SMED30008916

Overview
NameSMED30008916
Smed IDSMED30008916
Length (bp)2138
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 SMED30008916 (SMED30008916) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30008916 (SMED30008916) 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 SMED30008916 (SMED30008916) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30008916 (SMED30008916) 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



SMED30008916

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



PAGE Curations: 13

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30008916h1SMcG0010842 SmedASXL_010155SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30008916h1SMcG0010842 Contig37464newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30008916h1SMcG0010842 Contig37464uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
nervous systemSMED30008916h1SMcG0010842 dd_Smed_v4_9714_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30008916h1SMcG0010842 dd_Smed_v4_9714_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30008916h1SMcG0010842 dd_Smed_v4_9714_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
parapharyngeal regionSMED30008916h1SMcG0010842 dd_Smed_v4_9714_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30008916h1SMcG0010842 dd_Smed_v4_9714_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30008916h1SMcG0010842 dd_Smed_v4_9714_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30008916h1SMcG0010842 dd_Smed_v6_9714_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30008916h1SMcG0010842 OX_Smed_1.0.04584ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
cholinergic neuronSMED30008916h1SMcG0010842 dd_Smed_v6_9714_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
secretory systemSMED30008916h1SMcG0010842 dd_Smed_v6_9714_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
Alignments
SMED30008916 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002696:26208..43619 +10384
Homology
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BLAST of SMED30008916 vs. Planmine SMEST
Match: SMESG000061077.1 (SMESG000061077.1)

HSP 1 Score: 1102.04 bits (2849), Expect = 0.000e+0
Identity = 563/564 (99.82%), Postives = 563/564 (99.82%), Query Frame = 1 
Query:   70 MNNDNVTRDIFNALDVDKTGFVIKQHFINQMAEYLSQTEVSCTDYTLNKLNLVSRYPDMIDYENFKRFYEDLMEXXXXXXXXIAFSVSDEEAVIDNDSDSDVYESELGPCVDINSSRSTLQGSVINLIDFPNKNKPFSTNSVDRRRSIASYVPLHDTLMKKRFDYSSPAGSLRRRGFENLISARSSIPASGYSLSNQDEGKHINNEDFDEVSCMTDSGVSVATEEVDKLFNSYKSLVGELTDLKLKLEDSNNRYQKQRDITRLHNERIVMLEEQIRQLETSQSEELKIKKKELRVTMESLXXXXXXXXXXXXXXXXLFRQDVINRLNALESEYNASRTEYDRMKHECDILMKEKDDLRKELKISNRKCQELENTLQNYKEAVGSQIADLQRERDNAETINKELRDKVQELHSSNKCQNPNNWTSSSSLNSPVQNRPQSWAGPFNFLGHSNSVSKNSLDGGSGVSTSPSCTTISQLENIVYRLTMENRNLVEKVTHLEALEFYQRKRISNPNQLSVADEMDHLNVSDLKNELASEQEIAKRLQLYVMSLTNRLMMAGYIEAFRHG 1761
            MNNDNVTRDIFNALDVDKTGFVIKQHFINQMAEYLSQTEVSCTDYTLNKLNLVSRYPDMIDYENFKRFYEDLMESKKSSKSSIAFSVSDEEAVIDNDSDSDVYESELGPCVDINSSRSTLQGSVINLIDFPNKNKPFSTNSVDRRRSIASYVPLHDTLMKKRFDYSSPAGSLRRRGFENLISARSSIPASGYSLSNQDEGKHINNEDFDEVSCMTDSGVSVATEEVDKLFNSYKSLVGELTDLKLKLEDSNNRYQKQRDITRLHNERIVMLEEQIRQLETSQSEELKIKKKELRVTMESLHQKKEIEHEKHKYNEKLFRQDVINRLNALESEYNASRTEYDRMKHECDILMKEKDDLRKELKISNRKCQELENTLQNYKEAVGSQIADLQRERDNAETINKELRDKVQELHSSNKCQNPNNWTSSSSLNSPVQNRPQSWAGPFNFLGHSNSVSKNSLDGGSGVSTSPSCTTISQLENIVYRLTMENRNLVEKVTHLEALEFYQRKRISNPN LSVADEMDHLNVSDLKNELASEQEIAKRLQLYVMSLTNRLMMAGYIEAFRHG
Sbjct:    1 MNNDNVTRDIFNALDVDKTGFVIKQHFINQMAEYLSQTEVSCTDYTLNKLNLVSRYPDMIDYENFKRFYEDLMESKKSSKSSIAFSVSDEEAVIDNDSDSDVYESELGPCVDINSSRSTLQGSVINLIDFPNKNKPFSTNSVDRRRSIASYVPLHDTLMKKRFDYSSPAGSLRRRGFENLISARSSIPASGYSLSNQDEGKHINNEDFDEVSCMTDSGVSVATEEVDKLFNSYKSLVGELTDLKLKLEDSNNRYQKQRDITRLHNERIVMLEEQIRQLETSQSEELKIKKKELRVTMESLHQKKEIEHEKHKYNEKLFRQDVINRLNALESEYNASRTEYDRMKHECDILMKEKDDLRKELKISNRKCQELENTLQNYKEAVGSQIADLQRERDNAETINKELRDKVQELHSSNKCQNPNNWTSSSSLNSPVQNRPQSWAGPFNFLGHSNSVSKNSLDGGSGVSTSPSCTTISQLENIVYRLTMENRNLVEKVTHLEALEFYQRKRISNPNHLSVADEMDHLNVSDLKNELASEQEIAKRLQLYVMSLTNRLMMAGYIEAFRHG 564
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BLAST of SMED30008916 vs. Planmine SMEST
Match: SMESG000019783.1 (SMESG000019783.1)

HSP 1 Score: 109.383 bits (272), Expect = 7.517e-25
Identity = 109/418 (26.08%), Postives = 188/418 (44.98%), Query Frame = 1 
Query:  565 SSPAGSLRRRGFENLISARSSI------PASGYSLSNQDEGKHINNEDFDEVSCMTDSGVSVATEEVDKLFNSYKSLVGELTDLKLKLEDSNNRYQKQRDITRLHNERIVMLEEQIRQLETSQSEELKIKKKELRVTMESLXXXXXXXXXXXXXXXXLFRQD---VINRLNALESEYNASRTEYDRMKHECDILMKEKDDLRKELKISNRKCQELENTLQNYKEAVGSQIADLQRERDNAETINKELRDKVQELH------------SSNKCQNPNNWTSSSSLNSPVQNRPQSWAGPFNFLGHSNSVSKNSLDGGSGVSTSPSCTTISQLENIVYRLTMENRNLVEKVTHLEALEFYQRKRISNPNQLSVADEMDHLNVSDLKNELASEQEIAKRLQLYVMSLTNRLMMAGYIEAFR 1755
            SSP GS R+ G E + S++         P +G S+ + +    + N D +               +++ L  + ++L+ ++  L+ ++E+   RYQ Q++  +   E+I + E  I + E    ++++    E    ++S+  +  +   +        R+    V N   +L     AS  E   ++ EC  L   K               E EN L  YK+    Q+ +LQ ERD  E  N +L  ++Q +             S N+      + + S++ SPV++     +   N    +  +  +S D  S                +V  LTMENRNLVE++ HLE + FYQR+++   N LS+A EM+ LNV +LK  L  E+E  + LQ Y+ SLT +L+ AG+I+ F+
Sbjct:  137 SSP-GSARKHGQELMNSSKEKFLKIINSPLTGNSVDHAESDTILLNNDMET--------------KMENLSLTNENLMEKILKLQQEIEEDKRRYQTQKEENKSLKEKIYLQENVIHENEQRYKDKVRTNTSECNNKLQSMENELSLAKYQFDERSAEMRKQLATVTNENKSLLLRCEASDAEAAELRRECRNLQARKG--------------ETENILMEYKQVASKQVTELQAERDQLELANMKLNTELQTVKHISPSKSPSKHSSLNETPVAIRYRAKSTIESPVKSESSHSSNSMNTEYQNGKLRPDSKDLEST--------------RLVQILTMENRNLVERIAHLETVGFYQRQKLEAANCLSLAAEMEQLNVEELKKALTVERETVRNLQTYMESLTTKLLTAGHIDVFQ 511
The following BLAST results are available for this feature:
BLAST of SMED30008916 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 SMED30008916 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 SMED30008916 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 SMED30008916 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 SMED30008916 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 SMED30008916 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 SMED30008916 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 SMED30008916 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30008916 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 SMED30008916 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 SMED30008916 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 SMED30008916 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30008916 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 SMED30008916 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000061077.10.000e+099.82SMESG000061077.1[more]
SMESG000019783.17.517e-2526.08SMESG000019783.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30008916 ID=SMED30008916|Name=SMED30008916|organism=Schmidtea mediterranea sexual|type=transcript|length=2138bp
CGTATAATCTGAAATTAAATAAAAAAACTTTAACTACATAACATTTTATC
AAACATTATTTTTTTTGTAATGAACAACGACAATGTGACCCGAGATATTT
TCAATGCCCTTGATGTTGATAAAACAGGTTTTGTGATAAAACAGCATTTT
ATCAATCAAATGGCTGAATATCTTTCACAGACAGAAGTGTCTTGTACAGA
TTATACGCTAAACAAACTCAATCTAGTCAGCAGATATCCAGATATGATAG
ATTATGAAAATTTTAAAAGATTTTATGAAGATCTAATGGAATCAAAAAAG
AGTTCTAAAAGTTCTATTGCCTTTTCTGTGTCTGACGAAGAAGCTGTTAT
TGATAATGATTCTGACTCTGATGTATATGAATCTGAATTAGGACCATGTG
TGGATATCAATTCTTCTAGATCAACTTTACAAGGAAGCGTTATAAATCTT
ATCGACTTCCCAAACAAAAATAAACCATTTTCAACCAATTCTGTCGACAG
GAGAAGGAGTATCGCCTCATATGTTCCTCTGCATGATACATTAATGAAGA
AAAGATTTGATTACAGTTCACCAGCAGGCAGCTTACGAAGGCGAGGGTTT
GAGAATCTAATTTCTGCTAGATCTTCTATACCAGCAAGTGGATATTCCTT
ATCAAATCAAGATGAAGGAAAGCATATCAACAATGAAGACTTTGATGAAG
TTTCTTGCATGACTGATTCTGGAGTATCGGTGGCTACTGAAGAAGTTGAT
AAACTTTTTAACAGCTATAAATCACTTGTGGGAGAACTCACAGATTTAAA
ACTAAAACTTGAAGATAGTAATAATCGTTACCAAAAACAAAGAGATATTA
CAAGGTTGCACAATGAAAGAATAGTTATGTTAGAAGAACAAATTAGACAA
CTGGAAACTTCTCAGTCTGAAGAACTCAAAATTAAAAAAAAAGAATTAAG
GGTTACAATGGAATCCCTACATCAGAAAAAAGAAATCGAACATGAAAAGC
ACAAATATAACGAAAAGTTGTTTCGACAAGATGTTATAAACAGATTAAAT
GCCCTTGAATCTGAGTACAACGCCTCAAGGACAGAATATGATCGAATGAA
ACACGAATGTGATATTTTAATGAAGGAGAAAGATGATCTAAGGAAAGAAC
TCAAAATTTCTAACAGAAAATGTCAAGAACTCGAAAACACCTTGCAGAAT
TATAAAGAAGCAGTTGGCAGTCAAATTGCAGATTTGCAGAGAGAAAGAGA
TAATGCAGAGACAATCAATAAAGAATTACGTGATAAAGTTCAAGAACTTC
ACAGTTCAAATAAATGTCAGAATCCCAATAATTGGACGTCATCGTCGAGT
CTCAATTCTCCTGTCCAAAACAGACCTCAATCATGGGCTGGGCCTTTTAA
TTTCCTTGGGCATTCAAATTCCGTATCGAAAAATTCCTTGGATGGAGGTA
GTGGGGTTTCCACGTCTCCTTCTTGCACGACAATTTCTCAACTAGAAAAC
ATCGTCTATCGTTTGACAATGGAAAATCGGAACCTAGTAGAAAAAGTTAC
TCATTTAGAAGCTTTGGAGTTCTATCAGAGAAAGCGAATAAGTAATCCCA
ATCAGCTCAGTGTTGCCGATGAAATGGACCATTTAAACGTATCAGATTTA
AAAAACGAGCTGGCTTCAGAGCAGGAAATCGCAAAGCGACTCCAGCTCTA
TGTTATGAGTTTGACAAATCGCTTAATGATGGCGGGGTATATAGAGGCCT
TCCGGCATGGGTGATACGAGAAGAAAGTATAGAAGAAGATGATATGCTTG
ATTGTGTCAGCGATATTTCATTAAATTCCGTTAGAAATAAATCAGATGTT
GTAGATAATCATAAAAATTTTGTAGCAAGATGGCTTGATAAATTGAATGG
CTGGCGTAGCATACCTAGAATTATTTTATTGTCATTTTTACAATATTTAA
ATCGGCACCGGCCGGTTTTTGATATTTATACAGATATTGTCTTATTAGGC
TGTGCAATTTCTCTCATATCATATGATGATTTATTTACATTTTGTTAATT
ATCAACAAATTTGTTGTTTTATATTCACTATTATTTGTTGCATATTCAAT
GCCTGTTATTTTCTACTACTGCAAGATTTATTTATTTC
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protein sequence of SMED30008916-orf-1

>SMED30008916-orf-1 ID=SMED30008916-orf-1|Name=SMED30008916-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=565bp
MNNDNVTRDIFNALDVDKTGFVIKQHFINQMAEYLSQTEVSCTDYTLNKL
NLVSRYPDMIDYENFKRFYEDLMESKKSSKSSIAFSVSDEEAVIDNDSDS
DVYESELGPCVDINSSRSTLQGSVINLIDFPNKNKPFSTNSVDRRRSIAS
YVPLHDTLMKKRFDYSSPAGSLRRRGFENLISARSSIPASGYSLSNQDEG
KHINNEDFDEVSCMTDSGVSVATEEVDKLFNSYKSLVGELTDLKLKLEDS
NNRYQKQRDITRLHNERIVMLEEQIRQLETSQSEELKIKKKELRVTMESL
HQKKEIEHEKHKYNEKLFRQDVINRLNALESEYNASRTEYDRMKHECDIL
MKEKDDLRKELKISNRKCQELENTLQNYKEAVGSQIADLQRERDNAETIN
KELRDKVQELHSSNKCQNPNNWTSSSSLNSPVQNRPQSWAGPFNFLGHSN
SVSKNSLDGGSGVSTSPSCTTISQLENIVYRLTMENRNLVEKVTHLEALE
FYQRKRISNPNQLSVADEMDHLNVSDLKNELASEQEIAKRLQLYVMSLTN
RLMMAGYIEAFRHG*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000418head
PLANA:0000463cholinergic neuron
PLANA:0000484secretory system
PLANA:0003117parapharyngeal cell
Vocabulary: INTERPRO
TermDefinition
IPR002048EF_hand_dom
Vocabulary: molecular function
TermDefinition
GO:0005509calcium ion binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 319..413
NoneNo IPR availableCOILSCoilCoilcoord: 233..260
NoneNo IPR availableCOILSCoilCoilcoord: 283..303
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 408..434
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 412..434
IPR002048EF-hand domainPROSITEPS50222EF_HAND_2coord: 2..37
score: 8.879