Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2

Overview
NameRetrovirus-related Pol polyprotein from type-1 retrotransposable element R2
Smed IDSMED30015268
Length (bp)325
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast Population

 



 

Overview

 

Single cell RNA-seq of pluripotent neoblasts and its early progenies


We isolated X1 neoblasts cells enriched in high piwi-1 expression (Neoblast Population), and profiled ∼7,614 individual cells via scRNA-seq. Unsupervised analyses uncovered 12 distinct classes from 7,088 high-quality cells. We designated these classes Nb1 to Nb12 and ordered them based on high (Nb1) to low (Nb12) piwi-1 expression levels. We further defined groups of genes that best classified the cells parsed into 12 distinct cell clusters to generate a scaled expression heat map of discriminative gene sets for each cluster. Expression of each cluster’s gene signatures was validated using multiplex fluorescence in situ hybridization (FISH) co-stained with piwi-1 and largely confirmed the cell clusters revealed by scRNA-seq.

We also tested sub-lethal irradiation exposure. To profile rare pluripotent stem cells (PSCs) and avoid interference from immediate progenitor cells, we determined a time point after sub-lethal irradiation (7 DPI) with minimal piwi-1+ cells, followed by isolation and single-cell RNA-seq of 1,200 individual cells derived from X1 (Piwi-1 high) and X2 (Piwi-1 low) cell populations (Sub-lethal Irradiated Surviving X1 and X2 Cell Population)




Explore this single cell expression dataset with our NB Cluster Shiny App




 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 (SMED30015268) t-SNE clustered cells

Violin plots show distribution of expression levels for Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 (SMED30015268) in cells (dots) of each of the 12 neoblast clusters.

 

back to top


 

Embryonic Expression

Davies et. al., 2017




Hover the mouse over a column in the graph to view average RPKM values per sample.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult.
For further information about sample preparation and analysis for the single animal RNA-Seq experiment, please refer to the Materials and Methods

 

back to top
Anatomical Expression

PAGE et. al., 2020




SMED30015268

has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGE



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parenchymal cellSMED30015268 dd_Smed_v4_16441_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Ensembl Zebrafish
Match: CU462878.3 (pep chromosome:GRCz11:17:8542203:8545189:1 gene:ENSDARG00000103562.2 transcript:ENSDART00000158873.2 gene_biotype:protein_coding transcript_biotype:protein_coding gene_symbol:CU462878.3)

HSP 1 Score: 51.2174 bits (121), Expect = 2.316e-8
Identity = 26/83 (31.33%), Postives = 48/83 (57.83%), Query Frame = 2
Query:    2 PGEDNIPLRQWKEW--QEEDILYELFNYILQKRTFPDTWKDFPTILLVKPGKEKEAHIISNWRPIAILPTCYRIFTKIMNRRI 244
            PG D  P   +K +  Q   +L + FNY+L+    P +W++    ++ K GK+K     S++RPI++L   Y++F  I+++R+
Sbjct:  285 PGTDGYPSEMYKTFKPQITPMLLKCFNYVLRGGEIPQSWQEAVISIIPKQGKDKNE--CSSYRPISVLNVDYKLFASILSKRL 365          
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Ensembl Zebrafish
Match: BX547930.4 (pep chromosome:GRCz11:20:12830448:12834749:1 gene:ENSDARG00000098779.2 transcript:ENSDART00000164754.2 gene_biotype:protein_coding transcript_biotype:protein_coding gene_symbol:BX547930.4)

HSP 1 Score: 44.669 bits (104), Expect = 4.203e-6
Identity = 29/84 (34.52%), Postives = 45/84 (53.57%), Query Frame = 2
Query:    2 PGEDNIPLRQWKEW---QEEDILYELFNYILQKRTFPDTWKDFPTILLVKPGKEKEAHIISNWRPIAILPTCYRIFTKIMNRRI 244
            PG D +P+  +K +     ED+L E+ +  L K   P + +     LL K G  KE   + NWRP+A+L T Y+I +K +  R+
Sbjct:  489 PGLDGLPVEFYKAYWFFLGEDLL-EVLSNSLSKGKLPVSCRRAVLTLLPKKGDLKE---VKNWRPVALLCTDYKILSKALANRL 568          
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Ensembl Zebrafish
Match: BX548028.1 (pep chromosome:GRCz11:12:7865470:7870791:1 gene:ENSDARG00000103436.2 transcript:ENSDART00000161683.2 gene_biotype:protein_coding transcript_biotype:protein_coding gene_symbol:BX548028.1)

HSP 1 Score: 44.2838 bits (103), Expect = 6.624e-6
Identity = 27/103 (26.21%), Postives = 48/103 (46.60%), Query Frame = 2
Query:    2 PGEDNIPLRQWKEWQEED--ILYELFNYILQKRTFPDTWKDFPTILLVKPGKEKEAHIISNWRPIAILPTCYRIFTKIMNRRILAWATKGNLISRWQKAVNKS 304
            PG+D I     K   +    I+ +LFN + +    P  WK    I + KPGK++     +N+RPIA+     ++  +++  R++    K N  + +Q    K 
Sbjct:  463 PGKDEICNEMIKHLSDNSLCIILKLFNKVWESGILPAEWKHGVIIPIAKPGKDQSQP--NNYRPIALTSNICKLMERMVMSRLVYAIEKENFFAAYQSGFRKG 563          
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Ensembl Zebrafish
Match: BX511246.1 (pep chromosome:GRCz11:23:9353552:9357627:1 gene:ENSDARG00000100234.2 transcript:ENSDART00000163298.2 gene_biotype:protein_coding transcript_biotype:protein_coding gene_symbol:BX511246.1)

HSP 1 Score: 43.8986 bits (102), Expect = 7.368e-6
Identity = 30/93 (32.26%), Postives = 47/93 (50.54%), Query Frame = 2
Query:    2 PGEDNIPLRQWKE--WQEEDILYELFNYILQKRTFPDTWKDFPTILLVKPGKEKEAHIISNWRPIAILPTCYRIFTKIMNRRILAWATKGNLI 274
            PG D   +  +    +  +DIL  L+N  + ++    T K     L+ KP  EK++ +I NWRPI +L   Y+I   + + R+    TK NLI
Sbjct:  475 PGIDGFSVEFYTHFWYLIQDILLMLYNECIAEKEMSTTMKQGIISLIPKP--EKDSLLIDNWRPITLLTVDYKILALVFSNRL---KTKLNLI 562          
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Ensembl Zebrafish
Match: BX908731.1 (pep chromosome:GRCz11:22:17838913:17844117:-1 gene:ENSDARG00000099201.2 transcript:ENSDART00000159363.2 gene_biotype:protein_coding transcript_biotype:protein_coding gene_symbol:BX908731.1)

HSP 1 Score: 43.8986 bits (102), Expect = 9.767e-6
Identity = 28/103 (27.18%), Postives = 46/103 (44.66%), Query Frame = 2
Query:    2 PGEDNIPLRQWKEWQEE--DILYELFNYILQKRTFPDTWKDFPTILLVKPGKEKEAHIISNWRPIAILPTCYRIFTKIMNRRILAWATKGNLISRWQKAVNKS 304
            PG+D I  +      E   +I+  LFN I      P  WK    + ++KPGK       S++RPI++     +I  +++  RI  +    NL S +Q    + 
Sbjct:  458 PGKDEICYKMLSHMSEASLEIVLNLFNQIWDMGQLPIAWKQSIVVPILKPGKNPSDP--SSYRPISLTSHLCKIMERMITERITYFLESKNLFSPYQSGFRRG 558          
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Ensembl Xenopus
Match: txlna (taxilin alpha [Source:Xenbase;Acc:XB-GENE-992926])

HSP 1 Score: 47.3654 bits (111), Expect = 7.753e-7
Identity = 29/83 (34.94%), Postives = 46/83 (55.42%), Query Frame = 2
Query:    2 PGEDNIPLRQWKEWQE--EDILYELFNYILQKRTFPDTWKDFPTILLVKPGKEKEAHIISNWRPIAILPTCYRIFTKIMNRRI 244
            PG D IP+  +K++ +     + ELFN   Q  T PD+  D    L++KP K  E     ++RPI++L +  +IF KI+  R+
Sbjct:   66 PGPDGIPIEWYKKYADFLSPKMVELFNGNNQPNTLPDSCYDAYVTLILKPDKPPEQ--CESYRPISLLNSDIKIFAKILANRL 146          
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Ensembl Xenopus
Match: ENSXETT00000032317.1 (pep primary_assembly:Xenopus_tropicalis_v9.1:1:130520927:130524992:-1 gene:ENSXETG00000008594.1 transcript:ENSXETT00000032317.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 46.9802 bits (110), Expect = 1.030e-6
Identity = 27/88 (30.68%), Postives = 48/88 (54.55%), Query Frame = 2
Query:    5 GEDNIPLRQWKEWQE--EDILYELFNYILQKRTFPDTWKDFPTILLVKPGKEKEAHIISNWRPIAILPTCYRIFTKIMNRRILAWATK 262
            G D +P+  +K   +    +L +LF   +Q   FP++  +   +LL K GK+   H+  ++RPI++L    +IF K++ RR+    TK
Sbjct:  468 GADGLPIEIYKRHSKLLTPMLLKLFKEAVQLGQFPESLYEAAIVLLPKQGKDP--HLCESFRPISLLTADVKIFAKVLARRLSRVITK 553          
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Ensembl Xenopus
Match: ENSXETT00000002428.1 (pep primary_assembly:Xenopus_tropicalis_v9.1:3:15907829:15913358:1 gene:ENSXETG00000006437.1 transcript:ENSXETT00000002428.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 46.2098 bits (108), Expect = 1.740e-6
Identity = 24/82 (29.27%), Postives = 47/82 (57.32%), Query Frame = 2
Query:    5 GEDNIPLRQWKEWQEED--ILYELFNYILQKRTFPDTWKDFPTILLVKPGKEKEAHIISNWRPIAILPTCYRIFTKIMNRRI 244
            G D IP+  +K+  +    +L +++   +     P++  +   ILL KPGK+ +  +  ++RPI++L T  +I+ KI+ RR+
Sbjct:  468 GSDGIPIELYKKHAKSQTPLLTKMYGEAISTGILPESMYEAAIILLPKPGKDPQ--LCESFRPISLLTTDVKIYAKILARRL 547          
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Ensembl Xenopus
Match: ENSXETT00000008172.1 (pep primary_assembly:Xenopus_tropicalis_v9.1:5:143672566:143676425:-1 gene:ENSXETG00000002097.1 transcript:ENSXETT00000008172.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 44.669 bits (104), Expect = 5.848e-6
Identity = 29/102 (28.43%), Postives = 54/102 (52.94%), Query Frame = 2
Query:    2 PGEDNIPLRQWKEWQEE--DILYELFNYILQKRTFPDTWKDFPTILLVKPGKEKEAHIISNWRPIAILPTCYRIFTKIMNRRILAWATKGNLISRWQKAVNK 301
            PG D +    +K+++++   +L E+F   L+    P + ++   ILL    K K+   + NWRPIA+L T  ++  +I+  R++ ++  G L+S  Q    K
Sbjct:  485 PGPDGLTAEFYKKFKDQLAPVLVEVFRDCLEGGILPPSMRESSLILL---SKGKDPQRVENWRPIALLNTDRKLLARILFTRLILFS--GTLLSPVQSCTVK 581          
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Ensembl Xenopus
Match: tlr2 (toll like receptor 2 [Source:Xenbase;Acc:XB-GENE-481145])

HSP 1 Score: 44.669 bits (104), Expect = 7.231e-6
Identity = 27/89 (30.34%), Postives = 46/89 (51.69%), Query Frame = 2
Query:    2 PGEDNIPLRQWKEWQE--EDILYELFNYILQKRTFPDTWKDFPTILLVKPGKEKEAHIISNWRPIAILPTCYRIFTKIMNRRILAWATK 262
            PG D +    +K++ +     L E+FN  L++   P + +    ILL K   + +   + NWRPIA+L T  +I  K+M  R+  +A +
Sbjct:  456 PGPDGLTAEFYKQFVDVLAPRLTEVFNSTLEEGLLPPSMRHSALILLTKGLDQSK---VENWRPIALLNTDRKILAKVMFNRLFPFAER 541          
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. TrEMBL
Match: A0A159X4Q6 (ORF2-like protein (Fragment) OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 91.6633 bits (226), Expect = 9.319e-20
Identity = 46/109 (42.20%), Postives = 63/109 (57.80%), Query Frame = 2
Query:    2 PGEDNIPLRQWKEWQEED-ILYELFNYILQKRTFPDTWKDFPTILLVKPGKEKEAHIISNWRPIAILPTCYRIFTKIMNRRILAWATKGNLISRWQKAVNKSNGCDEHN 325
            PG+DNI  R  +    E  +L  LFN I+     P+ W  F TIL+ KPGK  +    S+WRPIA+L T Y+IFT I++RR+  W  +  L+   QK  ++  GC EHN
Sbjct:  190 PGDDNITYRDLRLLDPEGKLLARLFNIIIDSGQIPNDWLSFKTILIPKPGKSGDYDDTSSWRPIALLSTSYKIFTSILSRRLTKWIIENKLLHPGQKGGSRFEGCVEHN 298          
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. TrEMBL
Match: A0A4Y2WJK9 (Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 OS=Araneus ventricosus OX=182803 GN=PO21_26 PE=4 SV=1)

HSP 1 Score: 73.559 bits (179), Expect = 7.572e-13
Identity = 39/109 (35.78%), Postives = 59/109 (54.13%), Query Frame = 2
Query:    2 PGEDNIPLRQWKEWQEE-DILYELFNYILQKRTFPDTWKDFPTILLVKPGKEKEAHIISNWRPIAILPTCYRIFTKIMNRRILAWATKGNLISRWQKAVNKSNGCDEHN 325
            PG D I    WK        L  +FN  +  +  P +WK   T+LL K G   +A++ +NWRPIA+  T Y++FTK +  R+ AW  + +++S+ QK     +G  EHN
Sbjct: 1106 PGPDRITYADWKTIPASVKFLVTVFNACVHFQRIPPSWKTSTTVLLPKSG---DANVPNNWRPIALSSTMYKMFTKCLAARLSAWCERYDVLSKCQKGFTPHDGVIEHN 1211          
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. TrEMBL
Match: A0A147BLC2 (Putative reverse transcriptase (Fragment) OS=Ixodes ricinus OX=34613 PE=4 SV=1)

HSP 1 Score: 73.1738 bits (178), Expect = 1.078e-12
Identity = 38/109 (34.86%), Postives = 59/109 (54.13%), Query Frame = 2
Query:    2 PGEDNIPLRQWKEWQEE-DILYELFNYILQKRTFPDTWKDFPTILLVKPGKEKEAHIISNWRPIAILPTCYRIFTKIMNRRILAWATKGNLISRWQKAVNKSNGCDEHN 325
            PG+D +    W     +   L   FN  LQ R  PD+W+   TIL+ K G   E   I++WRPI++L T  ++F+ ++  R+ AW  + +++SR QK     +G  EHN
Sbjct:  163 PGDDRLTYHHWLAVDPDCRFLTAAFNICLQYRAIPDSWRQSRTILVPKKGDPAE---ITSWRPISLLRTASKLFSGVLAARLQAWLLEHDVLSRTQKGFLPYDGVFEHN 268          
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. TrEMBL
Match: A0A4Y2CJ97 (Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 OS=Araneus ventricosus OX=182803 GN=PO21_19 PE=4 SV=1)

HSP 1 Score: 73.1738 bits (178), Expect = 1.079e-12
Identity = 39/109 (35.78%), Postives = 58/109 (53.21%), Query Frame = 2
Query:    2 PGEDNIPLRQWKEWQEE-DILYELFNYILQKRTFPDTWKDFPTILLVKPGKEKEAHIISNWRPIAILPTCYRIFTKIMNRRILAWATKGNLISRWQKAVNKSNGCDEHN 325
            PG D I    WK        L  +FN  +  R  P +WK   T+LL K G   + ++ +NWRPIA+  T Y++FTK +  R+ AW  + +++S+ QK     +G  EHN
Sbjct:  355 PGPDRITYSDWKTIPASVKFLVTVFNACVHFRRIPPSWKTSTTVLLPKSG---DPNLPNNWRPIALSSTMYKMFTKCLAARLSAWCERYDVLSKCQKGFTPHDGVIEHN 460          
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. TrEMBL
Match: A0A131XRS2 (Putative reverse transcriptase (Fragment) OS=Ixodes ricinus OX=34613 PE=2 SV=1)

HSP 1 Score: 72.7886 bits (177), Expect = 1.363e-12
Identity = 38/109 (34.86%), Postives = 59/109 (54.13%), Query Frame = 2
Query:    2 PGEDNIPLRQWKEWQEE-DILYELFNYILQKRTFPDTWKDFPTILLVKPGKEKEAHIISNWRPIAILPTCYRIFTKIMNRRILAWATKGNLISRWQKAVNKSNGCDEHN 325
            PG+D +    W     +   L   FN  LQ R  PD+W+   TIL+ K G   E   I++WRPI++L T  ++F+ ++  R+ AW  + +++SR QK     +G  EHN
Sbjct:  123 PGDDRLTYHHWLAVDPDCRFLTAAFNICLQYRAIPDSWRQSRTILVPKKGDPAE---ITSWRPISLLRTASKLFSGVLAARLQAWLLEHDVLSRTQKGFLPYDGVFEHN 228          
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Ensembl Cavefish
Match: ENSAMXT00000029799.1 (pep primary_assembly:Astyanax_mexicanus-2.0:APWO02002288.1:29010:30180:-1 gene:ENSAMXG00000041014.1 transcript:ENSAMXT00000029799.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 49.6766 bits (117), Expect = 5.640e-8
Identity = 26/83 (31.33%), Postives = 48/83 (57.83%), Query Frame = 2
Query:    2 PGEDNIPLRQWKEW--QEEDILYELFNYILQKRTFPDTWKDFPTILLVKPGKEKEAHIISNWRPIAILPTCYRIFTKIMNRRI 244
            PG D  P+  +K++  Q   +L ++F + L +   PD+  +    LL+KPG  K+A    ++RPI++L T  +I +K++  R+
Sbjct:    7 PGPDGFPINFYKKFSKQLAPLLLDMFVHALSEGKLPDSLNEATITLLLKPG--KDASKCGSYRPISLLNTDIKILSKLLATRL 87          
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Ensembl Cavefish
Match: ENSAMXT00000052839.1 (pep primary_assembly:Astyanax_mexicanus-2.0:16:12653319:12657116:1 gene:ENSAMXG00000031230.1 transcript:ENSAMXT00000052839.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 49.6766 bits (117), Expect = 7.807e-8
Identity = 28/83 (33.73%), Postives = 49/83 (59.04%), Query Frame = 2
Query:    2 PGEDNIPLRQWKEWQEEDI--LYELFNYILQKRTFPDTWKDFPTILLVKPGKEKEAHIISNWRPIAILPTCYRIFTKIMNRRI 244
            PG D  P   +K ++ E +  L E+FN  L +R  P +WK+   I+ V P + K+A    ++RPI++L   Y+++T I+ +R+
Sbjct:  472 PGTDGFPNEWYKVFRAELVPYLLEVFNSALIERKMPPSWKE--AIISVIPKEGKDALDCGSYRPISVLNVDYKLYTSIIAKRL 552          
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Ensembl Cavefish
Match: ENSAMXT00000045927.1 (pep primary_assembly:Astyanax_mexicanus-2.0:APWO02000117.1:1373779:1377516:1 gene:ENSAMXG00000043500.1 transcript:ENSAMXT00000045927.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 49.2914 bits (116), Expect = 9.948e-8
Identity = 33/103 (32.04%), Postives = 58/103 (56.31%), Query Frame = 2
Query:    2 PGEDN---IPLRQWKEWQEEDILYELFNYILQKRTFPDTWKDFPTILLVKPGKEKEAHIISNWRPIAILPTCYRIFTKIMNRRILAWATKGNLISRWQKAVNK 301
            PG+D    I LR   +   + +L  LFN + ++ + P++WK    + +VKPGK+K +H  S++RPIA+     ++  K++ RR+L    +  L+S +Q    K
Sbjct:  457 PGKDEVCYIMLRNVSDTVLQCVL-ALFNKVWKEGSLPNSWKHGVVVPIVKPGKDK-SH-ASSYRPIALTSNLCKLMEKMIVRRLLYELERRGLLSPYQSGFRK 556          
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Ensembl Cavefish
Match: ENSAMXT00000040306.1 (pep primary_assembly:Astyanax_mexicanus-2.0:23:24916978:24919980:-1 gene:ENSAMXG00000037218.1 transcript:ENSAMXT00000040306.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 49.2914 bits (116), Expect = 1.003e-7
Identity = 28/83 (33.73%), Postives = 46/83 (55.42%), Query Frame = 2
Query:    2 PGEDNIPLRQWKEWQEE--DILYELFNYILQKRTFPDTWKDFPTILLVKPGKEKEAHIISNWRPIAILPTCYRIFTKIMNRRI 244
            PG D      +K +Q+E   IL   FN+ L+K   P +W+     ++ K GK+K      ++RPI++L   YR++T IM +R+
Sbjct:  224 PGSDGFTAEWYKAFQKELIPILLSAFNWALKKAEIPPSWRQAEISVIPKEGKDKLE--CGSYRPISVLNVDYRLYTSIMAKRL 304          
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Ensembl Cavefish
Match: ENSAMXT00000034831.1 (pep primary_assembly:Astyanax_mexicanus-2.0:3:16211297:16215948:1 gene:ENSAMXG00000034228.1 transcript:ENSAMXT00000034831.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 49.2914 bits (116), Expect = 1.032e-7
Identity = 34/111 (30.63%), Postives = 58/111 (52.25%), Query Frame = 2
Query:    2 PGEDNIPLRQWKEWQEE-DILYELFNYILQKRTFPDTWKDFPTILLVKPGKEKEAHIISNWRPIAILPTCYRIFTKIMNRRILAWATKGNLI-SRWQKA-VNKSNGCDEHN 325
            PG + +P R +K   +    L++L   + +K   P  W     +L+    KEK++  I  +RPI++L    +IF  ++ RR+  +  + NLI +  QKA +   +GC EHN
Sbjct:  390 PGPNGVPYRSYKSAPDVLKFLWKLMAIVWKKGIIPKEWHRAGGVLI---PKEKDSVAIDQFRPISLLNVEGKIFFSVVARRLATYLKRNNLIDTSVQKAGIAGFSGCIEHN 497          
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Ensembl Nematostella
Match: EDO32209 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7SVP6])

HSP 1 Score: 42.743 bits (99), Expect = 9.561e-7
Identity = 26/78 (33.33%), Postives = 39/78 (50.00%), Query Frame = 2
Query:    5 GEDNIPLRQWKEWQE--EDILYELFNYILQKRTFPDTWKDFPTILLVKPGKEKEAHIISNWRPIAILPTCYRIFTKIM 232
            G D IP R  +E  +     L  +FN  +    FPD WK      L K G+  +   I+N+RPI++ P   +IF +I+
Sbjct:   11 GLDRIPARILRECSDLIAASLCLIFNRSIISGIFPDEWKSAKVTPLFKNGQRSD---INNYRPISVTPIVAKIFERIV 85          
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Ensembl Medaka
Match: ENSORLT00000046447.1 (pep primary_assembly:ASM223467v1:15:12620570:12623341:-1 gene:ENSORLG00000023409.1 transcript:ENSORLT00000046447.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 55.0694 bits (131), Expect = 8.225e-10
Identity = 30/83 (36.14%), Postives = 50/83 (60.24%), Query Frame = 2
Query:    2 PGEDNIPLRQWKEWQEE--DILYELFNYILQKRTFPDTWKDFPTILLVKPGKEKEAHIISNWRPIAILPTCYRIFTKIMNRRI 244
            PG D  P   +K +++E   IL++  N+ LQ    P +W +    +L+KPGK K++   +N+RPI++L   Y+I+T I+  RI
Sbjct:  470 PGSDGFPAEWYKIFKDELTPILHKSLNWTLQNNKMPISWSEAIISVLLKPGKNKQS--CANYRPISVLNIDYKIYTSIICNRI 550          
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Ensembl Medaka
Match: ENSORLT00000041165.1 (pep primary_assembly:ASM223467v1:8:20886513:20892197:1 gene:ENSORLG00000024310.1 transcript:ENSORLT00000041165.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 55.0694 bits (131), Expect = 8.357e-10
Identity = 30/83 (36.14%), Postives = 50/83 (60.24%), Query Frame = 2
Query:    2 PGEDNIPLRQWKEWQEE--DILYELFNYILQKRTFPDTWKDFPTILLVKPGKEKEAHIISNWRPIAILPTCYRIFTKIMNRRI 244
            PG D  P   +K +++E   IL++  N+ LQ    P +W +    +L+KPGK K++   +N+RPI++L   Y+I+T I+  RI
Sbjct:  470 PGSDGFPAEWYKIFKDELTPILHKSLNWTLQNNKMPISWSEAIISVLLKPGKNKQS--CANYRPISVLNIDYKIYTSIICNRI 550          
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Ensembl Medaka
Match: ENSORLT00000042239.1 (pep primary_assembly:ASM223467v1:5:6656021:6661644:1 gene:ENSORLG00000029419.1 transcript:ENSORLT00000042239.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 52.373 bits (124), Expect = 8.134e-9
Identity = 33/83 (39.76%), Postives = 49/83 (59.04%), Query Frame = 2
Query:    2 PGEDNIPLRQWKEWQEE--DILYELFNYILQKRTFPDTWKDFPTILLVKPGKEKEAHIISNWRPIAILPTCYRIFTKIMNRRI 244
            PG D  P   +K ++EE   IL E FN+ L+    P +WK+    +L K GK KE     ++RPI+IL   Y+IFT I+++R+
Sbjct:  473 PGGDGYPNEWYKIFKEELAPILLESFNWTLKNAKTPPSWKEAIISVLPKEGKNKE--YCESYRPISILNVDYKIFTSIISKRL 553          
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Ensembl Medaka
Match: ENSORLT00000030476.1 (pep primary_assembly:ASM223467v1:6:31901344:31902456:1 gene:ENSORLG00000026399.1 transcript:ENSORLT00000030476.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 50.0618 bits (118), Expect = 4.344e-8
Identity = 26/75 (34.67%), Postives = 39/75 (52.00%), Query Frame = 2
Query:   68 LFNYILQKRTFPDTWKDFPTILLVKPGKEKEAHIISNWRPIAILPTCYRIFTKIMNRRILAWATKGNLISRWQKA 292
            +FN  L    FPD WK    I L+K   EK     SN RP+ +LP   +IF +++  ++L +    +L +R Q A
Sbjct:  103 IFNRALISGVFPDQWKQSKIIPLIK--DEKSEFTASNCRPVHVLPVLSKIFERLIFNQMLPYFISNDLFTRAQHA 175          
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Ensembl Medaka
Match: ENSORLT00000030752.1 (pep primary_assembly:ASM223467v1:11:7275367:7279110:1 gene:ENSORLG00000026314.1 transcript:ENSORLT00000030752.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 48.1358 bits (113), Expect = 2.371e-7
Identity = 28/105 (26.67%), Postives = 50/105 (47.62%), Query Frame = 2
Query:    2 PGEDNIPLRQWKEWQEEDIL--YELFNYILQKRTFPDTWKDFPTILLVKPGKEKEAHIISNWRPIAILPTCYRIFTKIMNRRILAWATKGNLISRWQKAVNKSNG 310
            PG D I     K    +  L   +++N +  +   P  WK+   I ++KPGK+  +    N+RPIA+     ++  +++N R+  +    NL+S +Q    K  G
Sbjct:  454 PGRDGISYVMLKHLGRKMKLKLLDMYNRVWSEGKLPTNWKEAVVIPILKPGKDPSSP--ENYRPIALTSHVGKVMERMINERLQYYLESKNLLSPYQNGFRKGRG 556          
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Planmine SMEST
Match: SMESG000025060.1 (SMESG000025060.1)

HSP 1 Score: 144.821 bits (364), Expect = 7.554e-46
Identity = 63/108 (58.33%), Postives = 84/108 (77.78%), Query Frame = 2
Query:    2 PGEDNIPLRQWKEWQEEDILYELFNYILQKRTFPDTWKDFPTILLVKPGKEKEAHIISNWRPIAILPTCYRIFTKIMNRRILAWATKGNLISRWQKAVNKSNGCDEHN 325
            PGED IPLRQW  W  +++L+++FNYI +    P+ WK++ T+LL+KPGK +E +  +N RPI+ILPT YRIF KI+NRR+L  A  GN ISRWQKAV+K+NGCDEH+
Sbjct:   33 PGEDGIPLRQWMIWHTDNVLFDMFNYIKRTHDIPEIWKNYTTMLLIKPGKSQETYNPANSRPISILPTSYRIFMKIINRRVLELANNGNFISRWQKAVDKANGCDEHS 140          
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Planmine SMEST
Match: SMESG000013875.1 (SMESG000013875.1)

HSP 1 Score: 156.377 bits (394), Expect = 1.800e-45
Identity = 65/108 (60.19%), Postives = 88/108 (81.48%), Query Frame = 2
Query:    2 PGEDNIPLRQWKEWQEEDILYELFNYILQKRTFPDTWKDFPTILLVKPGKEKEAHIISNWRPIAILPTCYRIFTKIMNRRILAWATKGNLISRWQKAVNKSNGCDEHN 325
            PGEDNIPLRQW  W  + +L+++FNYI +    PD WK++ T LL+KPGK +E++I +NWRPI+ILPT YRIF K++N+R+L WA +G LIS+WQKAV+K+NGCDEH+
Sbjct:  224 PGEDNIPLRQWIIWNNDGVLFDMFNYIKRTHDIPDMWKNYTTTLLIKPGKSQESNIPANWRPISILPTSYRIFMKVLNKRVLEWANRGELISKWQKAVDKANGCDEHS 331          
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Planmine SMEST
Match: SMESG000031457.1 (SMESG000031457.1)

HSP 1 Score: 156.377 bits (394), Expect = 2.114e-45
Identity = 66/108 (61.11%), Postives = 88/108 (81.48%), Query Frame = 2
Query:    2 PGEDNIPLRQWKEWQEEDILYELFNYILQKRTFPDTWKDFPTILLVKPGKEKEAHIISNWRPIAILPTCYRIFTKIMNRRILAWATKGNLISRWQKAVNKSNGCDEHN 325
            PGEDNIPLRQW  W  + +L+++FNYI +    PD WK++ T LL+KPGK +E++I +NWRPI+ILPT YRIF KI+N+R+L WA +G LIS+WQKAV+K+NGCDEH+
Sbjct:  596 PGEDNIPLRQWIIWNNDGVLFDMFNYIKRTHDIPDMWKNYTTTLLIKPGKSQESNIPANWRPISILPTSYRIFMKILNKRVLDWANRGELISKWQKAVDKANGCDEHS 703          
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Planmine SMEST
Match: SMESG000036894.1 (SMESG000036894.1)

HSP 1 Score: 152.14 bits (383), Expect = 2.299e-45
Identity = 63/108 (58.33%), Postives = 87/108 (80.56%), Query Frame = 2
Query:    2 PGEDNIPLRQWKEWQEEDILYELFNYILQKRTFPDTWKDFPTILLVKPGKEKEAHIISNWRPIAILPTCYRIFTKIMNRRILAWATKGNLISRWQKAVNKSNGCDEHN 325
            PG+DNIPLRQW  W  + +L+++FNYI +    PD WK++ T LL+K GK +E++I +NWRPI+ILPT YRIF K++N+R+L WA +G LIS+WQKAV+K+NGCDEH+
Sbjct:  142 PGDDNIPLRQWIIWNNDGVLFDMFNYIKRTHDIPDMWKNYTTTLLIKSGKSQESNIPTNWRPISILPTSYRIFMKVLNKRVLEWANRGELISKWQKAVDKANGCDEHS 249          
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Planmine SMEST
Match: SMESG000047667.1 (SMESG000047667.1)

HSP 1 Score: 154.066 bits (388), Expect = 1.490e-44
Identity = 64/108 (59.26%), Postives = 88/108 (81.48%), Query Frame = 2
Query:    2 PGEDNIPLRQWKEWQEEDILYELFNYILQKRTFPDTWKDFPTILLVKPGKEKEAHIISNWRPIAILPTCYRIFTKIMNRRILAWATKGNLISRWQKAVNKSNGCDEHN 325
            PGEDNIPLRQW  W  + +L+++FNYI +    P+ WK++ T LL+KPGK +E++I +NWRPI+ILPT YRIF K++N+R+L WA +G LIS+WQKAV+K+NGCDEH+
Sbjct:  827 PGEDNIPLRQWIIWNNDGVLFDMFNYIKRTHDIPEMWKNYTTTLLIKPGKSQESNIPANWRPISILPTSYRIFMKVLNKRVLDWANRGELISKWQKAVDKANGCDEHS 934          
The following BLAST results are available for this feature:
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 5
Match NameE-valueIdentityDescription
CU462878.32.316e-831.33pep chromosome:GRCz11:17:8542203:8545189:1 gene:EN... [more]
BX547930.44.203e-634.52pep chromosome:GRCz11:20:12830448:12834749:1 gene:... [more]
BX548028.16.624e-626.21pep chromosome:GRCz11:12:7865470:7870791:1 gene:EN... [more]
BX511246.17.368e-632.26pep chromosome:GRCz11:23:9353552:9357627:1 gene:EN... [more]
BX908731.19.767e-627.18pep chromosome:GRCz11:22:17838913:17844117:-1 gene... [more]
back to top
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 5
Match NameE-valueIdentityDescription
txlna7.753e-734.94taxilin alpha [Source:Xenbase;Acc:XB-GENE-992926][more]
ENSXETT00000032317.11.030e-630.68pep primary_assembly:Xenopus_tropicalis_v9.1:1:130... [more]
ENSXETT00000002428.11.740e-629.27pep primary_assembly:Xenopus_tropicalis_v9.1:3:159... [more]
ENSXETT00000008172.15.848e-628.43pep primary_assembly:Xenopus_tropicalis_v9.1:5:143... [more]
tlr27.231e-630.34toll like receptor 2 [Source:Xenbase;Acc:XB-GENE-4... [more]
back to top
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A159X4Q69.319e-2042.20ORF2-like protein (Fragment) OS=Schmidtea mediterr... [more]
A0A4Y2WJK97.572e-1335.78Retrovirus-related Pol polyprotein from type-1 ret... [more]
A0A147BLC21.078e-1234.86Putative reverse transcriptase (Fragment) OS=Ixode... [more]
A0A4Y2CJ971.079e-1235.78Retrovirus-related Pol polyprotein from type-1 ret... [more]
A0A131XRS21.363e-1234.86Putative reverse transcriptase (Fragment) OS=Ixode... [more]
back to top
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 5
Match NameE-valueIdentityDescription
ENSAMXT00000029799.15.640e-831.33pep primary_assembly:Astyanax_mexicanus-2.0:APWO02... [more]
ENSAMXT00000052839.17.807e-833.73pep primary_assembly:Astyanax_mexicanus-2.0:16:126... [more]
ENSAMXT00000045927.19.948e-832.04pep primary_assembly:Astyanax_mexicanus-2.0:APWO02... [more]
ENSAMXT00000040306.11.003e-733.73pep primary_assembly:Astyanax_mexicanus-2.0:23:249... [more]
ENSAMXT00000034831.11.032e-730.63pep primary_assembly:Astyanax_mexicanus-2.0:3:1621... [more]
back to top
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO322099.561e-733.33Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
back to top
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 5
Match NameE-valueIdentityDescription
ENSORLT00000046447.18.225e-1036.14pep primary_assembly:ASM223467v1:15:12620570:12623... [more]
ENSORLT00000041165.18.357e-1036.14pep primary_assembly:ASM223467v1:8:20886513:208921... [more]
ENSORLT00000042239.18.134e-939.76pep primary_assembly:ASM223467v1:5:6656021:6661644... [more]
ENSORLT00000030476.14.344e-834.67pep primary_assembly:ASM223467v1:6:31901344:319024... [more]
ENSORLT00000030752.12.371e-726.67pep primary_assembly:ASM223467v1:11:7275367:727911... [more]
back to top
BLAST of Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000025060.17.554e-4658.33SMESG000025060.1[more]
SMESG000013875.11.800e-4560.19SMESG000013875.1[more]
SMESG000031457.12.114e-4561.11SMESG000031457.1[more]
SMESG000036894.12.299e-4558.33SMESG000036894.1[more]
SMESG000047667.11.490e-4459.26SMESG000047667.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30015268 ID=SMED30015268|Name=Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2|organism=Schmidtea mediterranea sexual|type=transcript|length=325bp
ACCAGGAGAAGACAATATTCCGTTAAGACAATGGAAGGAGTGGCAAGAAG
AAGACATCCTTTATGAGCTATTCAACTACATACTCCAAAAAAGAACATTC
CCAGACACATGGAAAGATTTCCCCACGATTCTCTTAGTAAAACCAGGAAA
GGAAAAAGAAGCACATATCATATCAAACTGGAGACCAATAGCGATACTCC
CAACATGCTATAGGATATTTACAAAAATAATGAATAGAAGAATCCTCGCA
TGGGCCACAAAAGGAAATCTAATATCAAGATGGCAAAAGGCAGTCAACAA
ATCAAATGGATGTGATGAGCACAAC
back to top

protein sequence of SMED30015268-orf-1

>SMED30015268-orf-1 ID=SMED30015268-orf-1|Name=SMED30015268-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=108bp
PGEDNIPLRQWKEWQEEDILYELFNYILQKRTFPDTWKDFPTILLVKPGK
EKEAHIISNWRPIAILPTCYRIFTKIMNRRILAWATKGNLISRWQKAVNK
SNGCDEHN
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0003116parenchymal cell
Vocabulary: molecular function
TermDefinition
GO:0003676nucleic acid binding
GO:0003964RNA-directed DNA polymerase activity
GO:0046872metal ion binding
Vocabulary: biological process
TermDefinition
GO:0006278RNA-dependent DNA biosynthetic process