Retrovirus-related Pol polyprotein from transposon

Overview


Name	Retrovirus-related Pol polyprotein from transposon
Smed ID	SMED30018321
Length (bp)	689

Neoblast Clusters

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell 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 transposon (SMED30018321) t-SNE clustered cells

Violin plots show distribution of expression levels for Retrovirus-related Pol polyprotein from transposon (SMED30018321) in cells (dots) of each of the 12 neoblast clusters.

Sub-lethal Irradiated Surviving X1 and X2 Cell Population

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of Retrovirus-related Pol polyprotein from transposon (SMED30018321) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Embryonic Expression

Davies et. al., 2017

Hover the mouse over a column in the graph to view average RPKM values per sample.
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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

Anatomical Expression

PAGE et. al., 2020

SMED30018321

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

PAGE Curations: 3

Expressed In	Reference Transcript	Gene Models	Published Transcript	Transcriptome	Publication
epidermis	SMED30018321	h1SMcG0003271	dd_Smed_v4_8579_0_1	dd_Smed_v4	PMID:29674431 Fincher et al., 2018
cephalic ganglia	SMED30018321	h1SMcG0003271	dd_Smed_v4_8579_0_1	dd_Smed_v4	PMID:29674431 Fincher et al., 2018
muscle cell	SMED30018321	h1SMcG0003271	dd_Smed_v4_8579_0_1	dd_Smed_v4	PMID:29674431 Fincher et al., 2018

Note: Hover over icons to view figure legend

Homology

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BLAST of Retrovirus-related Pol polyprotein from transposon vs. TrEMBL
Match: A0A0V0RCI6 (Gypsy retrotransposon integrase-like protein 1 (Fragment) OS=Trichinella nelsoni OX=6336 GN=GIN1 PE=4 SV=1)

HSP 1 Score: 62.7734 bits (151), Expect = 2.693e-8
Identity = 36/123 (29.27%), Postives = 61/123 (49.59%), Query Frame = 3

Query:  324 VSNNFEMRNMRQTIQDVIQSYENYQKRKYTTPTKKIICKTMEL----RLFETIFIDFCGPLKQTLYGMKYIFGIIDKHSKYVSLHVFISQSEDTVVTI*KNSWILKYVAPEVIHCDRGKSFES 680
            V   F     R+ ++D  ++ +    R    PTK++    M++    + F+ + +D  GPL++TL G +YI  + D  SK+           DTV T   N    +Y APE +H D+G++FE+
Sbjct:   34 VRQRFYWPQQREDVEDWCRACQTCAAR--AAPTKRLQAP-MQIHPVGQPFQRVGMDLVGPLEETLRGNRYILVVCDYFSKWPEAFPLPDAEADTVATALVNGIFCRYGAPETLHSDQGRNFEA 153

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BLAST of Retrovirus-related Pol polyprotein from transposon vs. TrEMBL
Match: A0A0V1GMM2 (Pro-Pol polyprotein (Fragment) OS=Trichinella zimbabwensis OX=268475 GN=pol PE=4 SV=1)

HSP 1 Score: 62.3882 bits (150), Expect = 8.574e-8
Identity = 35/111 (31.53%), Postives = 55/111 (49.55%), Query Frame = 3

Query:  351 MRQTIQDVIQSYENYQKRKYTTPTKKIICKTMELR-LFETIFIDFCGPLKQTLYGMKYIFGIIDKHSKYVSLHVFISQSEDTVVTI*KNSWILKYVAPEVIHCDRGKSFES 680
            MR+ +    Q+      R  TT   K   +  E    F+T+ +DF GPL+ T  G +YI  + D  SK+   +   SQ+   V  +   +W  ++ AP  +H D+G+SFES
Sbjct:  167 MRKAVDAWCQACRTCAARNETTRKAKAPLQMPETSCAFQTMAMDFLGPLEATPKGYRYILVVCDYFSKWTEAYPTRSQAATEVADVLVGNWFSRFGAPIRLHSDQGRSFES 277

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BLAST of Retrovirus-related Pol polyprotein from transposon vs. TrEMBL
Match: A0A2G8LRM3 (Integrase catalytic domain-containing protein OS=Stichopus japonicus OX=307972 GN=BSL78_00208 PE=4 SV=1)

HSP 1 Score: 61.2326 bits (147), Expect = 1.650e-7
Identity = 37/114 (32.46%), Postives = 59/114 (51.75%), Query Frame = 3

Query:  351 MRQTIQDVIQSYENYQKRKYTTPTKKI---ICKTMELRLFETIFIDFCGPLKQTLYGMKYIFGIIDKHSKYVSLHVFISQSEDTVVTI*KNSWILKYVAPEVIHCDRGKSFESK 683
            MR+ I+D  +  E   +RK  TP  K    I K  E    + + ID  GPL +T  G KYI  + D  +K+   +   +Q   TV +    ++I ++  P++IH D+G +FES+
Sbjct:    1 MRRDIEDWCRRCELCSRRKPPTPRSKAPMEIVKAGEP--MQRVAIDVLGPLPETYNGNKYILVVADYFTKWTEAYPIPNQEAKTVASELVTNFIARFGVPQIIHSDQGSNFESE 112

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BLAST of Retrovirus-related Pol polyprotein from transposon vs. TrEMBL
Match: A0A3B3ST06 (Integrase catalytic domain-containing protein OS=Paramormyrops kingsleyae OX=1676925 PE=4 SV=1)

HSP 1 Score: 62.003 bits (149), Expect = 2.042e-7
Identity = 27/95 (28.42%), Postives = 48/95 (50.53%), Query Frame = 3

Query:  399 KRKYTTPTKKIICKTMELRLFETIFIDFCGPLKQTLYGMKYIFGIIDKHSKYVSLHVFISQSEDTVVTI*KNSWILKYVAPEVIHCDRGKSFESK 683
            +++     +  +  T+  R +E + +D  GPL +T  G KYI  + D  SK+       +Q   TV  +    W+ +Y  P  +H D+G++FES+
Sbjct:  228 RKEVGAAPRAPMVSTVSARPYERVALDILGPLPETGKGNKYILVVADYFSKWTEAFSLPNQEAITVARVLVEEWVCRYGTPRTLHSDQGRNFESR 322

[Close]

BLAST of Retrovirus-related Pol polyprotein from transposon vs. TrEMBL
Match: A0A0J7KHW9 (S68306 pol retrotransposon woot OS=Lasius niger OX=67767 GN=RF55_10460 PE=4 SV=1)

HSP 1 Score: 61.6178 bits (148), Expect = 3.766e-7
Identity = 38/123 (30.89%), Postives = 64/123 (52.03%), Query Frame = 3

Query:  309 KAEKYVSNNFEMRNMRQTIQDVIQSYENYQKRKY-TTPTKKIICKTMELRLFETIFIDFCGPLKQTLYGMKYIFGIIDKHSKYVSLHVFISQSEDTVVTI*KNSWILKYVAPEVIHCDRGKSF 674
            K   +VS+ FE++N+ + ++DV+ S E  Q  KY T PT+ I    +  +  + + +D  GPL QT  G KYI  ++D+ SK V  +   +Q  +T++   +  +  +   P  I  D G  F
Sbjct: 1175 KVSDFVSDYFEVQNLERVVRDVVASCETCQATKYYTRPTRGIEYYDLPSQPGQVVSLDIFGPLPQTPRGNKYILVLMDQFSKLVRFYAMKNQKLETILDCLQVEYFQEIGVPNEILTDNGGQF 1297

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BLAST of Retrovirus-related Pol polyprotein from transposon vs. Ensembl Cavefish
Match: ENSAMXT00000058127.1 (pep primary_assembly:Astyanax_mexicanus-2.0:16:35454045:35455481:1 gene:ENSAMXG00000038477.1 transcript:ENSAMXT00000058127.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 60.4622 bits (145), Expect = 2.012e-10
Identity = 36/139 (25.90%), Postives = 62/139 (44.60%), Query Frame = 3

Query:  267 FLQNRV*NCHAEPMKAEKYVSNNFEMRNMRQTIQDVIQSYENYQKRKYTTPTKKI-ICKTMELRLFETIFIDFCGPLKQTLYGMKYIFGIIDKHSKYVSLHVFISQSEDTVVTI*KNSWILKYVAPEVIHCDRGKSFES 680
             L N +   H    K ++ +   F      + ++   +   +   RK + P  +  +  ++  R +E I +D  GPL +T    +YI  + D  SK+       +Q   TV  +    WI +Y AP  IH D+G++FES
Sbjct:    8 MLHNDLTGGHLGVQKLKEKIRTRFYWPGWVEDVERWCRECTDCASRKTSGPAPRAPLLPSVTSRPYERIALDILGPLPETPQKNRYILVVGDYFSKWTEAFSLPNQEAKTVAKVLTEEWICRYGAPRSIHTDQGRNFES 146

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BLAST of Retrovirus-related Pol polyprotein from transposon vs. Ensembl Cavefish
Match: ENSAMXT00000031920.1 (pep primary_assembly:Astyanax_mexicanus-2.0:12:11094903:11101818:1 gene:ENSAMXG00000039354.1 transcript:ENSAMXT00000031920.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 60.077 bits (144), Expect = 2.573e-10
Identity = 31/94 (32.98%), Postives = 48/94 (51.06%), Query Frame = 3

Query:  402 RKYTTPTKKI-ICKTMELRLFETIFIDFCGPLKQTLYGMKYIFGIIDKHSKYVSLHVFISQSEDTVVTI*KNSWILKYVAPEVIHCDRGKSFES 680
            RK + P  +  +  ++  R +E I +D  GPL +T    +YI  + D  SK+       +Q   TV  +    WI +Y AP  IH D+G++FES
Sbjct:   17 RKTSGPAPRAPLLPSVTSRPYERIALDILGPLPETPQKNRYILVVGDYFSKWTEAFSLPNQEAKTVAKVLTEEWICRYGAPRSIHTDQGRNFES 110

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BLAST of Retrovirus-related Pol polyprotein from transposon vs. Ensembl Cavefish
Match: ENSAMXT00000054209.1 (pep primary_assembly:Astyanax_mexicanus-2.0:APWO02001944.1:84644:88116:-1 gene:ENSAMXG00000038678.1 transcript:ENSAMXT00000054209.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 55.0694 bits (131), Expect = 1.135e-8
Identity = 31/89 (34.83%), Postives = 49/89 (55.06%), Query Frame = 3

Query:  414 TPTKKIICKTMELRLFETIFIDFCGPLKQTLYGMKYIFGIIDKHSKYVSLHVFISQSEDTVVTI*KNSWILKYVAPEVIHCDRGKSFES 680
            TP   ++  ++  R F+ I +D  GPL  T  G KYI  I D  SK+   +   +Q   TV     + ++L++  P+VIH D+G++FES
Sbjct:    5 TPRAPLM-PSVATRPFQRIALDIVGPLPVTATGNKYILVIADYFSKWAESYAIPNQEATTVARAVVD-FLLRWGMPQVIHTDQGRTFES 91

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BLAST of Retrovirus-related Pol polyprotein from transposon vs. Ensembl Cavefish
Match: ENSAMXT00000037741.1 (pep primary_assembly:Astyanax_mexicanus-2.0:6:27788674:27792885:-1 gene:ENSAMXG00000029895.1 transcript:ENSAMXT00000037741.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 54.299 bits (129), Expect = 2.235e-8
Identity = 29/74 (39.19%), Postives = 39/74 (52.70%), Query Frame = 3

Query:  459 FETIFIDFCGPLKQTLYGMKYIFGIIDKHSKYVSLHVFISQSEDTVVTI*KNSWILKYVAPEVIHCDRGKSFES 680
            FE + ID  GPL  T  G KYI  I D  +K+       +Q  DTV       +IL++  P  IH D+GK+F+S
Sbjct:  157 FEKLGIDIVGPLPVTSQGNKYIIVIADYFTKWCEAFAMRAQDADTVARTVVEQFILRWGTPRSIHTDQGKNFDS 230

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BLAST of Retrovirus-related Pol polyprotein from transposon vs. Ensembl Cavefish
Match: ENSAMXT00000055645.1 (pep primary_assembly:Astyanax_mexicanus-2.0:APWO02001353.1:7814:9808:1 gene:ENSAMXG00000036557.1 transcript:ENSAMXT00000055645.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 54.299 bits (129), Expect = 3.171e-8
Identity = 24/75 (32.00%), Postives = 40/75 (53.33%), Query Frame = 3

Query:  459 FETIFIDFCGPLKQTLYGMKYIFGIIDKHSKYVSLHVFISQSEDTVVTI*KNSWILKYVAPEVIHCDRGKSFESK 683
             E I ID  GP+ +T    +YI    D  +K+V  +   +    TV  +  + W+ +Y AP+ +H D+G +FES+
Sbjct:  270 MERIAIDLMGPMNETDRHNRYILVAQDYFTKWVEAYALPNDQAVTVAEVLTSEWVCRYGAPQTLHSDQGSNFESE 344

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BLAST of Retrovirus-related Pol polyprotein from transposon vs. Ensembl Medaka
Match: ENSORLT00000045127.1 (pep primary_assembly:ASM223467v1:10:587855:593081:1 gene:ENSORLG00000029202.1 transcript:ENSORLT00000045127.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 55.4546 bits (132), Expect = 9.099e-9
Identity = 25/76 (32.89%), Postives = 40/76 (52.63%), Query Frame = 3

Query:  453 RLFETIFIDFCGPLKQTLYGMKYIFGIIDKHSKYVSLHVFISQSEDTVVTI*KNSWILKYVAPEVIHCDRGKSFES 680
            R FE + ++  GPL +T    KYI  I D  SK+       +Q   ++  +    W+ ++ AP  IH D+G++FES
Sbjct:   36 RPFERVALEILGPLPETPNKNKYILVISDYFSKWTEAFPLPNQEAQSIAKVLTEEWVCRFGAPRSIHSDQGRNFES 111

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BLAST of Retrovirus-related Pol polyprotein from transposon vs. Ensembl Medaka
Match: ENSORLT00000032021.1 (pep primary_assembly:ASM223467v1:7:3496795:3498971:-1 gene:ENSORLG00000027527.1 transcript:ENSORLT00000032021.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 55.4546 bits (132), Expect = 1.111e-8
Identity = 30/126 (23.81%), Postives = 58/126 (46.03%), Query Frame = 3

Query:  309 KAEKYVSNNFEMRNMRQTIQDVIQSYENYQKRKYTTPTKKIICKTMELR-LFETIFIDFCGPLKQTLYGMKYIFGIIDKHSKYVSLHVFISQSEDTVVTI*KNSWILKYVAPEVIHCDRGKSFESK 683
            K  + +   F     R+ ++D  +  +    RK  +       +  ++R   E + +D  GPL ++  G +YI   ID  +++   +    Q  +TV+       I ++  PE IH D+G++FES+
Sbjct:  119 KTLRRLRQGFYWGRCRRDVEDFCRQCDPCIARKGPSGQSHAPLQPFQVRGPMERVAVDIVGPLPRSSRGNRYILSAIDYFTRWPEAYALPDQEAETVLDALLGGMISRFGVPETIHSDQGRNFESR 244

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BLAST of Retrovirus-related Pol polyprotein from transposon vs. Ensembl Medaka
Match: ENSORLT00000040305.1 (pep primary_assembly:ASM223467v1:1:25459511:25466649:-1 gene:ENSORLG00000028409.1 transcript:ENSORLT00000040305.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 48.521 bits (114), Expect = 2.767e-6
Identity = 25/73 (34.25%), Postives = 39/73 (53.42%), Query Frame = 3

Query:  462 ETIFIDFCGPLKQTLYGMKYIFGIIDKHSKYVSLHVFISQSEDTVVTI*KNSWILKYVAPEVIHCDRGKSFES 680
            E I +D  GPL +T    +YI  + D  SK+V  +   ++   TV     + W+ +Y AP  +H D+G +FES
Sbjct: 1482 ERIAVDVMGPLNETDRHNRYILVVQDYFSKWVEAYPVPNEQATTVAEKIVSEWVCRYGAPYELHSDQGANFES 1554

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BLAST of Retrovirus-related Pol polyprotein from transposon vs. Planmine SMEST
Match: SMESG000029259.1 (SMESG000029259.1)

HSP 1 Score: 97.8265 bits (242), Expect = 3.789e-23
Identity = 57/134 (42.54%), Postives = 80/134 (59.70%), Query Frame = 3

Query:  291 CHAEPMKAEKYVSNNFEMRNMRQTIQDVIQSYENYQKRKYTTPTKKIICKTME-LRLFETIFIDFCGPLKQTLYGMKYIFGIIDKHSKYVSLHVFISQSEDTVVTI*KNSWILKYVAPEVIHCDRGKSFESKGM 689
            CHA   K  KY+ NN +M N+   ++ VI++ E  QK K  T   K   +T++    FE I++D CGPLK+T    KYI GIID +SKY+SL     Q E T+     N WILK+ AP+ +H D GK+FE++ +
Sbjct: 3236 CHAGAQKVTKYIQNNCDMENLATEVKKVIENCERCQKMKTITTKTKEETQTIKSTEPFEKIYMDICGPLKETFNKKKYICGIIDHYSKYISLTAINKQDERTISETLLNKWILKFGAPKELHVDCGKNFEARSI 3369

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BLAST of Retrovirus-related Pol polyprotein from transposon vs. Planmine SMEST
Match: SMESG000074789.1 (SMESG000074789.1)

HSP 1 Score: 63.5438 bits (153), Expect = 1.800e-11
Identity = 40/99 (40.40%), Postives = 56/99 (56.57%), Query Frame = 3

Query:  396 QKRKYTTPT-KKIICKTMELRLFETIFIDFCGPLKQTLYGMKYIFGIIDKHSKYVSLHVFISQSEDTVVTI*KNSWILKYVAPEVIHCDRGKSFESKGM 689
            QK K TT T K+ + K     +FE IF+D CG  ++T    KYI G+ID++SKY  L   I Q E+T+        IL++  P+ I  D GK++ES  M
Sbjct:  620 QKTKVTTITMKEPVKKLKSTEMFEIIFVDDCGLPQETKRRKKYILGMIDQYSKYQILTTIIRQDEETIKRTIYEKSILRFGCPKEIKVDCGKAYESTMM 718

[Close]

BLAST of Retrovirus-related Pol polyprotein from transposon vs. Planmine SMEST
Match: SMESG000074789.1 (SMESG000074789.1)

HSP 1 Score: 63.5438 bits (153), Expect = 1.802e-11
Identity = 40/99 (40.40%), Postives = 56/99 (56.57%), Query Frame = 3

Query:  396 QKRKYTTPT-KKIICKTMELRLFETIFIDFCGPLKQTLYGMKYIFGIIDKHSKYVSLHVFISQSEDTVVTI*KNSWILKYVAPEVIHCDRGKSFESKGM 689
            QK K TT T K+ + K     +FE IF+D CG  ++T    KYI G+ID++SKY  L   I Q E+T+        IL++  P+ I  D GK++ES  M
Sbjct:  656 QKTKVTTITMKEPVKKLKSTEMFEIIFVDDCGLPQETKRRKKYILGMIDQYSKYQILTTIIRQDEETIKRTIYEKSILRFGCPKEIKVDCGKAYESTMM 754

[Close]

BLAST of Retrovirus-related Pol polyprotein from transposon vs. Planmine SMEST
Match: SMESG000074789.1 (SMESG000074789.1)

HSP 1 Score: 63.5438 bits (153), Expect = 1.951e-11
Identity = 40/99 (40.40%), Postives = 56/99 (56.57%), Query Frame = 3

Query:  396 QKRKYTTPT-KKIICKTMELRLFETIFIDFCGPLKQTLYGMKYIFGIIDKHSKYVSLHVFISQSEDTVVTI*KNSWILKYVAPEVIHCDRGKSFESKGM 689
            QK K TT T K+ + K     +FE IF+D CG  ++T    KYI G+ID++SKY  L   I Q E+T+        IL++  P+ I  D GK++ES  M
Sbjct:  672 QKTKVTTITMKEPVKKLKSTEMFEIIFVDDCGLPQETKRRKKYILGMIDQYSKYQILTTIIRQDEETIKRTIYEKSILRFGCPKEIKVDCGKAYESTMM 770

[Close]

BLAST of Retrovirus-related Pol polyprotein from transposon vs. Planmine SMEST
Match: SMESG000057289.1 (SMESG000057289.1)

HSP 1 Score: 59.6918 bits (143), Expect = 2.528e-10
Identity = 44/131 (33.59%), Postives = 62/131 (47.33%), Query Frame = 3

Query:  291 CHAEPMKAEKYVSNNFEMRNMRQTIQDVIQSYENYQKRK-YTTPTKKIICKTMELRLFETIFIDFCGPLKQTLYGMKYIFGIIDKHSKYVSLHVFISQSEDTVVTI*KNSWILKYVAPEVIHCDRGKSFES 680
            CH    K   Y+ + F   +M Q I + I   +    RK Y   TK+I+      R  E I +D      +T    KY+  IID  SK VSL V  +Q E T++    N+WI ++  PE I  D G++FE 
Sbjct:   29 CHLGIKKTLFYLKDFFFWPSMNQIIAEFINKCKICASRKIYQGQTKEILLPRTGERFLEQIVVDIA--YMETKESNKYMIVIIDSFSKLVSLSVASTQDEATILNFILNNWIYRFGRPESILTDIGRTFEG 157

The following BLAST results are available for this feature:

BLAST of Retrovirus-related Pol polyprotein from transposon vs. Ensembl Human
BLAST of Retrovirus-related Pol polyprotein from transposon vs. Ensembl Celegans
BLAST of Retrovirus-related Pol polyprotein from transposon vs. Ensembl Fly
BLAST of Retrovirus-related Pol polyprotein from transposon vs. Ensembl Zebrafish
BLAST of Retrovirus-related Pol polyprotein from transposon vs. Ensembl Xenopus
BLAST of Retrovirus-related Pol polyprotein from transposon vs. Ensembl Mouse
BLAST of Retrovirus-related Pol polyprotein from transposon vs. UniProt/SwissProt
BLAST of Retrovirus-related Pol polyprotein from transposon vs. TrEMBL
BLAST of Retrovirus-related Pol polyprotein from transposon vs. Ensembl Cavefish
BLAST of Retrovirus-related Pol polyprotein from transposon vs. Ensembl Sea Lamprey
BLAST of Retrovirus-related Pol polyprotein from transposon vs. Ensembl Yeast
BLAST of Retrovirus-related Pol polyprotein from transposon vs. Ensembl Nematostella
BLAST of Retrovirus-related Pol polyprotein from transposon vs. Ensembl Medaka
BLAST of Retrovirus-related Pol polyprotein from transposon vs. Planmine SMEST

BLAST of Retrovirus-related Pol polyprotein from transposon vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0


Match Name	E-value	Identity	Description

BLAST of Retrovirus-related Pol polyprotein from transposon vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0


Match Name	E-value	Identity	Description

BLAST of Retrovirus-related Pol polyprotein from transposon vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0


Match Name	E-value	Identity	Description

BLAST of Retrovirus-related Pol polyprotein from transposon vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0


Match Name	E-value	Identity	Description

BLAST of Retrovirus-related Pol polyprotein from transposon vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0


Match Name	E-value	Identity	Description

BLAST of Retrovirus-related Pol polyprotein from transposon vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0


Match Name	E-value	Identity	Description

BLAST of Retrovirus-related Pol polyprotein from transposon vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0


Match Name	E-value	Identity	Description

BLAST of Retrovirus-related Pol polyprotein from transposon vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5


Match Name	E-value	Identity	Description
A0A0V0RCI6	2.693e-8	29.27	Gypsy retrotransposon integrase-like protein 1 (Fr...	[more]
A0A0V1GMM2	8.574e-8	31.53	Pro-Pol polyprotein (Fragment) OS=Trichinella zimb...	[more]
A0A2G8LRM3	1.650e-7	32.46	Integrase catalytic domain-containing protein OS=S...	[more]
A0A3B3ST06	2.042e-7	28.42	Integrase catalytic domain-containing protein OS=P...	[more]
A0A0J7KHW9	3.766e-7	30.89	S68306 pol retrotransposon woot OS=Lasius niger OX...	[more]

BLAST of Retrovirus-related Pol polyprotein from transposon vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 5


Match Name	E-value	Identity	Description
ENSAMXT00000058127.1	2.012e-10	25.90	pep primary_assembly:Astyanax_mexicanus-2.0:16:354...	[more]
ENSAMXT00000031920.1	2.573e-10	32.98	pep primary_assembly:Astyanax_mexicanus-2.0:12:110...	[more]
ENSAMXT00000054209.1	1.135e-8	34.83	pep primary_assembly:Astyanax_mexicanus-2.0:APWO02...	[more]
ENSAMXT00000037741.1	2.235e-8	39.19	pep primary_assembly:Astyanax_mexicanus-2.0:6:2778...	[more]
ENSAMXT00000055645.1	3.171e-8	32.00	pep primary_assembly:Astyanax_mexicanus-2.0:APWO02...	[more]

BLAST of Retrovirus-related Pol polyprotein from transposon vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0


Match Name	E-value	Identity	Description

BLAST of Retrovirus-related Pol polyprotein from transposon vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0


Match Name	E-value	Identity	Description

BLAST of Retrovirus-related Pol polyprotein from transposon vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0


Match Name	E-value	Identity	Description

BLAST of Retrovirus-related Pol polyprotein from transposon vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 3


Match Name	E-value	Identity	Description
ENSORLT00000045127.1	9.099e-9	32.89	pep primary_assembly:ASM223467v1:10:587855:593081:...	[more]
ENSORLT00000032021.1	1.111e-8	23.81	pep primary_assembly:ASM223467v1:7:3496795:3498971...	[more]
ENSORLT00000040305.1	2.767e-6	34.25	pep primary_assembly:ASM223467v1:1:25459511:254666...	[more]

BLAST of Retrovirus-related Pol polyprotein from transposon vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5


Match Name	E-value	Identity	Description
SMESG000029259.1	3.789e-23	42.54	SMESG000029259.1	[more]
SMESG000074789.1	1.800e-11	40.40	SMESG000074789.1	[more]
SMESG000074789.1	1.802e-11	40.40	SMESG000074789.1	[more]
SMESG000074789.1	1.951e-11	40.40	SMESG000074789.1	[more]
SMESG000057289.1	2.528e-10	33.59	SMESG000057289.1	[more]

Analyses

This transcript is derived from or has results from the following analyses


Analysis Name	Date Performed
Embryonic Stages	2016-07-25
Schmidtea mediterranea smed_20140614 BLASTX Human e!99	2016-08-08
Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99	2020-05-01
Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99	2020-05-01
Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99	2016-08-08
Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99	2020-05-01
Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99	2020-05-01
Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt	2020-05-01
Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL	2020-05-01
Schmidtea mediterranea Sexual smed_20140614 transcriptome	2016-07-25
Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99	2020-05-08
Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99	2020-05-08
Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46	2020-05-08
Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46	2020-05-08
Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99	2020-05-08
Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST	2020-05-08

Sequences

The following sequences are available for this feature:

transcript sequence
protein sequence

transcript sequence

>SMED30018321 ID=SMED30018321|Name=Retrovirus-related Pol polyprotein from transposon|organism=Schmidtea mediterranea sexual|type=transcript|length=689bp
TGATTATTTACATAATTTATTTTATTTTGCTTTTGTCAAATTTAGAAGAA
AACACCGAAAGTAATTACCGTACAATTCTAAATATGAATCAACTTTTTAA
GCAGTTCAGATATAGATTATCAATGTAGAAAAGGAAAAGATCATTCTAAA
GCAAATACATTATCAAAGGGTAAATATGCCAAGTATATTCAATGTCAAAA
ATGAAAAAACCAAATTCAAAATAAAAGATAATAAACCATTAATAGTCAAT
AGTCGAAAAATAGATTTTTCTACAAAATCGTGTATAAAACTGTCATGCTG
AACCAATGAAAGCAGAAAAGTATGTATCAAATAATTTTGAAATGAGAAAT
ATGAGACAAACAATACAAGATGTGATTCAAAGTTATGAAAATTATCAGAA
GCGCAAATATACAACTCCAACAAAAAAAATAATTTGTAAAACCATGGAAC
TCAGATTATTTGAAACTATATTTATTGATTTTTGTGGCCCATTGAAACAA
ACACTATATGGAATGAAATATATTTTCGGAATCATCGACAAGCATAGTAA
ATATGTATCCCTTCATGTCTTTATATCGCAAAGCGAAGATACCGTTGTTA
CAATTTAAAAAAATAGTTGGATATTAAAATATGTTGCTCCAGAGGTTATA
CACTGTGATAGAGGGAAATCATTTGAAAGTAAAGGTATG

protein sequence of SMED30018321-orf-1

>SMED30018321-orf-1 ID=SMED30018321-orf-1|Name=SMED30018321-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=101bp
MKAEKYVSNNFEMRNMRQTIQDVIQSYENYQKRKYTTPTKKIICKTMELR
LFETIFIDFCGPLKQTLYGMKYIFGIIDKHSKYVSLHVFISQSEDTVVTI
*

Annotated Terms

The following terms have been associated with this transcript:

Vocabulary: **molecular function**
Term	Definition
GO:0004190	aspartic-type endopeptidase activity
GO:0008270	zinc ion binding
GO:0003676	nucleic acid binding
GO:0003964	RNA-directed DNA polymerase activity

Vocabulary: **biological process**
Term	Definition
GO:0006508	proteolysis
GO:0006278	RNA-dependent DNA biosynthetic process
GO:0015074	DNA integration

Vocabulary: **INTERPRO**
Term	Definition
IPR012337	RNaseH-like_sf

Main menu

Retrovirus-related Pol polyprotein from transposon

Zeng et. al., 2018

▻ Overview

▻ Neoblast Population

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell Population

Overview

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

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

Neoblast Population

Sub-lethal Irradiated Surviving X1 and X2 Cell Population

Davies et. al., 2017

PAGE et. al., 2020

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

PAGE Curations: 3

Owlery

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