SMED30030512

Overview


Name	SMED30030512
Smed ID	SMED30030512
Length (bp)	309

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

SMED30030512

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

PAGE Curations: 4

Expressed In	Reference Transcript	Gene Models	Published Transcript	Transcriptome	Publication
nervous system	SMED30030512	h1SMcG0004612	dd_Smed_v4_18799_0_1	dd_Smed_v4	PMID:29674431 Fincher et al., 2018
cephalic ganglia	SMED30030512	h1SMcG0004612	dd_Smed_v4_18799_0_1	dd_Smed_v4	PMID:29674431 Fincher et al., 2018
non-ciliated neuron	SMED30030512	h1SMcG0004612	dd_Smed_v4_18799_0_1	dd_Smed_v4	PMID:29674431 Fincher et al., 2018
cilated neuron	SMED30030512	h1SMcG0004612	dd_Smed_v4_18799_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 SMED30030512 vs. Ensembl Zebrafish
Match: tmtopsb (teleost multiple tissue opsin b [Source:ZFIN;Acc:ZDB-GENE-091118-50])

HSP 1 Score: 53.5286 bits (127), Expect = 2.105e-9
Identity = 26/80 (32.50%), Postives = 46/80 (57.50%), Query Frame = 2

Query:   47 SQTSHSEKRFIFVGIFLSYLLGLGMALVPILTDFSSYVPEGVG--CSVDWSSRKLGNIIYISIMFVIDFVIPLMIILTTY 280
            +Q   +  R + +GI  S++  +   L P+   +S Y PEG G  CSV+W++R   N+ YI  +FV   ++P ++I+ +Y
Sbjct:   45 TQADSTNYRKVVIGIAFSWIYSMVWTLPPLF-GWSCYGPEGPGTTCSVNWAARTPNNVSYIVCLFVFCLILPFIVIVYSY 123

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BLAST of SMED30030512 vs. Ensembl Zebrafish
Match: tmtopsb (teleost multiple tissue opsin b [Source:ZFIN;Acc:ZDB-GENE-091118-50])

HSP 1 Score: 53.5286 bits (127), Expect = 2.914e-9
Identity = 27/84 (32.14%), Postives = 48/84 (57.14%), Query Frame = 2

Query:   47 SQTSHSEKRFIFVGIFLSYLLGLGMALVPILTDFSSYVPEGVG--CSVDWSSRKLGNIIYISIMFVIDFVIPLMIILTTYISIL 292
            +Q   +  R + +GI  S++  +   L P+   +S Y PEG G  CSV+W++R   N+ YI  +FV   ++P ++I+ +Y  +L
Sbjct:  195 TQADSTNYRKVVIGIAFSWIYSMVWTLPPLF-GWSCYGPEGPGTTCSVNWAARTPNNVSYIVCLFVFCLILPFIVIVYSYGRLL 277

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BLAST of SMED30030512 vs. Ensembl Zebrafish
Match: tmtopsb (teleost multiple tissue opsin b [Source:ZFIN;Acc:ZDB-GENE-091118-50])

HSP 1 Score: 53.1434 bits (126), Expect = 3.284e-9
Identity = 27/84 (32.14%), Postives = 48/84 (57.14%), Query Frame = 2

Query:   47 SQTSHSEKRFIFVGIFLSYLLGLGMALVPILTDFSSYVPEGVG--CSVDWSSRKLGNIIYISIMFVIDFVIPLMIILTTYISIL 292
            +Q   +  R + +GI  S++  +   L P+   +S Y PEG G  CSV+W++R   N+ YI  +FV   ++P ++I+ +Y  +L
Sbjct:  144 TQADSTNYRKVVIGIAFSWIYSMVWTLPPLF-GWSCYGPEGPGTTCSVNWAARTPNNVSYIVCLFVFCLILPFIVIVYSYGRLL 226

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BLAST of SMED30030512 vs. Ensembl Zebrafish
Match: CABZ01063651.1 (pep chromosome:GRCz11:2:4631335:4642407:-1 gene:ENSDARG00000103674.2 transcript:ENSDART00000162044.2 gene_biotype:protein_coding transcript_biotype:protein_coding gene_symbol:CABZ01063651.1)

HSP 1 Score: 49.6766 bits (117), Expect = 4.134e-8
Identity = 25/84 (29.76%), Postives = 47/84 (55.95%), Query Frame = 2

Query:   47 SQTSHSEKRFIFVGIFLSYLLGLGMALVPILTDFSSYVPEGVG--CSVDWSSRKLGNIIYISIMFVIDFVIPLMIILTTYISIL 292
            ++   +  + +  G+ +S++  L   L P+   +S Y PEG G  CSVDW+++   NI YI  +F+   ++P ++I+  Y  +L
Sbjct:  146 TEADATNYKKVIGGVLMSWIYSLIWTLPPLF-GWSRYGPEGPGTTCSVDWTTKTANNISYIICLFIFCLIVPFLVIIFCYGKLL 228

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BLAST of SMED30030512 vs. Ensembl Zebrafish
Match: opn1sw2 (opsin 1 (cone pigments), short-wave-sensitive 2 [Source:NCBI gene;Acc:30435])

HSP 1 Score: 46.9802 bits (110), Expect = 3.730e-7
Identity = 25/79 (31.65%), Postives = 40/79 (50.63%), Query Frame = 2

Query:   83 VGIFLSYLLGLGMALVPILTDFSSYVPEGVGCSV--DW--SSRKLGNIIYISIMFVIDFVIPLMIILTTYISILIKVNI 307
             G  L + + L   L P+L  +S Y+PEG+ CS   DW  ++ K  N  Y+  +F   F +P   I+  Y  +LI + +
Sbjct:   34 AGCILPWCMALAAGLPPLL-GWSRYIPEGLQCSCGPDWYTTNNKFNNESYVMFLFCFCFAVPFSTIVFCYGQLLITLKL 111

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BLAST of SMED30030512 vs. Ensembl Xenopus
Match: ttll8 (tubulin tyrosine ligase like 8 [Source:Xenbase;Acc:XB-GENE-6258704])

HSP 1 Score: 51.6026 bits (122), Expect = 1.632e-8
Identity = 32/102 (31.37%), Postives = 53/102 (51.96%), Query Frame = 2

Query:    2 LALTRARTVHRTQIVSQTSHSEKRFIFVGIFLSYLLGLGMALVPILTDFSSYVPEGVG--CSVDWSSRKLGNIIYISIMFVIDFVIPLMIILTTYISILIKV 301
            L+  R  T+ R+     T++ +    ++GI +S++  L   L P+   +S Y PEG G  CSV+W SR   NI YI  +F+    +P  +I+  Y  +L  +
Sbjct:  146 LSYERYCTMLRSTEADLTNYKKA---WLGILVSWIYSLVWTLPPLF-GWSKYGPEGPGTTCSVNWHSRDANNISYIVCLFIFCLALPFAVIVYCYGRLLFAI 243

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BLAST of SMED30030512 vs. Ensembl Xenopus
Match: ENSXETT00000039933.1 (blue-sensitive opsin-like [Source:NCBI gene;Acc:100485989])

HSP 1 Score: 46.2098 bits (108), Expect = 1.236e-6
Identity = 27/78 (34.62%), Postives = 45/78 (57.69%), Query Frame = 2

Query:   83 VGIFLSYLLGLGMALVPILTDFSSYVPEGVGCSV--DWSS--RKLGNIIYISIMFVIDFVIPLMIILTTYISILIKVN 304
            +G  L++++GL +A  P L  +S Y+PEG+ CS   DW +   K  N  Y+  +F   F  PL II+ +Y  +L+ ++
Sbjct:  164 LGCILTWVMGL-LAATPPLLGWSRYIPEGLQCSCGPDWYTVNNKWNNESYVIFLFCFCFGFPLAIIVFSYGRLLLTLH 240

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BLAST of SMED30030512 vs. Ensembl Xenopus
Match: ENSXETT00000039908.1 (blue-sensitive opsin-like [Source:NCBI gene;Acc:100485989])

HSP 1 Score: 46.2098 bits (108), Expect = 1.270e-6
Identity = 27/78 (34.62%), Postives = 45/78 (57.69%), Query Frame = 2

Query:   83 VGIFLSYLLGLGMALVPILTDFSSYVPEGVGCSV--DWSS--RKLGNIIYISIMFVIDFVIPLMIILTTYISILIKVN 304
            +G  L++++GL +A  P L  +S Y+PEG+ CS   DW +   K  N  Y+  +F   F  PL II+ +Y  +L+ ++
Sbjct:  160 LGCILTWVMGL-LAATPPLLGWSRYIPEGLQCSCGPDWYTVNNKWNNESYVIFLFCFCFGFPLAIIVFSYGRLLLTLH 236

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BLAST of SMED30030512 vs. Ensembl Xenopus
Match: ENSXETT00000039895.1 (blue-sensitive opsin-like [Source:NCBI gene;Acc:100485989])

HSP 1 Score: 46.2098 bits (108), Expect = 1.307e-6
Identity = 27/78 (34.62%), Postives = 45/78 (57.69%), Query Frame = 2

Query:   83 VGIFLSYLLGLGMALVPILTDFSSYVPEGVGCSV--DWSS--RKLGNIIYISIMFVIDFVIPLMIILTTYISILIKVN 304
            +G  L++++GL +A  P L  +S Y+PEG+ CS   DW +   K  N  Y+  +F   F  PL II+ +Y  +L+ ++
Sbjct:  159 LGCILTWVMGL-LAATPPLLGWSRYIPEGLQCSCGPDWYTVNNKWNNESYVIFLFCFCFGFPLAIIVFSYGRLLLTLH 235

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BLAST of SMED30030512 vs. Ensembl Xenopus
Match: ENSXETT00000039873.1 (blue-sensitive opsin-like [Source:NCBI gene;Acc:100485989])

HSP 1 Score: 46.2098 bits (108), Expect = 1.331e-6
Identity = 27/78 (34.62%), Postives = 45/78 (57.69%), Query Frame = 2

Query:   83 VGIFLSYLLGLGMALVPILTDFSSYVPEGVGCSV--DWSS--RKLGNIIYISIMFVIDFVIPLMIILTTYISILIKVN 304
            +G  L++++GL +A  P L  +S Y+PEG+ CS   DW +   K  N  Y+  +F   F  PL II+ +Y  +L+ ++
Sbjct:  163 LGCILTWVMGL-LAATPPLLGWSRYIPEGLQCSCGPDWYTVNNKWNNESYVIFLFCFCFGFPLAIIVFSYGRLLLTLH 239

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BLAST of SMED30030512 vs. Ensembl Mouse
Match: Rho (rhodopsin [Source:MGI Symbol;Acc:MGI:97914])

HSP 1 Score: 43.8986 bits (102), Expect = 5.680e-6
Identity = 24/78 (30.77%), Postives = 45/78 (57.69%), Query Frame = 2

Query:   83 VGIFLSYLLGLGMALVPILTDFSSYVPEGVGCS--VDWSSRK--LGNIIYISIMFVIDFVIPLMIILTTYISILIKVN 304
            +G+  ++++ L  A  P L  +S Y+PEG+ CS  +D+ + K  + N  ++  MFV+ F IP+++I   Y  ++  V 
Sbjct:   13 MGVVFTWIMALACA-APPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVK 89

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BLAST of SMED30030512 vs. UniProt/SwissProt
Match: sp|O42307|OPSD_COTBO (Rhodopsin (Fragment) OS=Cottinella boulengeri OX=61639 GN=rho PE=3 SV=1)

HSP 1 Score: 51.2174 bits (121), Expect = 9.912e-8
Identity = 34/99 (34.34%), Postives = 56/99 (56.57%), Query Frame = 2

Query:   20 RTVHRTQIVSQTSHSEKRFIFVGIFLSYLLGLGMALVPILTDFSSYVPEGVGCS--VDWSSRKLG--NIIYISIMFVIDFVIPLMIILTTYISILIKVN 304
            R +   + +S+   +E   I +G+  S+++GL  A VP L  +S Y+PEG+ CS  VD+ +R  G  N  ++  MF++ F+IPL +I   Y  +L  V 
Sbjct:  106 RWIVVCKPISKFRFTEDHAI-MGLAFSWVMGLACA-VPPLVGWSRYIPEGMKCSCGVDYYTRAEGFNNESFVIYMFIVHFLIPLSVIFFCYGRLLCAVK 202

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BLAST of SMED30030512 vs. UniProt/SwissProt
Match: sp|O42427|OPSD_LIMBE (Rhodopsin (Fragment) OS=Limnocottus bergianus OX=61633 GN=rho PE=3 SV=1)

HSP 1 Score: 48.521 bits (114), Expect = 9.526e-7
Identity = 29/78 (37.18%), Postives = 46/78 (58.97%), Query Frame = 2

Query:   83 VGIFLSYLLGLGMALVPILTDFSSYVPEGVGCS--VDWSSRKLG--NIIYISIMFVIDFVIPLMIILTTYISILIKVN 304
            +G+  S+++ L  A VP L  +S Y+PEG+ CS  VD+ +R  G  N  ++  MF++ F+IPL +I   Y  +L  V 
Sbjct:  126 MGLAFSWVMALACA-VPPLVGWSRYIPEGMQCSCGVDYYTRAEGFNNESFVIYMFIVHFLIPLSVIFFCYGRLLCAVK 202

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BLAST of SMED30030512 vs. UniProt/SwissProt
Match: sp|P79807|OPSD_MYRVI (Rhodopsin (Fragment) OS=Myripristis violacea OX=47701 GN=rho PE=2 SV=1)

HSP 1 Score: 48.521 bits (114), Expect = 1.278e-6
Identity = 30/77 (38.96%), Postives = 47/77 (61.04%), Query Frame = 2

Query:   83 VGIFLSYLLGLGMALVPILTDFSSYVPEGVGCS--VDWSSRKLG--NIIYISIMFVIDFVIPLMIILTTYISILIKV 301
            +G+ L++++GL    VP L  +S Y+PEG+ CS  +D+ +R  G  N  Y+  MFV  F+IPL++I   Y  +L  V
Sbjct:  152 MGVTLTWVMGLACT-VPPLVGWSRYIPEGMQCSCGIDYYTRAEGFNNDSYVLYMFVCHFLIPLVVIFFCYGRLLCAV 227

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BLAST of SMED30030512 vs. UniProt/SwissProt
Match: sp|O42294|OPSD_ABYKO (Rhodopsin (Fragment) OS=Abyssocottus korotneffi OX=61637 GN=rho PE=3 SV=1)

HSP 1 Score: 47.7506 bits (112), Expect = 2.151e-6
Identity = 28/78 (35.90%), Postives = 46/78 (58.97%), Query Frame = 2

Query:   83 VGIFLSYLLGLGMALVPILTDFSSYVPEGVGCS--VDWSSRKLG--NIIYISIMFVIDFVIPLMIILTTYISILIKVN 304
            +G+  ++++ L  A VP L  +S Y+PEG+ CS  VD+ +R  G  N  ++  MF++ F+IPL +I   Y  +L  V 
Sbjct:  126 MGLAFTWVMALACA-VPPLVGWSRYIPEGMQCSCGVDYYTRAEGFNNESFVIYMFIVHFLIPLSVIFFCYGRLLCAVK 202

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BLAST of SMED30030512 vs. UniProt/SwissProt
Match: sp|O42300|OPSD_BATMU (Rhodopsin (Fragment) OS=Batrachocottus multiradiatus OX=61628 GN=rho PE=3 SV=1)

HSP 1 Score: 46.595 bits (109), Expect = 4.485e-6
Identity = 29/78 (37.18%), Postives = 45/78 (57.69%), Query Frame = 2

Query:   83 VGIFLSYLLGLGMALVPILTDFSSYVPEGVGCS--VDWSSRKLG--NIIYISIMFVIDFVIPLMIILTTYISILIKVN 304
            +G+  S+++ L  A VP L  +S Y+PEG+ CS  VD+ +R  G  N  ++  MF++ F IPL +I   Y  +L  V 
Sbjct:  126 MGLAFSWVMALTCA-VPPLVGWSRYIPEGMQCSCGVDYYTRAEGFNNESFVIYMFIVHFPIPLSVIFFCYGRLLCAVK 202

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BLAST of SMED30030512 vs. TrEMBL
Match: G1KAU7 (G_PROTEIN_RECEP_F1_2 domain-containing protein OS=Anolis carolinensis OX=28377 GN=LOC100558074 PE=3 SV=2)

HSP 1 Score: 60.8474 bits (146), Expect = 1.660e-8
Identity = 32/88 (36.36%), Postives = 52/88 (59.09%), Query Frame = 2

Query:   47 SQTSHSEKRFIFVGIFLSYLLGLGMALVPILTDFSSYVPEGVG--CSVDWSSRKLGNIIYISIMFVIDFVIPLMIILTTYISILIKVN 304
            ++   +  + +++GIFLS++  L  +L P+   +SSY PEG G  CSV+W SR   NI YI  +F+   VIP ++I+  Y  +L  + 
Sbjct:  149 TEADATNYKKVWMGIFLSWIYSLFWSLPPLF-GWSSYGPEGPGTTCSVNWHSRDANNISYIICLFIFCLVIPFIVIVYCYGKLLCAIK 235

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BLAST of SMED30030512 vs. TrEMBL
Match: A0A1A8CT77 (Teleost multiple tissue opsin a (Fragment) OS=Nothobranchius kadleci OX=1051664 GN=TMTOPSA PE=3 SV=1)

HSP 1 Score: 60.4622 bits (145), Expect = 1.706e-8
Identity = 33/88 (37.50%), Postives = 51/88 (57.95%), Query Frame = 2

Query:   47 SQTSHSEKRFIFVGIFLSYLLGLGMALVPILTDFSSYVPEGVG--CSVDWSSRKLGNIIYISIMFVIDFVIPLMIILTTYISILIKVN 304
            ++   S  R I +GI LS++  L M  +P L  +S Y PEG G  CSVDW+++   NI YI  +FV  F++P ++I+  Y  +L  + 
Sbjct:   46 AEADSSNYRKISLGILLSWVYSL-MWTLPPLFGWSHYGPEGPGTTCSVDWTAKTANNISYIICLFVFCFIVPFLVIVLCYGKLLYAIK 132

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BLAST of SMED30030512 vs. TrEMBL
Match: A0A091EH85 (Pinopsin (Fragment) OS=Corvus brachyrhynchos OX=85066 GN=N302_05998 PE=3 SV=1)

HSP 1 Score: 59.3066 bits (142), Expect = 1.786e-8
Identity = 40/102 (39.22%), Postives = 54/102 (52.94%), Query Frame = 2

Query:    2 LALTRARTVHRTQIVSQTSHSEKRFIFVGIFLSYLLGLGMALVPILTDFSSYVPEGVG--CSVDWSSRKLGNIIYISIMFVIDFVIPLMIILTTYISILIKV 301
            L+  R  T+ RT     T++   R  + GI LS+   L +  VP L  +SSY PEG G  CSV+W S+   N  YI  +FV   VIP  II+ +Y  +L  V
Sbjct:   11 LSYERYCTMTRTTEADTTNY---RKTWTGIILSWTYSL-LWTVPPLFGWSSYGPEGPGITCSVNWHSKDANNASYIVCLFVFCLVIPFAIIVYSYGKLLCAV 108

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BLAST of SMED30030512 vs. TrEMBL
Match: A0A1A8ULH4 (Teleost multiple tissue opsin a (Fragment) OS=Nothobranchius furzeri OX=105023 GN=TMTOPSA PE=3 SV=1)

HSP 1 Score: 60.4622 bits (145), Expect = 1.858e-8
Identity = 33/88 (37.50%), Postives = 51/88 (57.95%), Query Frame = 2

Query:   47 SQTSHSEKRFIFVGIFLSYLLGLGMALVPILTDFSSYVPEGVG--CSVDWSSRKLGNIIYISIMFVIDFVIPLMIILTTYISILIKVN 304
            ++   S  R I +GI LS++  L M  +P L  +S Y PEG G  CSVDW+++   NI YI  +FV  F++P ++I+  Y  +L  + 
Sbjct:   37 AEADSSNYRKISLGILLSWVYSL-MWTLPPLFGWSHYGPEGPGTTCSVDWTAKTANNISYIICLFVFCFIVPFLVIVLCYGKLLYAIK 123

[Close]

BLAST of SMED30030512 vs. TrEMBL
Match: A0A1A7Z938 (Teleost multiple tissue opsin a (Fragment) OS=Nothobranchius furzeri OX=105023 GN=TMTOPSA PE=3 SV=1)

HSP 1 Score: 60.4622 bits (145), Expect = 2.022e-8
Identity = 33/88 (37.50%), Postives = 51/88 (57.95%), Query Frame = 2

Query:   47 SQTSHSEKRFIFVGIFLSYLLGLGMALVPILTDFSSYVPEGVG--CSVDWSSRKLGNIIYISIMFVIDFVIPLMIILTTYISILIKVN 304
            ++   S  R I +GI LS++  L M  +P L  +S Y PEG G  CSVDW+++   NI YI  +FV  F++P ++I+  Y  +L  + 
Sbjct:   51 AEADSSNYRKISLGILLSWVYSL-MWTLPPLFGWSHYGPEGPGTTCSVDWTAKTANNISYIICLFVFCFIVPFLVIVLCYGKLLYAIK 137

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BLAST of SMED30030512 vs. Ensembl Cavefish
Match: ENSAMXT00000055655.1 (vertebrate ancient opsin-like [Source:NCBI gene;Acc:103036092])

HSP 1 Score: 53.9138 bits (128), Expect = 1.567e-9
Identity = 28/84 (33.33%), Postives = 47/84 (55.95%), Query Frame = 2

Query:   47 SQTSHSEKRFIFVGIFLSYLLGLGMALVPILTDFSSYVPEGVG--CSVDWSSRKLGNIIYISIMFVIDFVIPLMIILTTYISIL 292
            ++   +  R + VG+ LS+   L    VP    +S Y PEG G  CSVDW+++   NI YI  +F+   ++P ++I+ +Y  +L
Sbjct:  129 TEADATNYRKVAVGVALSWAYSLAWT-VPPFFGWSRYGPEGPGTTCSVDWTTKTANNISYIICLFIFCLILPFLVIVYSYGKLL 211

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BLAST of SMED30030512 vs. Ensembl Cavefish
Match: tmtopsb (pinopsin-like [Source:NCBI gene;Acc:103030045])

HSP 1 Score: 48.9062 bits (115), Expect = 9.033e-8
Identity = 25/85 (29.41%), Postives = 46/85 (54.12%), Query Frame = 2

Query:   44 VSQTSHSEKRFIFVGIFLSYLLGLGMALVPILTDFSSYVPEGVG--CSVDWSSRKLGNIIYISIMFVIDFVIPLMIILTTYISIL 292
             +Q   +  R + +GI  S++  +   L P+   +S Y PEG G  CSV+W+++   N+ YI  +F    ++P  +I+ +Y  +L
Sbjct:  146 ATQADSTNYRKVIMGITFSWIYSMIWTLPPLF-GWSRYGPEGPGTTCSVNWAAKTANNVSYIICLFFFCLILPFFVIIYSYGKLL 229

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BLAST of SMED30030512 vs. Ensembl Cavefish
Match: opn9 (opsin 9 [Source:ZFIN;Acc:ZDB-GENE-141216-390])

HSP 1 Score: 48.9062 bits (115), Expect = 1.073e-7
Identity = 32/94 (34.04%), Postives = 55/94 (58.51%), Query Frame = 2

Query:   41 IVSQTSHS---EKRFIFVGIFLSYLLGLGMALVPILTDFSSYVPE--GVGCSVDWS--SRKLGNIIYISIMFVIDFVIPLMIILTTYISILIKV 301
            ++ QT +S   E++ + + I + +   L  A +P+   F SY PE  G  CS++W   +  L   IYI +M ++ F++P +IILT+Y +I+I V
Sbjct:  120 LIKQTFYSQWIERKHVSMSIVVMWAYTLFWASLPVF-GFGSYGPEPYGTSCSINWWRMNSSLNERIYIYLMLLMCFIMPTLIILTSYTAIIITV 212

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BLAST of SMED30030512 vs. Ensembl Cavefish
Match: opn4xb (opsin 4xb [Source:NCBI gene;Acc:563080])

HSP 1 Score: 45.4394 bits (106), Expect = 1.442e-6
Identity = 33/103 (32.04%), Postives = 53/103 (51.46%), Query Frame = 2

Query:    2 LALTRARTVHRTQIVSQTSHSEKRFIFVGIFLSYLLGLGMALVPILTDFSSYVPEGV--GCSVDWSSRKLGNIIYISIMFVIDFVIPLMIILTTYISILIKVN 304
            LA++  R +  T+ +     + K   F+ I L ++  L  +L P L  +S+YVPEG+   C+ D++S   GN  Y   +    F IPL+IIL  Y  + + V 
Sbjct:  111 LAISVDRYLVITRPLQAMQWNSKCRTFIIITLVWIYSLAWSLAP-LIGWSAYVPEGLMTSCTWDYASPAAGNRSYTLSLCCCVFFIPLIIILYCYTCMFLSVR 212

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BLAST of SMED30030512 vs. Ensembl Cavefish
Match: rhol (blue-sensitive opsin-like [Source:NCBI gene;Acc:103047117])

HSP 1 Score: 44.669 bits (104), Expect = 2.428e-6
Identity = 27/78 (34.62%), Postives = 44/78 (56.41%), Query Frame = 2

Query:   83 VGIFLSYLLGLGMALVPILTDFSSYVPEGVGCS--VDW--SSRKLGNIIYISIMFVIDFVIPLMIILTTYISILIKVN 304
            +G+  S+++    AL P+L ++S ++PEG+ CS  VD+   S  L N  ++  MF + F IPL +I   Y  +L  V 
Sbjct:  155 LGVGFSWMMAFSCALPPLL-EWSRFIPEGLQCSCGVDYYTESPHLFNESFVIYMFAVHFTIPLTVISFCYTWLLCTVK 231

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BLAST of SMED30030512 vs. Ensembl Sea Lamprey
Match: parapinopsina (parapinopsin a [Source:ZFIN;Acc:ZDB-GENE-101129-1])

HSP 1 Score: 41.5874 bits (96), Expect = 6.164e-6
Identity = 22/76 (28.95%), Postives = 39/76 (51.32%), Query Frame = 2

Query:   83 VGIFLSYLLGLGMALVPILTDFSSYVPEGVG--CSVDWSSRKLGNIIYISIMFVIDFVIPLMIILTTYISILIKVN 304
             G+ +S+   L  +  P L  +  Y  EGVG  C+ DW+        Y++  F+  F +P++IIL  Y  ++I ++
Sbjct:   35 CGVAISWTWALAWS-APPLFGWGRYHYEGVGTSCAPDWADSSPSGRSYMTTYFIFCFALPMIIILFCYTKLMIAIH 109

[Close]

BLAST of SMED30030512 vs. Ensembl Nematostella
Match: EDO41487 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7S4B1])

HSP 1 Score: 41.2022 bits (95), Expect = 9.900e-6
Identity = 30/99 (30.30%), Postives = 50/99 (50.51%), Query Frame = 2

Query:    2 LALTRARTVHRTQIVSQTSHSEKRFIFVGIFLSYLLGLGMALVPILTDFSSYVPEGVG--CSVDWSSRKLGNIIYISIMFVIDFVIPLMIILTTYISIL 292
            L++ R    HR Q         +R I   +F+ +L  +     P    +S++VPE     C+VDW S K  +IIYI  + ++ +VIP+ + + +Y SI 
Sbjct:   33 LSIKRKIVHHRIQ--------RRRLIRTSVFI-WLTAILWGAFPFF-GWSNFVPESKQKVCAVDWGSSKPLDIIYIVCILLLFYVIPIAVTVISYSSIF 121

[Close]

BLAST of SMED30030512 vs. Ensembl Medaka
Match: ENSORLT00000031545.1 (vertebrate ancient opsin [Source:NCBI gene;Acc:101168518])

HSP 1 Score: 55.4546 bits (132), Expect = 3.992e-10
Identity = 32/88 (36.36%), Postives = 49/88 (55.68%), Query Frame = 2

Query:   47 SQTSHSEKRFIFVGIFLSYLLGLGMALVPILTDFSSYVPEGVG--CSVDWSSRKLGNIIYISIMFVIDFVIPLMIILTTYISILIKVN 304
            ++   S  R I +GI LS+   L +  +P L  +S Y PEG G  CSVDW+++   NI YI  +FV   ++P M+I+  Y  +L  + 
Sbjct:  147 AEADSSNYRKISLGIILSWGYSL-LWTLPPLFGWSHYGPEGPGTTCSVDWTAKTANNISYIICLFVFCLIVPFMVIVFCYGKLLYAIK 233

[Close]

BLAST of SMED30030512 vs. Ensembl Medaka
Match: tmtops1b (pinopsin-like [Source:NCBI gene;Acc:101172366])

HSP 1 Score: 48.1358 bits (113), Expect = 2.047e-7
Identity = 27/76 (35.53%), Postives = 41/76 (53.95%), Query Frame = 2

Query:   71 RFIFVGIFLSYLLGLGMALVPILTDFSSYVPEGVG--CSVDWSSRKLGNIIYISIMFVIDFVIPLMIILTTYISIL 292
            R    GI  S+L  +   + P+L  +S Y PEG G  CSVDW ++   NI YI  +F    ++P  +I+ +Y  +L
Sbjct:  252 RPALGGICFSWLYSVAWTVPPLL-GWSRYGPEGPGTTCSVDWKTQTPNNISYIICLFTFCLLLPFGVIVYSYGKML 326

[Close]

BLAST of SMED30030512 vs. Ensembl Medaka
Match: opn4xb (melanopsin-A [Source:NCBI gene;Acc:101173945])

HSP 1 Score: 46.595 bits (109), Expect = 6.399e-7
Identity = 31/87 (35.63%), Postives = 46/87 (52.87%), Query Frame = 2

Query:   50 QTSH-SEKRFIFVGIFLSYLLGLGMALVPILTDFSSYVPEGV--GCSVDWSSRKLGNIIYISIMFVIDFVIPLMIILTTYISILIKV 301
            QT H S KR   + IFL +   L  +L P L  +SSY+PEG+   C+ D+ +    N  Y  ++    F IPL IIL  Y+ + + +
Sbjct:  135 QTIHWSSKRKTTLAIFLVWFYSLAWSLAP-LVGWSSYIPEGLMTSCTWDYVTYTPANRSYTMMLCCFVFFIPLGIILYCYLRMFLSI 220

[Close]

BLAST of SMED30030512 vs. Ensembl Medaka
Match: opn4xb (melanopsin-A [Source:NCBI gene;Acc:101173945])

HSP 1 Score: 46.595 bits (109), Expect = 6.920e-7
Identity = 31/87 (35.63%), Postives = 46/87 (52.87%), Query Frame = 2

Query:   50 QTSH-SEKRFIFVGIFLSYLLGLGMALVPILTDFSSYVPEGV--GCSVDWSSRKLGNIIYISIMFVIDFVIPLMIILTTYISILIKV 301
            QT H S KR   + IFL +   L  +L P L  +SSY+PEG+   C+ D+ +    N  Y  ++    F IPL IIL  Y+ + + +
Sbjct:  128 QTIHWSSKRKTTLAIFLVWFYSLAWSLAP-LVGWSSYIPEGLMTSCTWDYVTYTPANRSYTMMLCCFVFFIPLGIILYCYLRMFLSI 213

[Close]

BLAST of SMED30030512 vs. Ensembl Medaka
Match: tmtops3a (pinopsin-like [Source:NCBI gene;Acc:101167300])

HSP 1 Score: 45.4394 bits (106), Expect = 1.571e-6
Identity = 29/87 (33.33%), Postives = 47/87 (54.02%), Query Frame = 2

Query:   47 SQTSHSEKRFIFVGIFLSYLLGLGMALVPILTDFSSYVPEGVG--CSVDWSSRKLGNIIYISIMFVIDFVIPLMIILTTYISILIKV 301
            SQ   S  R  +  +  S+L  L   L P L  +SSY PEG G  CS+ W  R   ++ Y+  +F+   V+PL++++ +Y  IL+ +
Sbjct:  142 SQADLSNFRKAWFCVGGSWLYSLLWTLPPFL-GWSSYGPEGPGTTCSIQWHLRSPTSVSYVLCLFIFCLVLPLVLMVYSYGRILVAL 227

The following BLAST results are available for this feature:

BLAST of SMED30030512 vs. Ensembl Human
BLAST of SMED30030512 vs. Ensembl Celegans
BLAST of SMED30030512 vs. Ensembl Fly
BLAST of SMED30030512 vs. Ensembl Zebrafish
BLAST of SMED30030512 vs. Ensembl Xenopus
BLAST of SMED30030512 vs. Ensembl Mouse
BLAST of SMED30030512 vs. UniProt/SwissProt
BLAST of SMED30030512 vs. TrEMBL
BLAST of SMED30030512 vs. Ensembl Cavefish
BLAST of SMED30030512 vs. Ensembl Sea Lamprey
BLAST of SMED30030512 vs. Ensembl Yeast
BLAST of SMED30030512 vs. Ensembl Nematostella
BLAST of SMED30030512 vs. Ensembl Medaka
BLAST of SMED30030512 vs. Planmine SMEST

BLAST of SMED30030512 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 SMED30030512 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 SMED30030512 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 SMED30030512 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 5


Match Name	E-value	Identity	Description
tmtopsb	2.105e-9	32.50	teleost multiple tissue opsin b [Source:ZFIN;Acc:Z...	[more]
tmtopsb	2.914e-9	32.14	teleost multiple tissue opsin b [Source:ZFIN;Acc:Z...	[more]
tmtopsb	3.284e-9	32.14	teleost multiple tissue opsin b [Source:ZFIN;Acc:Z...	[more]
CABZ01063651.1	4.134e-8	29.76	pep chromosome:GRCz11:2:4631335:4642407:-1 gene:EN...	[more]
opn1sw2	3.730e-7	31.65	opsin 1 (cone pigments), short-wave-sensitive 2 [S...	[more]

BLAST of SMED30030512 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 5


Match Name	E-value	Identity	Description
ttll8	1.632e-8	31.37	tubulin tyrosine ligase like 8 [Source:Xenbase;Acc...	[more]
ENSXETT00000039933.1	1.236e-6	34.62	blue-sensitive opsin-like [Source:NCBI gene;Acc:10...	[more]
ENSXETT00000039908.1	1.270e-6	34.62	blue-sensitive opsin-like [Source:NCBI gene;Acc:10...	[more]
ENSXETT00000039895.1	1.307e-6	34.62	blue-sensitive opsin-like [Source:NCBI gene;Acc:10...	[more]
ENSXETT00000039873.1	1.331e-6	34.62	blue-sensitive opsin-like [Source:NCBI gene;Acc:10...	[more]

BLAST of SMED30030512 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 1


Match Name	E-value	Identity	Description
Rho	5.680e-6	30.77	rhodopsin [Source:MGI Symbol;Acc:MGI:97914]	[more]

BLAST of SMED30030512 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 5


Match Name	E-value	Identity	Description
sp\|O42307\|OPSD_COTBO	9.912e-8	34.34	Rhodopsin (Fragment) OS=Cottinella boulengeri OX=6...	[more]
sp\|O42427\|OPSD_LIMBE	9.526e-7	37.18	Rhodopsin (Fragment) OS=Limnocottus bergianus OX=6...	[more]
sp\|P79807\|OPSD_MYRVI	1.278e-6	38.96	Rhodopsin (Fragment) OS=Myripristis violacea OX=47...	[more]
sp\|O42294\|OPSD_ABYKO	2.151e-6	35.90	Rhodopsin (Fragment) OS=Abyssocottus korotneffi OX...	[more]
sp\|O42300\|OPSD_BATMU	4.485e-6	37.18	Rhodopsin (Fragment) OS=Batrachocottus multiradiat...	[more]

BLAST of SMED30030512 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5


Match Name	E-value	Identity	Description
G1KAU7	1.660e-8	36.36	G_PROTEIN_RECEP_F1_2 domain-containing protein OS=...	[more]
A0A1A8CT77	1.706e-8	37.50	Teleost multiple tissue opsin a (Fragment) OS=Noth...	[more]
A0A091EH85	1.786e-8	39.22	Pinopsin (Fragment) OS=Corvus brachyrhynchos OX=85...	[more]
A0A1A8ULH4	1.858e-8	37.50	Teleost multiple tissue opsin a (Fragment) OS=Noth...	[more]
A0A1A7Z938	2.022e-8	37.50	Teleost multiple tissue opsin a (Fragment) OS=Noth...	[more]

BLAST of SMED30030512 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
ENSAMXT00000055655.1	1.567e-9	33.33	vertebrate ancient opsin-like [Source:NCBI gene;Ac...	[more]
tmtopsb	9.033e-8	29.41	pinopsin-like [Source:NCBI gene;Acc:103030045]	[more]
opn9	1.073e-7	34.04	opsin 9 [Source:ZFIN;Acc:ZDB-GENE-141216-390]	[more]
opn4xb	1.442e-6	32.04	opsin 4xb [Source:NCBI gene;Acc:563080]	[more]
rhol	2.428e-6	34.62	blue-sensitive opsin-like [Source:NCBI gene;Acc:10...	[more]

BLAST of SMED30030512 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 1


Match Name	E-value	Identity	Description
parapinopsina	6.164e-6	28.95	parapinopsin a [Source:ZFIN;Acc:ZDB-GENE-101129-1]	[more]

BLAST of SMED30030512 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 SMED30030512 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1


Match Name	E-value	Identity	Description
EDO41487	9.900e-6	30.30	Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7...	[more]

BLAST of SMED30030512 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
ENSORLT00000031545.1	3.992e-10	36.36	vertebrate ancient opsin [Source:NCBI gene;Acc:101...	[more]
tmtops1b	2.047e-7	35.53	pinopsin-like [Source:NCBI gene;Acc:101172366]	[more]
opn4xb	6.399e-7	35.63	melanopsin-A [Source:NCBI gene;Acc:101173945]	[more]
opn4xb	6.920e-7	35.63	melanopsin-A [Source:NCBI gene;Acc:101173945]	[more]
tmtops3a	1.571e-6	33.33	pinopsin-like [Source:NCBI gene;Acc:101167300]	[more]

BLAST of SMED30030512 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0


Match Name	E-value	Identity	Description

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
protein sequence

transcript sequence

>SMED30030512 ID=SMED30030512|Name=SMED30030512|organism=Schmidtea mediterranea sexual|type=transcript|length=309bp
GTTGGCATTGACGAGAGCAAGAACTGTCCACAGGACTCAAATTGTTTCGC
AAACATCTCACTCAGAAAAACGGTTTATATTCGTTGGAATATTCCTTTCA
TATCTACTAGGACTCGGGATGGCACTTGTTCCGATTTTAACAGATTTTTC
AAGTTATGTTCCTGAAGGAGTCGGTTGCAGTGTCGATTGGAGCTCTAGGA
AATTAGGAAATATTATTTATATTTCAATTATGTTTGTAATTGATTTCGTG
ATACCGTTGATGATAATATTGACGACATACATAAGCATATTAATAAAAGT
GAATATTCA

protein sequence of SMED30030512-orf-1

>SMED30030512-orf-1 ID=SMED30030512-orf-1|Name=SMED30030512-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=102bp
LALTRARTVHRTQIVSQTSHSEKRFIFVGIFLSYLLGLGMALVPILTDFS
SYVPEGVGCSVDWSSRKLGNIIYISIMFVIDFVIPLMIILTTYISILIKV
NI

Annotated Terms

The following terms have been associated with this transcript:

Vocabulary: **INTERPRO**
Term	Definition
IPR000276	GPCR_Rhodpsn
IPR017452	GPCR_Rhodpsn_7TM

Vocabulary: **cellular component**
Term	Definition
GO:0016021	integral component of membrane

Vocabulary: **molecular function**
Term	Definition
GO:0004930	G-protein coupled receptor activity

Vocabulary: **biological process**
Term	Definition
GO:0007186	G-protein coupled receptor signaling pathway

InterPro

Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
None	No IPR available	GENE3D	G3DSA:1.20.1070.10		coord: 1..99 e-value: 1.4E-11 score: 45.7
None	No IPR available	PANTHER	PTHR24240:SF133		coord: 1..97
None	No IPR available	PANTHER	PTHR24240	OPSIN	coord: 1..97
None	No IPR available	CDD	cd14969	7tmA_Opsins_type2_animals	coord: 23..99 e-value: 9.2525E-11 score: 54.1344
None	No IPR available	SUPERFAMILY	SSF81321	Family A G protein-coupled receptor-like	coord: 13..98
None	No IPR available	TMHMM	TMhelix		coord: 25..47
None	No IPR available	TMHMM	TMhelix		coord: 76..98
IPR017452	GPCR, rhodopsin-like, 7TM	PROSITE	PS50262	G_PROTEIN_RECEP_F1_2	coord: 1..99 score: 10.562

Main menu

SMED30030512

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: 4

Owlery

blazegraph-runner