Sel1

Overview
NameSel1
Smed IDSMED30006840
Length (bp)863
Neoblast Clusters

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


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 Sel1 (SMED30006840) t-SNE clustered cells

Violin plots show distribution of expression levels for Sel1 (SMED30006840) in cells (dots) of each of the 12 neoblast clusters.

 

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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 Sel1 (SMED30006840) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Sel1 (SMED30006840) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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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

 

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Anatomical Expression

PAGE et. al., 2020




SMED30006840

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



PAGE Curations: 11

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30006840SMESG000003789.1 SmedASXL_012961SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30006840SMESG000003789.1 dd_Smed_v4_9387_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30006840SMESG000003789.1 dd_Smed_v4_9387_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30006840SMESG000003789.1 dd_Smed_v4_9387_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult colorimetric in situ hybridization evidence
cilated neuronSMED30006840SMESG000003789.1 dd_Smed_v4_9387_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30006840SMESG000003789.1 dd_Smed_v4_9387_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30006840SMESG000003789.1 Contig46398newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30006840SMESG000003789.1 Contig46398uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30006840SMESG000003789.1 dd_Smed_v6_9387_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
head regionSMED30006840SMESG000003789.1 OX_Smed_1.0.01458ox_Smed_v2PMID:24238224
Kao et al., 2013
whole organism asexual adult RNA-sequencing evidence
GABAergic neuronSMED30006840SMESG000003789.1 dd_Smed_v6_9387_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of Sel1 vs. TrEMBL
Match: A0A267F2L0 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig026715g1 PE=4 SV=1)

HSP 1 Score: 159.073 bits (401), Expect = 1.049e-44
Identity = 88/167 (52.69%), Postives = 110/167 (65.87%), Query Frame = 2
Query:  287 DWDPLLPYGGKVYLPRKRKPDSWLVFGIEIALISFAVXXXXXXXXXXXXXXXXTIKLYAHMGFKVRTIFELYFYKMFQEAQHQLGQRYLRGIGVPLHHQHAVHWFKKAAEQGHPHSAYNLAVAKLKGYH-DLKKGETRKLLHHASKNGVKEAADLIEEACNRGKCYD 784
            DWDP +PYGGKV+L R++KPD W V  IEI ++       YY+YY+ D+L+ H  K YAHMGFK              EAQHQ+GQRYL G GV  HH  A+ WF KAAEQGHPH++YNLAV  LKG   +LK+G+ R+ LH A+  G+ +A D+I EAC RG C D
Sbjct:   27 DWDPSMPYGGKVFLARRKKPDPWWVTAIEITVLVGTACFAYYAYYYFDHLHFHVTKAYAHMGFK--------------EAQHQIGQRYLHGKGVEQHHPEAMRWFHKAAEQGHPHASYNLAVGHLKGIQTELKRGDVRRFLHSAANQGIAQAHDIINEACARGACDD 179          
BLAST of Sel1 vs. TrEMBL
Match: A0A267GSG2 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig026715g3 PE=4 SV=1)

HSP 1 Score: 159.844 bits (403), Expect = 1.336e-44
Identity = 88/167 (52.69%), Postives = 110/167 (65.87%), Query Frame = 2
Query:  287 DWDPLLPYGGKVYLPRKRKPDSWLVFGIEIALISFAVXXXXXXXXXXXXXXXXTIKLYAHMGFKVRTIFELYFYKMFQEAQHQLGQRYLRGIGVPLHHQHAVHWFKKAAEQGHPHSAYNLAVAKLKGYH-DLKKGETRKLLHHASKNGVKEAADLIEEACNRGKCYD 784
            DWDP +PYGGKV+L R++KPD W V  IEI ++       YY+YY+ D+L+ H  K YAHMGFK              EAQHQ+GQRYL G GV  HH  A+ WF KAAEQGHPH++YNLAV  LKG   +LK+G+ R+ LH A+  G+ +A D+I EAC RG C D
Sbjct:   58 DWDPSMPYGGKVFLARRKKPDPWWVTAIEITVLVGTACFAYYAYYYFDHLHFHVTKAYAHMGFK--------------EAQHQIGQRYLHGKGVEQHHPEAMRWFHKAAEQGHPHASYNLAVGHLKGIQTELKRGDVRRFLHSAANQGIAQAHDIINEACARGACDD 210          
BLAST of Sel1 vs. TrEMBL
Match: A0A210QMX3 (Uncharacterized protein YbeT OS=Mizuhopecten yessoensis OX=6573 GN=KP79_PYT14051 PE=4 SV=1)

HSP 1 Score: 139.043 bits (349), Expect = 6.151e-37
Identity = 86/191 (45.03%), Postives = 113/191 (59.16%), Query Frame = 2
Query:  230 YYKMTSEENVRHRERYIAKD---WDPLLPYGGKVYLPRKRKPDSWLVFGIE----IALISFAVXXXXXXXXXXXXXXXXTIKLYAHMGFKVRTIFELYFYKMFQEAQHQLGQRYLRGIGVPLHHQHAVHWFKKAAEQGHPHSAYNLAVAKLKGYH-DLKKGETRKLLHHASKNGVKEAADLIEEACNRGKC 778
            + +  +E+ VR  +R I ++   +D  LPYGGKVYL RK+K D W +   E    I  +SFA+   Y                + H+ F V      Y Y  + +AQHQ+GQRYL G GV  HHQ AV WF+KA++QGHPH+AYNLAVA LKGY  DLK GE  +L+ HA+  GVKEA  ++ E C+RG C
Sbjct:    4 FSRSGAEQEVR--QRLIPENEPEYDQSLPYGGKVYLARKKKADPWHIRIAEALIIILTLSFAIYAYY---------------YFDHLHFHVTYA---YGYLGYPQAQHQVGQRYLHGKGVEKHHQKAVEWFRKASDQGHPHAAYNLAVAHLKGYKTDLKPGEAHQLISHAASKGVKEAHQVLHEVCSRGGC 174          
BLAST of Sel1 vs. TrEMBL
Match: A0A087SWK3 (Uncharacterized protein (Fragment) OS=Stegodyphus mimosarum OX=407821 GN=X975_25420 PE=4 SV=1)

HSP 1 Score: 129.028 bits (323), Expect = 3.377e-33
Identity = 77/173 (44.51%), Postives = 108/173 (62.43%), Query Frame = 2
Query:  266 RERYIA-KDWDPLLPYGGKVYLPRKRKPDSWLVFGIEIALISFAVXXXXXXXXXXXXXXXXTIKLYAHMGFKVRTIFELYFYKMFQEAQHQLGQRYLRGIGVPLHHQHAVHWFKKAAEQGHPHSAYNLAVAKLKGYH-DLKKGETRKLLHHASKNGVKEAADLIEEACNRGKC 778
            R RY+   D++  LPYGGKV L +K+KP SW+   +E+A  SF V L YYSY+H ++L+ H    YA +G                 AQH +G +YL G G+  +H  A  WF+KAA+QGHPHSAYNLAV  ++GY  D+KKGE   L+ +A++ GV+EA D++   C++G C
Sbjct:    4 RRRYVPDSDFNDNLPYGGKVVLAKKKKPQSWIYTLLEVAAFSFVVALLYYSYFHFEHLHFHVTHFYAQLGHA--------------HAQHAMGHKYLNGAGITRNHTAAFTWFRKAADQGHPHSAYNLAVGHMQGYDTDVKKGEAHDLIKYAAEQGVEEAHDVLHRVCSKGHC 162          
BLAST of Sel1 vs. TrEMBL
Match: A0A433SXH7 (Uncharacterized protein (Fragment) OS=Elysia chlorotica OX=188477 GN=EGW08_018213 PE=4 SV=1)

HSP 1 Score: 127.487 bits (319), Expect = 1.240e-32
Identity = 77/183 (42.08%), Postives = 110/183 (60.11%), Query Frame = 2
Query:  236 KMTSEENVRHRERYIAKDWDPLLPYGGKVYLPRKRKPDSWLVFGIEIALISFAVXXXXXXXXXXXXXXXXTIKLYAHMGFKVRTIFELYFYKMFQEAQHQLGQRYLRGIGVPLHHQHAVHWFKKAAEQGHPHSAYNLAVAKLKGYH-DLKKGETRKLLHHASKNGVKEAADLIEEACNRGKCY 781
            ++  ++     E  +  D+D L P   K+ L RK K D   +  +EI ++ F +I G Y +++ + ++ H    YAH+G+ V              AQHQ+GQRYL G GV  H Q A+ WFKKAA+QGHPH+AYNLAV  LKGY  DLK GE+ +L+HHA+ NGV+EA +++   C +G CY
Sbjct:    2 RLLPKDKNEEEEGSLKGDFDNL-PLKAKLKLARKAKADPAYILILEILMVIFVIIGGLYCWFYFENVHFHVTHAYAHLGYDV--------------AQHQVGQRYLHGKGVDKHPQKAMEWFKKAADQGHPHAAYNLAVGHLKGYKTDLKAGESHRLIHHAAANGVREAHEVLNSVCTKGGCY 169          
BLAST of Sel1 vs. Ensembl Nematostella
Match: EDO34903 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7SMY9])

HSP 1 Score: 107.071 bits (266), Expect = 1.759e-28
Identity = 68/181 (37.57%), Postives = 104/181 (57.46%), Query Frame = 2
Query:  239 MTSEENVRHRERYIAKDW-------DPLLPYGGKVYLPRKRKPDSWLVFGIEIALISFAVXXXXXXXXXXXXXXXXTIKLYAHMGFKVRTIFELYFYKMFQEAQHQLGQRYLRGIGVPLHHQHAVHWFKKAAEQGHPHSAYNLAVAKLKGYH-DLKKGETRKLLHHASKNGVKEAADLIEE 757
            M+++E VR R R     W       DP LPYG KVYL RK+KPD W V  IE+A++   ++   Y YY++++L+ H ++ YA++G                 AQH LG ++L+G G       A++WF++AA+ GHPH AYNL    ++GY+ D+++ E   LL  A+ NGV EA   +++
Sbjct:    1 MSAKEEVRKRSRNETPSWAPGQPDYDPNLPYGPKVYLARKKKPDPWWVTCIEVAVVVGVLLFFVYMYYYMEHLHFHVVRAYAYVGS--------------SHAQHHLGHKFLKGHGTSKDENQAMYWFREAAKNGHPHGAYNLVAGHIQGYNTDVEEHEVEPLLQMAADNGVDEAKQALKD 167          
BLAST of Sel1 vs. Planmine SMEST
Match: SMESG000003789.1 (SMESG000003789.1)

HSP 1 Score: 298.13 bits (762), Expect = 4.179e-103
Identity = 167/182 (91.76%), Postives = 168/182 (92.31%), Query Frame = 2
Query:  239 MTSEENVRHRERYIAKDWDPLLPYGGKVYLPRKRKPDSWLVFGIEIALISFAVXXXXXXXXXXXXXXXXTIKLYAHMGFKVRTIFELYFYKMFQEAQHQLGQRYLRGIGVPLHHQHAVHWFKKAAEQGHPHSAYNLAVAKLKGYHDLKKGETRKLLHHASKNGVKEAADLIEEACNRGKCYD 784
            MTSEENVRHRERYIAKDWDPLLPYGGKVYLPRKRKPDSWLVFGIEIALISFAVILGYYSYYHIDYLYSHTIKLYAHMGFK              EAQHQLGQRYLRGIGVPLHHQHAVHWFKKAAEQGHPHSAYNLAVAKLKGYHDL+KGETRKLLHHASKNGVKEAADLIEEACNRGKCYD
Sbjct:    1 MTSEENVRHRERYIAKDWDPLLPYGGKVYLPRKRKPDSWLVFGIEIALISFAVILGYYSYYHIDYLYSHTIKLYAHMGFK--------------EAQHQLGQRYLRGIGVPLHHQHAVHWFKKAAEQGHPHSAYNLAVAKLKGYHDLEKGETRKLLHHASKNGVKEAADLIEEACNRGKCYD 168          
The following BLAST results are available for this feature:
BLAST of Sel1 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Sel1 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Sel1 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Sel1 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Sel1 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Sel1 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Sel1 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Sel1 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A267F2L01.049e-4452.69Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267GSG21.336e-4452.69Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
A0A210QMX36.151e-3745.03Uncharacterized protein YbeT OS=Mizuhopecten yesso... [more]
A0A087SWK33.377e-3344.51Uncharacterized protein (Fragment) OS=Stegodyphus ... [more]
A0A433SXH71.240e-3242.08Uncharacterized protein (Fragment) OS=Elysia chlor... [more]
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BLAST of Sel1 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Sel1 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Sel1 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Sel1 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO349031.759e-2837.57Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of Sel1 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Sel1 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000003789.14.179e-10391.76SMESG000003789.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30006840 ID=SMED30006840|Name=Sel1|organism=Schmidtea mediterranea sexual|type=transcript|length=863bp
AAAATAGTTAGATTAATTTTTAAAAGATGTTTTCGCTGTCAAAAATATTT
GAACTTAGATGTTAAAGTTTTTAAAATTTGATATATTTCCTATTGCATTT
AAAAATTCTATTGTTAATCTTTTAAAATAAATACTATCGAGTAAAATTAA
TAAAAATTATATTTGCTGTGTTTTGGTTTCTAAGCAACTACATTGTTATC
TGGAACTATCCTATTTGTTAATTTTTATTTACTATAAAATGACTTCCGAG
GAAAATGTGAGACACAGAGAACGCTATATAGCAAAAGATTGGGACCCACT
ATTACCTTATGGCGGTAAAGTTTACCTTCCTCGAAAAAGGAAACCTGATT
CATGGTTAGTTTTTGGGATTGAAATAGCATTAATTTCTTTCGCTGTAATA
TTGGGATATTATTCATATTATCATATTGATTATCTCTATTCTCATACTAT
AAAGCTCTATGCTCACATGGGTTTCAAAGTAAGAACAATTTTCGAGTTAT
ACTTTTATAAAATGTTTCAGGAAGCACAACATCAACTTGGACAGAGATAT
TTAAGAGGTATTGGAGTGCCTCTTCATCATCAACACGCGGTTCATTGGTT
CAAAAAAGCGGCAGAGCAAGGTCATCCTCATTCTGCATACAATTTGGCCG
TGGCCAAACTGAAAGGTTATCATGACTTAAAGAAAGGAGAAACTCGAAAA
CTTCTGCACCATGCATCTAAAAATGGTGTAAAAGAAGCTGCTGATTTAAT
TGAAGAGGCATGCAATCGAGGGAAATGCTATGATTGAAATTAGAATAGTT
TGTTATGTGCCTTCAGTTCATCTTACAATGTTACATTTATAAAAAATAAA
AATTTGTTCACTC
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protein sequence of SMED30006840-orf-1

>SMED30006840-orf-1 ID=SMED30006840-orf-1|Name=SMED30006840-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=183bp
MTSEENVRHRERYIAKDWDPLLPYGGKVYLPRKRKPDSWLVFGIEIALIS
FAVILGYYSYYHIDYLYSHTIKLYAHMGFKVRTIFELYFYKMFQEAQHQL
GQRYLRGIGVPLHHQHAVHWFKKAAEQGHPHSAYNLAVAKLKGYHDLKKG
ETRKLLHHASKNGVKEAADLIEEACNRGKCYD*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000418head
PLANA:0000464GABAergic neuron
Vocabulary: INTERPRO
TermDefinition
IPR006597Sel1-like
IPR011990TPR-like_helical_dom_sf
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR006597Sel1-like repeatSMARTSM00671sel1coord: 94..129
e-value: 2.0E-9
score: 47.3
IPR006597Sel1-like repeatPFAMPF08238Sel1coord: 130..148
e-value: 67.0
score: 4.4
coord: 95..129
e-value: 4.6E-8
score: 33.5
IPR011990Tetratricopeptide-like helical domain superfamilyGENE3DG3DSA:1.25.40.10coord: 91..177
e-value: 8.6E-16
score: 60.5
NoneNo IPR availableSUPERFAMILYSSF81901HCP-likecoord: 94..146
NoneNo IPR availableTMHMMTMhelixcoord: 39..61