Transposon Ty3-I Gag-Pol poly

Overview


Name	Transposon Ty3-I Gag-Pol poly
Smed ID	SMED30000810
Length (bp)	713

Neoblast Clusters

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

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

SMED30000810

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

PAGE Curations: 1

Expressed In	Reference Transcript	Gene Models	Published Transcript	Transcriptome	Publication	Specimen	Lifecycle	Evidence
epidermis	SMED30000810		dd_Smed_v4_38928_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 Transposon Ty3-I Gag-Pol poly vs. TrEMBL
Match: A0A2H8TVW1 (Retrovirus-related Pol polyprotein from transposon 412 OS=Melanaphis sacchari OX=742174 GN=POL_5 PE=4 SV=1)

HSP 1 Score: 48.1358 bits (113), Expect = 1.465e-10
Identity = 29/85 (34.12%), Postives = 47/85 (55.29%), Query Frame = 3

Query:  276 DKILDPLNKVKYLSFIDIESAYYQVELEEESKLKAAFII-QC*FCFNMMHLGIGAELQTSQKFMTLII*DMT*IKA*VLLYNILI 527
            D+ILD L + +Y S +D+ S Y+QV + EE + K AF   +  + F  M  G+     T Q+ M  ++  +  +KA V L +I+I
Sbjct:  323 DEILDQLGRSRYYSTLDLASGYHQVPIREEDRQKTAFSTDKGHYEFIQMPFGLSGAPSTFQRLMNSVLIGINGVKAFVYLDDIII 407

HSP 2 Score: 34.6538 bits (78), Expect = 1.465e-10
Identity = 14/24 (58.33%), Postives = 20/24 (83.33%), Query Frame = 2

Query:  122 LDENKIIEKSESPWNSLVVRAPKK 193
            L+ENKII+ S+SPWN+ ++  PKK
Sbjct:  267 LEENKIIQPSDSPWNAPLIVVPKK 290

HSP 3 Score: 31.187 bits (69), Expect = 1.465e-10
Identity = 13/23 (56.52%), Postives = 16/23 (69.57%), Query Frame = 1

Query:  208 RMSLDFIALNSNTVGSAFPIPNL 276
            R+ +DF  LN  TVG AFPIP +
Sbjct:  300 RVCVDFRRLNQITVGDAFPIPRI 322

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BLAST of Transposon Ty3-I Gag-Pol poly vs. TrEMBL
Match: X1WLD0 (Uncharacterized protein OS=Acyrthosiphon pisum OX=7029 PE=4 SV=1)

HSP 1 Score: 45.0542 bits (105), Expect = 9.116e-9
Identity = 28/85 (32.94%), Postives = 45/85 (52.94%), Query Frame = 3

Query:  276 DKILDPLNKVKYLSFIDIESAYYQVELEEESKLKAAFII-QC*FCFNMMHLGIGAELQTSQKFMTLII*DMT*IKA*VLLYNILI 527
            + ILD L K KY + +D+ S Y+QV +  E + K AF   Q  + FN M  G+     T Q+ M  ++  +   +A V L +I++
Sbjct:  600 NSILDQLGKAKYFTCLDMASGYHQVLIRPEDREKTAFSTDQGHYEFNRMCFGLKGAPATFQRLMNRVLQGINGYRAFVYLDDIIV 684

HSP 2 Score: 31.5722 bits (70), Expect = 9.116e-9
Identity = 13/26 (50.00%), Postives = 19/26 (73.08%), Query Frame = 1

Query:  199 SDIRMSLDFIALNSNTVGSAFPIPNL 276
            S  R+ +DF  LN+ TVG AFP+P++
Sbjct:  574 SKYRVVVDFRKLNNLTVGDAFPMPDI 599

HSP 3 Score: 30.8018 bits (68), Expect = 9.116e-9
Identity = 14/27 (51.85%), Postives = 20/27 (74.07%), Query Frame = 2

Query:  113 VRNLDENKIIEKSESPWNSLVVRAPKK 193
            V+ L ++KII  SESPWN+ ++  PKK
Sbjct:  541 VKQLMQDKIISPSESPWNAPLLIVPKK 567

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BLAST of Transposon Ty3-I Gag-Pol poly vs. TrEMBL
Match: A0A2S2QW04 (Retrovirus-related Pol polyprotein OS=Sipha flava OX=143950 GN=POL_31 PE=4 SV=1)

HSP 1 Score: 42.3578 bits (98), Expect = 2.660e-8
Identity = 28/83 (33.73%), Postives = 43/83 (51.81%), Query Frame = 3

Query:  282 ILDPLNKVKYLSFIDIESAYYQVELEEESKLKAAFII-QC*FCFNMMHLGIGAELQTSQKFMTLII*DMT*IKA*VLLYNILI 527
            ILD L K KY + +D+   Y+QV +  E   K AF   +  F F  +  G+     T Q+ M  ++  +T +KA V L +I+I
Sbjct:  145 ILDQLGKSKYYTTLDLAQGYHQVRMHPEHTAKTAFSTDRGHFEFLRVPFGLKGAPATFQRLMNTVLAGLTGMKAFVYLDDIII 227

HSP 2 Score: 33.4982 bits (75), Expect = 2.660e-8
Identity = 14/29 (48.28%), Postives = 21/29 (72.41%), Query Frame = 2

Query:  107 RIVRNLDENKIIEKSESPWNSLVVRAPKK 193
            R V+ L+E+K+I  S SPWN+ ++  PKK
Sbjct:   82 RQVKQLEEDKVIAPSRSPWNAPLLVVPKK 110

HSP 3 Score: 30.4166 bits (67), Expect = 2.660e-8
Identity = 11/23 (47.83%), Postives = 17/23 (73.91%), Query Frame = 1

Query:  208 RMSLDFIALNSNTVGSAFPIPNL 276
            R+ +DF  LN  +VG A+P+PN+
Sbjct:  120 RVCVDFRKLNQISVGDAYPLPNI 142

[Close]

BLAST of Transposon Ty3-I Gag-Pol poly vs. TrEMBL
Match: A0A2S2NWU7 (Retrovirus-related Pol polyprotein OS=Schizaphis graminum OX=13262 GN=POL_27 PE=4 SV=1)

HSP 1 Score: 41.9726 bits (97), Expect = 5.202e-8
Identity = 26/83 (31.33%), Postives = 44/83 (53.01%), Query Frame = 3

Query:  282 ILDPLNKVKYLSFIDIESAYYQVELEEESKLKAAF-IIQC*FCFNMMHLGIGAELQTSQKFMTLII*DMT*IKA*VLLYNILI 527
            ILD L K KY S +D+ S Y+Q+E++ +   K AF   +  + F  M  G+     T Q+ M  ++  +   +A V L +I++
Sbjct:  307 ILDQLGKAKYFSCLDLASGYHQIEIDPKDMEKTAFSTSEGHYEFKRMCFGLKGAPATFQRLMNRVLNGINGSRAFVYLDDIIV 389

HSP 2 Score: 33.4982 bits (75), Expect = 5.202e-8
Identity = 15/27 (55.56%), Postives = 21/27 (77.78%), Query Frame = 2

Query:  113 VRNLDENKIIEKSESPWNSLVVRAPKK 193
            V+ L++NKII  SESPWN+ ++  PKK
Sbjct:  246 VKQLEQNKIIVPSESPWNAPLLIVPKK 272

HSP 3 Score: 29.261 bits (64), Expect = 5.202e-8
Identity = 11/27 (40.74%), Postives = 19/27 (70.37%), Query Frame = 1

Query:  196 ASDIRMSLDFIALNSNTVGSAFPIPNL 276
            +   R+ +DF  LN+ T+G AFP+P++
Sbjct:  278 SKKYRVVVDFRKLNNITIGDAFPMPDI 304

[Close]

BLAST of Transposon Ty3-I Gag-Pol poly vs. TrEMBL
Match: A0A2S2NNZ3 (Retrovirus-related Pol polyprotein OS=Schizaphis graminum OX=13262 GN=POL_0 PE=4 SV=1)

HSP 1 Score: 41.9726 bits (97), Expect = 7.015e-8
Identity = 28/83 (33.73%), Postives = 43/83 (51.81%), Query Frame = 3

Query:  282 ILDPLNKVKYLSFIDIESAYYQVELEEESKLKAAFII-QC*FCFNMMHLGIGAELQTSQKFMTLII*DMT*IKA*VLLYNILI 527
            ILD L K KY + +D+   Y+QV +  E   K AF   +  F F  +  G+     T Q+ M  ++  +T +KA V L +I+I
Sbjct:  349 ILDQLGKSKYYTTLDLAQGYHQVRMHPEHTEKTAFSTDKGHFEFLRVPFGLKGAPATFQRLMNTVLAGLTGLKAFVYLDDIII 431

HSP 2 Score: 31.5722 bits (70), Expect = 7.015e-8
Identity = 12/24 (50.00%), Postives = 18/24 (75.00%), Query Frame = 1

Query:  208 RMSLDFIALNSNTVGSAFPIPNLI 279
            R+ +DF  LN  +VG A+P+PN+I
Sbjct:  324 RVCVDFRKLNQISVGDAYPLPNII 347

HSP 3 Score: 30.8018 bits (68), Expect = 7.015e-8
Identity = 13/29 (44.83%), Postives = 20/29 (68.97%), Query Frame = 2

Query:  107 RIVRNLDENKIIEKSESPWNSLVVRAPKK 193
            R ++ L+E+ II  S SPWN+ ++  PKK
Sbjct:  286 RQMKQLEEDNIIAPSRSPWNAPLLVVPKK 314

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BLAST of Transposon Ty3-I Gag-Pol poly vs. Ensembl Cavefish
Match: ENSAMXT00000057694.1 (pep primary_assembly:Astyanax_mexicanus-2.0:APWO02002300.1:326161:328805:1 gene:ENSAMXG00000038480.1 transcript:ENSAMXT00000057694.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 45.8246 bits (107), Expect = 1.393e-8
Identity = 23/58 (39.66%), Postives = 34/58 (58.62%), Query Frame = 3

Query:  294 LNKVKYLSFIDIESAYYQVELEEESKLKAAFIIQC*FC-FNMMHLGIGAELQTSQKFM 464
            L+  ++ S +D++S YYQVE+EEE K K AF+    F  FN +  G+     T Q+ M
Sbjct:   56 LHGSRWFSVMDLKSGYYQVEVEEEDKHKTAFVTPMGFWEFNRLPQGVTNAPSTFQRVM 113

HSP 2 Score: 31.5722 bits (70), Expect = 1.393e-8
Identity = 11/30 (36.67%), Postives = 21/30 (70.00%), Query Frame = 1

Query:  187 QKEASDIRMSLDFIALNSNTVGSAFPIPNL 276
            +K++  IR+ +D+  LNS T+  A+ +PN+
Sbjct:   20 KKKSGAIRLCVDYRKLNSQTIKDAYALPNI 49

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BLAST of Transposon Ty3-I Gag-Pol poly vs. Ensembl Cavefish
Match: ENSAMXT00000032063.1 (pep primary_assembly:Astyanax_mexicanus-2.0:APWO02001664.1:281551:284311:1 gene:ENSAMXG00000035893.1 transcript:ENSAMXT00000032063.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 43.8986 bits (102), Expect = 2.784e-8
Identity = 24/65 (36.92%), Postives = 34/65 (52.31%), Query Frame = 3

Query:  273 FDKILDPLNKVKYLSFIDIESAYYQVELEEESKLKAAFIIQC*FC-FNMMHLGIGAELQTSQKFM 464
             ++ L  L   K+ S +D++S YYQ+E+ E  K K AF+    F  FN M  GI     T Q+ M
Sbjct:  403 LEETLSALAGSKWFSVLDLKSGYYQIEVAESDKHKTAFVCPLGFWEFNRMPQGITNAPSTFQRLM 467

HSP 2 Score: 32.3426 bits (72), Expect = 2.784e-8
Identity = 11/31 (35.48%), Postives = 20/31 (64.52%), Query Frame = 1

Query:  184 AQKEASDIRMSLDFIALNSNTVGSAFPIPNL 276
             +K+  D+R+ +D+  LN  T+  A+ +PNL
Sbjct:  373 VKKKTGDVRLCIDYRKLNLQTIKDAYALPNL 403

[Close]

BLAST of Transposon Ty3-I Gag-Pol poly vs. Ensembl Cavefish
Match: ENSAMXT00000047000.1 (pep primary_assembly:Astyanax_mexicanus-2.0:21:9985706:9990085:1 gene:ENSAMXG00000032330.1 transcript:ENSAMXT00000047000.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 43.8986 bits (102), Expect = 6.793e-8
Identity = 24/65 (36.92%), Postives = 34/65 (52.31%), Query Frame = 3

Query:  273 FDKILDPLNKVKYLSFIDIESAYYQVELEEESKLKAAFIIQC*FC-FNMMHLGIGAELQTSQKFM 464
             ++    L   K+ S +D++S YYQ+E+EE  K K AF+    F  FN M  GI     T Q+ M
Sbjct:  429 LEETFSTLTGSKWFSVLDLKSGYYQIEVEETDKPKTAFVCPLGFWEFNRMPQGITNAPSTFQRLM 493

HSP 2 Score: 30.8018 bits (68), Expect = 6.793e-8
Identity = 12/30 (40.00%), Postives = 20/30 (66.67%), Query Frame = 1

Query:  187 QKEASDIRMSLDFIALNSNTVGSAFPIPNL 276
            +K+  D+R+ +D+  LN  TV  A+ +PNL
Sbjct:  400 RKKNGDVRLCIDYRKLNLQTVKDAYALPNL 429

[Close]

BLAST of Transposon Ty3-I Gag-Pol poly vs. Ensembl Cavefish
Match: ENSAMXT00000041729.1 (pep primary_assembly:Astyanax_mexicanus-2.0:20:22787350:22790973:1 gene:ENSAMXG00000030022.1 transcript:ENSAMXT00000041729.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 43.8986 bits (102), Expect = 1.437e-7
Identity = 26/86 (30.23%), Postives = 44/86 (51.16%), Query Frame = 3

Query:  273 FDKILDPLNKVKYLSFIDIESAYYQVELEEESKLKAAFIIQC*FC-FNMMHLGIGAELQTSQKFMTLII*DMT*IKA*VLLYNILI 527
             ++    L   K+ S +D++S YYQ+E+EE  K K AF+    F  FN M  G+     T Q+ M   + D+   +  V L ++++
Sbjct:  102 LEEAFSALTGSKWFSVLDLKSGYYQIEVEETDKPKTAFVCPLGFWEFNRMPQGVTNAPSTFQRLMERCMGDINLKEVLVFLDDLIV 187

HSP 2 Score: 29.6462 bits (65), Expect = 1.437e-7
Identity = 11/30 (36.67%), Postives = 20/30 (66.67%), Query Frame = 1

Query:  187 QKEASDIRMSLDFIALNSNTVGSAFPIPNL 276
            +K+  D+R+ +D+  LN  T+  A+ +PNL
Sbjct:   73 RKKNGDVRLCIDYRKLNLRTIKDAYALPNL 102

[Close]

BLAST of Transposon Ty3-I Gag-Pol poly vs. Ensembl Cavefish
Match: ENSAMXT00000042297.1 (pep primary_assembly:Astyanax_mexicanus-2.0:APWO02002193.1:21:2557:1 gene:ENSAMXG00000030761.1 transcript:ENSAMXT00000042297.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 43.5134 bits (101), Expect = 1.474e-7
Identity = 23/64 (35.94%), Postives = 36/64 (56.25%), Query Frame = 3

Query:  276 DKILDPLNKVKYLSFIDIESAYYQVELEEESKLKAAFIIQC*FC-FNMMHLGIGAELQTSQKFM 464
            ++    L+  ++ S +D++S YYQVE+EEE K K AF+    F  FN +  G+     T Q+ M
Sbjct:  199 EETFSALHGSRWFSVMDLKSGYYQVEVEEEDKHKTAFVTPMGFWEFNRLPQGVTNAPSTFQRVM 262

HSP 2 Score: 30.0314 bits (66), Expect = 1.474e-7
Identity = 11/30 (36.67%), Postives = 21/30 (70.00%), Query Frame = 1

Query:  187 QKEASDIRMSLDFIALNSNTVGSAFPIPNL 276
            +K++  IR+ +D+  LNS T+  A+ +PN+
Sbjct:  169 KKKSGAIRLCVDYRKLNSQTIKDAYALPNI 198

[Close]

BLAST of Transposon Ty3-I Gag-Pol poly vs. Ensembl Medaka
Match: ENSORLT00000033871.1 (pep primary_assembly:ASM223467v1:5:24767545:24770648:1 gene:ENSORLG00000024878.1 transcript:ENSORLT00000033871.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 42.743 bits (99), Expect = 1.599e-7
Identity = 26/86 (30.23%), Postives = 44/86 (51.16%), Query Frame = 3

Query:  273 FDKILDPLNKVKYLSFIDIESAYYQVELEEESKLKAAFIIQC*FC-FNMMHLGIGAELQTSQKFMTLII*DMT*IKA*VLLYNILI 527
             ++    L   K+ S +D++S YYQ+E++E  K K AF+    F  FN M  GI     T Q+ M   + D+   +  V L ++++
Sbjct:  259 LEETFSALTGSKWFSVLDLKSGYYQIEVDEVDKQKTAFVCPLGFWEFNRMPQGITNAPSTFQRLMEKCMGDINLKEVLVFLDDLIV 344

HSP 2 Score: 30.8018 bits (68), Expect = 1.599e-7
Identity = 11/30 (36.67%), Postives = 20/30 (66.67%), Query Frame = 1

Query:  187 QKEASDIRMSLDFIALNSNTVGSAFPIPNL 276
            +K+  D+R+ +D+  LN  T+  A+ +PNL
Sbjct:  230 RKKNGDVRLCIDYRKLNMQTIKDAYALPNL 259

[Close]

BLAST of Transposon Ty3-I Gag-Pol poly vs. Ensembl Medaka
Match: ENSORLT00000034814.1 (uncharacterized LOC111946697 [Source:NCBI gene;Acc:111946697])

HSP 1 Score: 48.9062 bits (115), Expect = 1.817e-7
Identity = 34/89 (38.20%), Postives = 48/89 (53.93%), Query Frame = 3

Query:  276 DKILDPLNKVKYLSFIDIESAYYQVELEEESKLKAAFIIQC*FC-FNMMHLGIGAELQTSQKFMTLII*DMT*IKA*VLLY-NILIPFG 536
            ++ LD L+  K+ S +D+ S YYQ+ + EE K K AFI    F  F  M  GI     T Q+ M   + DM  ++  VL+Y + LI FG
Sbjct:  924 EEALDSLSGSKWFSVLDLRSGYYQIAMAEEDKEKTAFICPLGFFQFERMPQGITGAPATFQRLMEKTVGDMNLLE--VLVYLDDLIVFG 1010

HSP 2 Score: 24.2534 bits (51), Expect = 1.817e-7
Identity = 11/28 (39.29%), Postives = 16/28 (57.14%), Query Frame = 1

Query:  187 QKEASDIRMSLDFIALNSNTVGSAFPIP 270
            +K+   IRM +D+  LNS TV   +  P
Sbjct:  894 RKKNGAIRMCIDYRLLNSRTVPDQYTTP 921

[Close]

BLAST of Transposon Ty3-I Gag-Pol poly vs. Ensembl Medaka
Match: ENSORLT00000040080.1 (pep primary_assembly:ASM223467v1:4:6109106:6115792:1 gene:ENSORLG00000022989.1 transcript:ENSORLT00000040080.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 42.743 bits (99), Expect = 4.593e-7
Identity = 25/79 (31.65%), Postives = 43/79 (54.43%), Query Frame = 3

Query:  294 LNKVKYLSFIDIESAYYQVELEEESKLKAAFIIQC*FC-FNMMHLGIGAELQTSQKFMTLII*DMT*IKA*VLLYNILI 527
            L+   + S +D++S +YQ+E+EE  K K AF+    F  FN M  GI     T Q+ M   + ++   +A V L ++++
Sbjct:  450 LSGSHWFSVLDLKSGFYQIEMEEADKQKTAFVCPLGFFEFNRMPQGITNAPSTFQRLMERCVGELNLKQALVFLDDLIV 528

HSP 2 Score: 29.261 bits (64), Expect = 4.593e-7
Identity = 11/30 (36.67%), Postives = 20/30 (66.67%), Query Frame = 1

Query:  187 QKEASDIRMSLDFIALNSNTVGSAFPIPNL 276
            +K+  D+R+ +D+  LN  TV  ++ +PNL
Sbjct:  414 RKKNGDVRLCIDYRKLNLQTVKDSYALPNL 443

[Close]

BLAST of Transposon Ty3-I Gag-Pol poly vs. Ensembl Medaka
Match: ENSORLT00000036641.1 (pep primary_assembly:ASM223467v1:3:12394909:12399588:1 gene:ENSORLG00000024795.1 transcript:ENSORLT00000036641.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 42.743 bits (99), Expect = 4.593e-7
Identity = 25/79 (31.65%), Postives = 43/79 (54.43%), Query Frame = 3

Query:  294 LNKVKYLSFIDIESAYYQVELEEESKLKAAFIIQC*FC-FNMMHLGIGAELQTSQKFMTLII*DMT*IKA*VLLYNILI 527
            L+   + S +D++S +YQ+E+EE  K K AF+    F  FN M  GI     T Q+ M   + ++   +A V L ++++
Sbjct:  450 LSGSHWFSVLDLKSGFYQIEMEEADKQKTAFVCPLGFFEFNRMPQGITNAPSTFQRLMERCVGELNLKQALVFLDDLIV 528

HSP 2 Score: 29.261 bits (64), Expect = 4.593e-7
Identity = 11/30 (36.67%), Postives = 20/30 (66.67%), Query Frame = 1

Query:  187 QKEASDIRMSLDFIALNSNTVGSAFPIPNL 276
            +K+  D+R+ +D+  LN  TV  ++ +PNL
Sbjct:  414 RKKNGDVRLCIDYRKLNLQTVKDSYALPNL 443

[Close]

BLAST of Transposon Ty3-I Gag-Pol poly vs. Ensembl Medaka
Match: ENSORLT00000041485.1 (pep primary_assembly:ASM223467v1:15:30019002:30023522:-1 gene:ENSORLG00000028547.1 transcript:ENSORLT00000041485.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 41.2022 bits (95), Expect = 1.161e-6
Identity = 23/79 (29.11%), Postives = 43/79 (54.43%), Query Frame = 3

Query:  294 LNKVKYLSFIDIESAYYQVELEEESKLKAAFIIQC*FC-FNMMHLGIGAELQTSQKFMTLII*DMT*IKA*VLLYNILI 527
            L   K+ + +D++S YYQ+E++E+ + K AF+    F  +N M  G+     T Q+ M   + D+   +  V L +I++
Sbjct:  398 LTGSKWFTVLDLKSGYYQIEMDEKDRAKTAFVTPLGFWEWNRMPQGVTNAPSTFQRLMEKCMGDLNLREVLVFLDDIIV 476

HSP 2 Score: 29.6462 bits (65), Expect = 1.161e-6
Identity = 11/30 (36.67%), Postives = 19/30 (63.33%), Query Frame = 1

Query:  187 QKEASDIRMSLDFIALNSNTVGSAFPIPNL 276
            +K   D+R+ +D+  LN  T+  A+ +PNL
Sbjct:  362 RKRNGDVRLCIDYRKLNLQTIKDAYALPNL 391

[Close]

BLAST of Transposon Ty3-I Gag-Pol poly vs. Planmine SMEST
Match: SMESG000080238.1 (SMESG000080238.1)

HSP 1 Score: 73.559 bits (179), Expect = 6.105e-15
Identity = 45/85 (52.94%), Postives = 53/85 (62.35%), Query Frame = 3

Query:  276 DKILDPLNKVKYLSFIDIESAYYQVELEEESKLKAAFII-QC*FCFNMMHLGIGAELQTSQKFMTLII*DMT*IKA*VLLYNILI 527
            D++LD LN  KY S  D+ +A YQVEL++ESKLK AF   Q  FCFN M   I     T QK MTLII DM   +A V L NIL+
Sbjct:  164 DEMLDSLNGAKYFSLTDLGNANYQVELDQESKLKTAFSTRQDQFCFNTMPFRIAVAPSTFQKLMTLIIGDMMWNEAQVYLDNILL 248

[Close]

BLAST of Transposon Ty3-I Gag-Pol poly vs. Planmine SMEST
Match: SMESG000052960.1 (SMESG000052960.1)

HSP 1 Score: 68.5514 bits (166), Expect = 2.705e-14
Identity = 50/124 (40.32%), Postives = 65/124 (52.42%), Query Frame = 3

Query:   15 NLGKTNILKHLIETSCYPIRLLPRKQTMYYEELLEIWTKTK*LRKVSHLGIH*LYVRP-KRSF*HTNVFRFYSFKFKYGWISFSDS*FDKILDPLNKVKYLSFIDIESAYYQVELEEESKLKAA 383
            ++GK +ILKH IET+C P+ +  R+Q M+YEE LE   K     K++       Y  P  R         F          +F     D+ LD LN  KY S ID+++AYYQVELEEESKLK  
Sbjct:   16 DIGKVDILKHRIETNCGPVPIKSRQQPMHYEEKLEEIVKNLAKNKITE-KCESPYNSPIARVPKKGTSIDFRILISNTVRPAFQIPNVDETLDSLNGTKYFSSIDLKNAYYQVELEEESKLKTV 138

[Close]

BLAST of Transposon Ty3-I Gag-Pol poly vs. Planmine SMEST
Match: SMESG000033479.1 (SMESG000033479.1)

HSP 1 Score: 67.3958 bits (163), Expect = 1.066e-12
Identity = 42/85 (49.41%), Postives = 56/85 (65.88%), Query Frame = 3

Query:  276 DKILDPLNKVKYLSFIDIESAYYQVELEEESKLKAAFII-QC*FCFNMMHLGIGAELQTSQKFMTLII*DMT*IKA*VLLYNILI 527
            D++ D L+  KY S ID+ +AYYQVEL++E+KLK AF   Q  F FN+M  GI +   T QK +TLII D+   +A V L +ILI
Sbjct:  271 DEMFDSLSGAKYFSSIDLGNAYYQVELDKENKLKTAFSTRQGQFRFNIMPFGIASAPLTFQKLITLIIGDVMWNEAVVYLDDILI 355

[Close]

BLAST of Transposon Ty3-I Gag-Pol poly vs. Planmine SMEST
Match: SMESG000029259.1 (SMESG000029259.1)

HSP 1 Score: 65.855 bits (159), Expect = 4.410e-12
Identity = 59/187 (31.55%), Postives = 94/187 (50.27%), Query Frame = 3

Query:   12 MNLGKTNILKHLIETSCYPIRLLPRKQTMYYEELLEIWTKTK*LRKVSHLGIH*LYVRPKRSF*HTNVFRFYSFKFK--------------YGWISFSDS*FDKILDPLNKVKYLSFIDIESAYYQVELEEESKLKAAFII-QC*FCFNMMHLGIGAELQTSQKFMTLII*DMT*IKA*VLLYNILI 527
             ++G TN++KH I T   PI + PR+Q +  E+ +E     + ++ + + GI    +R   S  +T +   +  + K                  +F     D+ILD L+  +Y S ID+ +AYYQV+L++ES+ K AF   +  FCFN M  GI A   T Q+ MT ++ D+      V L +ILI
Sbjct: 2709 WDIGCTNLIKHKIITKGEPIMIKPRRQPINLEDKIE-----EAIKNLENNGI----IRKCNSPWNTPLVCVWKKEKKDIRLCLDFRQLNKITERQAFPMPNVDEILDILHGSRYFSSIDLGNAYYQVKLDKESQEKTAFSTKEGQFCFNRMPFGIAAAPGTFQELMTKVLKDLWKDGVMVYLDDILI 2886

[Close]

BLAST of Transposon Ty3-I Gag-Pol poly vs. Planmine SMEST
Match: SMESG000062996.1 (SMESG000062996.1)

HSP 1 Score: 62.003 bits (149), Expect = 2.665e-11
Identity = 56/162 (34.57%), Postives = 77/162 (47.53%), Query Frame = 3

Query:   15 NLGKTNILKHLIETSCYPIRLLPRKQTMY----YEELLEIWTKTK*LRKVSHLGIH*LYV--RPKRSF*HTNVFRFY-SFKFKYGWISFSDS*FDKILDPLNKVKYLSFIDIESAYYQVELEEESKLKAAFII-QC*FCFNMMHLGIGAELQTSQKFMTLII 476
            +LG T ++ H I+TS  PI   PR+Q M+     EEL++   +   +RK        L +  +P  S      FR   S   K+   SF       +LD L K    S ID+  AYYQVEL E S++KA F   +  FCFN +  G+     T QK M  I+
Sbjct:   93 DLGHTKVITHEIKTSGPPILQNPRRQPMHLEGKVEELVQNLLEAGVVRKCQSPWNTPLVIVGKPDGSIRMCLDFRLLNSVTEKF---SFPIPEMQLLLDCLGKSMIFSSIDLRQAYYQVELNENSQIKAEFSTKEGQFCFNRLPFGLSTAPATFQKRMHQIL 251

The following BLAST results are available for this feature:

BLAST of Transposon Ty3-I Gag-Pol poly vs. Ensembl Human
BLAST of Transposon Ty3-I Gag-Pol poly vs. Ensembl Celegans
BLAST of Transposon Ty3-I Gag-Pol poly vs. Ensembl Fly
BLAST of Transposon Ty3-I Gag-Pol poly vs. Ensembl Zebrafish
BLAST of Transposon Ty3-I Gag-Pol poly vs. Ensembl Xenopus
BLAST of Transposon Ty3-I Gag-Pol poly vs. Ensembl Mouse
BLAST of Transposon Ty3-I Gag-Pol poly vs. UniProt/SwissProt
BLAST of Transposon Ty3-I Gag-Pol poly vs. TrEMBL
BLAST of Transposon Ty3-I Gag-Pol poly vs. Ensembl Cavefish
BLAST of Transposon Ty3-I Gag-Pol poly vs. Ensembl Sea Lamprey
BLAST of Transposon Ty3-I Gag-Pol poly vs. Ensembl Yeast
BLAST of Transposon Ty3-I Gag-Pol poly vs. Ensembl Nematostella
BLAST of Transposon Ty3-I Gag-Pol poly vs. Ensembl Medaka
BLAST of Transposon Ty3-I Gag-Pol poly vs. Planmine SMEST

BLAST of Transposon Ty3-I Gag-Pol poly 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 Transposon Ty3-I Gag-Pol poly 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 Transposon Ty3-I Gag-Pol poly 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 Transposon Ty3-I Gag-Pol poly 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 Transposon Ty3-I Gag-Pol poly 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 Transposon Ty3-I Gag-Pol poly 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 Transposon Ty3-I Gag-Pol poly 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 Transposon Ty3-I Gag-Pol poly vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5


Match Name	E-value	Identity	Description
A0A2H8TVW1	1.465e-10	34.12	Retrovirus-related Pol polyprotein from transposon...	[more]
X1WLD0	9.116e-9	32.94	Uncharacterized protein OS=Acyrthosiphon pisum OX=...	[more]
A0A2S2QW04	2.660e-8	33.73	Retrovirus-related Pol polyprotein OS=Sipha flava ...	[more]
A0A2S2NWU7	5.202e-8	31.33	Retrovirus-related Pol polyprotein OS=Schizaphis g...	[more]
A0A2S2NNZ3	7.015e-8	33.73	Retrovirus-related Pol polyprotein OS=Schizaphis g...	[more]

BLAST of Transposon Ty3-I Gag-Pol poly 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
ENSAMXT00000057694.1	1.393e-8	39.66	pep primary_assembly:Astyanax_mexicanus-2.0:APWO02...	[more]
ENSAMXT00000032063.1	2.784e-8	36.92	pep primary_assembly:Astyanax_mexicanus-2.0:APWO02...	[more]
ENSAMXT00000047000.1	6.793e-8	36.92	pep primary_assembly:Astyanax_mexicanus-2.0:21:998...	[more]
ENSAMXT00000041729.1	1.437e-7	30.23	pep primary_assembly:Astyanax_mexicanus-2.0:20:227...	[more]
ENSAMXT00000042297.1	1.474e-7	35.94	pep primary_assembly:Astyanax_mexicanus-2.0:APWO02...	[more]

BLAST of Transposon Ty3-I Gag-Pol poly 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 Transposon Ty3-I Gag-Pol poly 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 Transposon Ty3-I Gag-Pol poly 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 Transposon Ty3-I Gag-Pol poly vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 5


Match Name	E-value	Identity	Description
ENSORLT00000033871.1	1.599e-7	30.23	pep primary_assembly:ASM223467v1:5:24767545:247706...	[more]
ENSORLT00000034814.1	1.817e-7	38.20	uncharacterized LOC111946697 [Source:NCBI gene;Acc...	[more]
ENSORLT00000040080.1	4.593e-7	31.65	pep primary_assembly:ASM223467v1:4:6109106:6115792...	[more]
ENSORLT00000036641.1	4.593e-7	31.65	pep primary_assembly:ASM223467v1:3:12394909:123995...	[more]
ENSORLT00000041485.1	1.161e-6	29.11	pep primary_assembly:ASM223467v1:15:30019002:30023...	[more]

BLAST of Transposon Ty3-I Gag-Pol poly vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5


Match Name	E-value	Identity	Description
SMESG000080238.1	6.105e-15	52.94	SMESG000080238.1	[more]
SMESG000052960.1	2.705e-14	40.32	SMESG000052960.1	[more]
SMESG000033479.1	1.066e-12	49.41	SMESG000033479.1	[more]
SMESG000029259.1	4.410e-12	31.55	SMESG000029259.1	[more]
SMESG000062996.1	2.665e-11	34.57	SMESG000062996.1	[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 mediteranean smed_20140614 Interproscan	2020-05-01
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

transcript sequence

>SMED30000810 ID=SMED30000810|Name=Transposon Ty3-I Gag-Pol poly|organism=Schmidtea mediterranea sexual|type=transcript|length=713bp
ATATGTACTAAATGAATTTAGGAAAAACAAATATTTTAAAACACCTTATT
GAAACGAGTTGTTATCCGATACGATTATTACCTCGGAAACAAACTATGTA
CTATGAAGAATTGTTAGAAATTTGGACGAAAACAAAATAATTGAGAAAAG
TGAGTCACCTTGGAATTCATTAGTTGTACGTGCGCCCAAAAAGAAGCTTC
TGACATACGAATGTCTTTAGATTTTATAGCTTTAAATTCAAATACGGTTG
GATCAGCTTTTCCGATTCCTAATTTGATAAAATTCTAGATCCTCTGAATA
AAGTAAAATATTTATCATTTATAGATATAGAAAGTGCTTATTATCAAGTT
GAATTAGAGGAGGAAAGTAAATTGAAAGCAGCATTTATAATACAGTGTTA
ATTTTGCTTCAATATGATGCATCTTGGCATAGGTGCTGAACTACAAACAT
CTCAAAAATTCATGACATTGATAATTTGAGATATGACGTGAATTAAAGCA
TGAGTTTTGTTATACAATATACTGATACCTTTTGGTGGGTTATCGGTGTT
GTGATCTTGATATTTTACTAGCGCCATCTTGACTTCATTAACACATGCAT
ACGAAGTCGTCAATCCTTTGTTAGGCAATGATGGTATTGTGACAAAGGGT
TTTTAATCCGATACCGAAACTGTTCCACTTCGGGTGTATCTTGGATTCAG
CGAGCTGCCGAGA

Annotated Terms

The following terms have been associated with this transcript:

Vocabulary: **molecular function**
Term	Definition
GO:0003676	nucleic acid binding
GO:0004190	aspartic-type endopeptidase activity

Vocabulary: **biological process**
Term	Definition
GO:0015074	DNA integration
GO:0006508	proteolysis

Vocabulary: **Planarian Anatomy**
Term	Definition
PLANA:0002032	epidermal cell

Main menu

Transposon Ty3-I Gag-Pol poly

Zeng et. al., 2018

Overview

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

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

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: 1

Owlery

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