SMED30018750

Overview
NameSMED30018750
Smed IDSMED30018750
Length (bp)1689
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast 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 SMED30018750 (SMED30018750) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30018750 (SMED30018750) in cells (dots) of each of the 12 neoblast clusters.

 

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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




SMED30018750

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



PAGE Curations: 8

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30018750SMESG000032765.1 SMESG000032764.1 SmedASXL_010686SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
nervous systemSMED30018750SMESG000032765.1 SMESG000032764.1 dd_Smed_v4_9225_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30018750SMESG000032765.1 SMESG000032764.1 dd_Smed_v4_9225_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30018750SMESG000032765.1 SMESG000032764.1 dd_Smed_v4_9225_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30018750SMESG000032765.1 SMESG000032764.1 dd_Smed_v4_9225_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
zeta neoblastSMED30018750SMESG000032765.1 SMESG000032764.1 dd_Smed_v4_9225_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
neoblastSMED30018750SMESG000032765.1 SMED_09519_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30018750SMESG000032765.1 SMED_09519_V2_1GPL14150PMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30018750 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000355:60210..65225 -8220
Homology
BLAST of SMED30018750 vs. Planmine SMEST
Match: SMESG000032765.1 (SMESG000032765.1)

HSP 1 Score: 404.831 bits (1039), Expect = 1.960e-140
Identity = 196/196 (100.00%), Postives = 196/196 (100.00%), Query Frame = 1
Query:  967 DFKPESIIAVHRLVNHFQIALGNGEICTFDYTRNKLSNVFSWKLRLKSIITKLNQSVALTSDHRVYRSIDNGNPVEIKYLEGCQHISLSFNKQFVAIFPQTICWVNWKSCNIVKQTRIKVPIKSVFYSPLLLTVDVKNAIVTFQQGGQIRYPTGALVKEFPHNKEVTALSNVFFKKIYVAIDNEVHLLSRQPLQAA 1554
            DFKPESIIAVHRLVNHFQIALGNGEICTFDYTRNKLSNVFSWKLRLKSIITKLNQSVALTSDHRVYRSIDNGNPVEIKYLEGCQHISLSFNKQFVAIFPQTICWVNWKSCNIVKQTRIKVPIKSVFYSPLLLTVDVKNAIVTFQQGGQIRYPTGALVKEFPHNKEVTALSNVFFKKIYVAIDNEVHLLSRQPLQAA
Sbjct:    4 DFKPESIIAVHRLVNHFQIALGNGEICTFDYTRNKLSNVFSWKLRLKSIITKLNQSVALTSDHRVYRSIDNGNPVEIKYLEGCQHISLSFNKQFVAIFPQTICWVNWKSCNIVKQTRIKVPIKSVFYSPLLLTVDVKNAIVTFQQGGQIRYPTGALVKEFPHNKEVTALSNVFFKKIYVAIDNEVHLLSRQPLQAA 199          
BLAST of SMED30018750 vs. Planmine SMEST
Match: SMESG000032764.1 (SMESG000032764.1)

HSP 1 Score: 396.356 bits (1017), Expect = 6.399e-137
Identity = 196/196 (100.00%), Postives = 196/196 (100.00%), Query Frame = 1
Query:   19 MLEKGSQELEILMNRLIECNENEKKIITKISCQQEEINKTINIIQKFQQCLSEQYQMMSTLKENENVAKLNKKKIFQEIRNLDDEMQNVNEIDQSQLDSNKENRFSIHECQSKTANDNNEIPSTPAEVQLQFDGNNEIEVIRESPQPKRRKLIDYSDLNVIDLTDEGDPLAIRASQSQADNNVHNRQPLPNCKHKP 606
            MLEKGSQELEILMNRLIECNENEKKIITKISCQQEEINKTINIIQKFQQCLSEQYQMMSTLKENENVAKLNKKKIFQEIRNLDDEMQNVNEIDQSQLDSNKENRFSIHECQSKTANDNNEIPSTPAEVQLQFDGNNEIEVIRESPQPKRRKLIDYSDLNVIDLTDEGDPLAIRASQSQADNNVHNRQPLPNCKHKP
Sbjct:    1 MLEKGSQELEILMNRLIECNENEKKIITKISCQQEEINKTINIIQKFQQCLSEQYQMMSTLKENENVAKLNKKKIFQEIRNLDDEMQNVNEIDQSQLDSNKENRFSIHECQSKTANDNNEIPSTPAEVQLQFDGNNEIEVIRESPQPKRRKLIDYSDLNVIDLTDEGDPLAIRASQSQADNNVHNRQPLPNCKHKP 196          
BLAST of SMED30018750 vs. Planmine SMEST
Match: SMESG000032764.1 (SMESG000032764.1)

HSP 1 Score: 332.413 bits (851), Expect = 1.772e-112
Identity = 167/167 (100.00%), Postives = 167/167 (100.00%), Query Frame = 1
Query:   19 MLEKGSQELEILMNRLIECNENEKKIITKISCQQEEINKTINIIQKFQQCLSEQYQMMSTLKENENVAKLNKKKIFQEIRNLDDEMQNVNEIDQSQLDSNKENRFSIHECQSKTANDNNEIPSTPAEVQLQFDGNNEIEVIRESPQPKRRKLIDYSDLNVIDLTDEG 519
            MLEKGSQELEILMNRLIECNENEKKIITKISCQQEEINKTINIIQKFQQCLSEQYQMMSTLKENENVAKLNKKKIFQEIRNLDDEMQNVNEIDQSQLDSNKENRFSIHECQSKTANDNNEIPSTPAEVQLQFDGNNEIEVIRESPQPKRRKLIDYSDLNVIDLTDEG
Sbjct:    1 MLEKGSQELEILMNRLIECNENEKKIITKISCQQEEINKTINIIQKFQQCLSEQYQMMSTLKENENVAKLNKKKIFQEIRNLDDEMQNVNEIDQSQLDSNKENRFSIHECQSKTANDNNEIPSTPAEVQLQFDGNNEIEVIRESPQPKRRKLIDYSDLNVIDLTDEG 167          
BLAST of SMED30018750 vs. Planmine SMEST
Match: SMESG000032769.1 (SMESG000032769.1)

HSP 1 Score: 247.284 bits (630), Expect = 1.307e-76
Identity = 131/295 (44.41%), Postives = 193/295 (65.42%), Query Frame = 1
Query:  682 EGNPNEKCDRIMKLFASEIGIFSAGTGGSLRIHGWGNNTQSIPTGTTDDIHGFYIIKKKILLHTASQLILADWRPFWPNGNVLERNN---NNSFQIVSDFKPESIIAVHRLVNHFQIALGNGEICTFDYTRNKLSNVFSWKLRLKSIITKLNQSVALTSDHRVYRSIDNGNPVEIKYLEGCQHISLSFNKQFVAIFPQTICWVNWKSCNIVKQTRIKVPIKSV-FYSPLLLTVDVKNAIVTFQ--QGGQIRYPTGALVKEFPHNKEVTALSNVFFKKIYVAIDNEVHLLSRQPLQ 1548
            +G PN    ++ K+F  +  ++++G GG+L +H +   T++IP+GTTDDI GFY+I +K+LL+TAS+LIL           +  RN     +  +++ DFKP++II V RL   FQ+ L NGE   +++     +NVFSWKLRLKSIITKLNQSVALTSD R+YRSI  G P+EIK L GCQ I  S +++FV IFP  ICWV+WK+  I K+ +I VP+KS   Y  + +TVDV+N + TFQ  +G ++      +V+ +    EVTA+S+   +K+YVA++N++ L++    Q
Sbjct:   81 DGKPNVTSAKLTKIFVGKHEVYTSGCGGALEVHKYNKATKTIPSGTTDDILGFYLISEKLLLYTASELILTT--------KLYGRNMLHCADPPEVLRDFKPDTIINVLRLNKLFQVTLENGESWDYNFYEKTFTNVFSWKLRLKSIITKLNQSVALTSDLRLYRSIGYGTPLEIKSLGGCQDIYPSSSEEFVVIFPTEICWVDWKTYIIKKRKKIYVPVKSFSTYCDMFMTVDVENTVKTFQKHKGSEM------VVRMYGRENEVTAISDHQSQKLYVAVNNQIKLIASPSYQ 361          
BLAST of SMED30018750 vs. Planmine SMEST
Match: SMESG000053453.1 (SMESG000053453.1)

HSP 1 Score: 149.058 bits (375), Expect = 2.212e-39
Identity = 96/273 (35.16%), Postives = 147/273 (53.85%), Query Frame = 1
Query:  706 DRIMKLFASEIGIFSAGTGGSLRIHGWGNNTQSIPTGTTDDIHGFYIIKKKILLHTASQLILADWRPFWPNGNVLERNNNNSFQIVSDFKPESIIAVHRLVNHFQIALGNGEICTFDYTRNKLSNVFSWKLRLKSIITKLNQSVALTSDHRVYRSIDNGNPVEIKYLEGCQHISLSFNKQFVAIFPQTICWVNWKSCNIVKQTRIKVPIKSV-FYSPLLLTVDVKNAIVTFQQGGQIRYPTGALVKEFPHNKEVTALSNVFFKKIYVAIDNEV 1521
            +RI K+F+ + GI + G+ GS+     G   +++   T  DI  F+ I+ KILL T   LIL +++             N   +IV  F+P  I+ + R    FQI L NGEI  +++  N      +    LK+IIT L++SVAL+ D +VY+  D  N  EIK LEGC  I    NK FVAIF   IC VN +   I  +  I  PIK +      L+TV+++N +  F     ++  +   +++F  N E+TA+ NV+ KKIY++++NE+
Sbjct:  145 ERINKIFSGKPGIGACGSSGSIAFFKKGT-VKTMKAVTDKDIFDFFFIEGKILLQTEYLLILTEFK-------------NKVEKIVKGFQPWKILDICRNEKKFQITLQNGEIWIYEFPENIFLKYSTGIRNLKAIITYLSRSVALSLDQKVYQITDYKNVKEIKDLEGCDKIYKFCNKSFVAIFSTKICIVNLEDYKIQTEITINFPIKQLAICGSYLVTVNMENTVEKF----NVKNLSRKFIEQFSQNDEITAIPNVYQKKIYISVNNEI 399          

HSP 2 Score: 74.3294 bits (181), Expect = 5.433e-14
Identity = 50/109 (45.87%), Postives = 72/109 (66.06%), Query Frame = 1
Query:   19 MLEKGSQELEILMNRLIECNENEKKIITKISCQQEEINKTINIIQKFQQCLSEQYQMMSTLKENENVAKLNKKKIFQEIRNL----DDE--MQNVNEIDQSQLDSNKEN 327
            M E  SQ  + L+N L+E  + E KI  KI  QQEEI KT N+I++FQ+C  EQ QM+S LK++    +++K KI +++RNL    DDE  +QN N  +Q+QLD+N+ N
Sbjct:    1 MPETTSQIFKNLLNELVEIRDEEIKIENKIYIQQEEIIKTNNVIEQFQKCHVEQTQMLSKLKDDGIKFRISKNKILKKLRNLNHESDDEVDIQNENVTEQTQLDNNECN 109          
The following BLAST results are available for this feature:
BLAST of SMED30018750 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 SMED30018750 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 SMED30018750 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 SMED30018750 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 SMED30018750 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 SMED30018750 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 SMED30018750 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 SMED30018750 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 SMED30018750 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 SMED30018750 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 SMED30018750 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 SMED30018750 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 SMED30018750 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 SMED30018750 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000032765.11.960e-140100.00SMESG000032765.1[more]
SMESG000032764.16.399e-137100.00SMESG000032764.1[more]
SMESG000032764.11.772e-112100.00SMESG000032764.1[more]
SMESG000032769.11.307e-7644.41SMESG000032769.1[more]
SMESG000053453.12.212e-3935.16SMESG000053453.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30018750 ID=SMED30018750|Name=SMED30018750|organism=Schmidtea mediterranea sexual|type=transcript|length=1689bp
TAAATTCATAAATTTGCCATGCTTGAAAAGGGATCACAAGAGCTTGAAAT
TTTAATGAATAGGCTAATTGAATGCAATGAGAATGAAAAAAAAATCATAA
CTAAAATATCTTGCCAACAAGAAGAAATCAATAAAACTATTAATATAATT
CAGAAATTTCAACAATGCCTCAGTGAACAATATCAAATGATGTCAACACT
GAAAGAAAACGAAAATGTCGCGAAACTTAATAAAAAAAAAATTTTCCAAG
AAATCCGAAATTTGGATGATGAAATGCAAAATGTGAATGAAATTGATCAG
TCACAATTAGACAGCAACAAAGAAAATCGATTTTCAATCCATGAATGTCA
ATCCAAAACCGCTAATGACAATAATGAGATTCCTTCCACACCAGCAGAAG
TCCAATTGCAATTCGATGGCAACAATGAAATTGAGGTGATTCGTGAATCT
CCACAACCTAAACGAAGGAAATTAATTGATTATTCTGATTTGAATGTCAT
AGATCTGACTGATGAGGGCGACCCGCTAGCAATCCGTGCCAGCCAATCAC
AAGCCGATAATAATGTCCATAACCGACAGCCGCTGCCAAACTGCAAGCAC
AAGCCCGTCAAGCAATTTCCACCCAGGAAAAGGAAGGAACTTACTGATAA
TGCTAAATCAGAAACGATCGATCTCACTGACGAGGGAAATCCCAATGAGA
AATGCGACAGGATCATGAAATTATTTGCTAGCGAAATCGGCATATTCAGT
GCCGGAACTGGGGGATCCCTGAGGATTCACGGCTGGGGTAATAACACGCA
GTCTATACCAACCGGCACAACCGACGATATCCACGGTTTCTATATAATCA
AGAAGAAAATATTGCTACATACCGCTAGCCAACTGATTCTCGCCGATTGG
AGACCTTTCTGGCCAAATGGAAATGTATTAGAGAGAAATAATAATAATTC
ATTCCAAATCGTCAGCGACTTCAAGCCCGAGTCTATCATAGCTGTGCACC
GATTGGTCAATCATTTCCAGATCGCTCTTGGAAACGGCGAGATCTGCACG
TTTGATTACACTAGAAACAAATTATCAAACGTTTTCTCCTGGAAATTGAG
ATTAAAATCGATAATCACAAAACTCAATCAGTCCGTGGCACTCACATCGG
ATCACAGGGTTTATCGCTCAATCGATAATGGAAATCCAGTGGAAATAAAA
TACCTGGAAGGTTGCCAGCACATTTCTTTATCTTTCAATAAGCAATTTGT
TGCGATTTTCCCACAGACAATTTGCTGGGTTAATTGGAAGAGCTGCAATA
TTGTCAAGCAAACAAGAATAAAAGTCCCAATCAAAAGCGTATTCTATTCA
CCCCTGTTGCTGACAGTCGATGTCAAGAACGCAATCGTGACATTCCAGCA
AGGGGGGCAAATCAGATATCCCACCGGAGCTCTGGTGAAGGAATTCCCTC
ATAATAAGGAAGTCACTGCACTTTCAAATGTTTTCTTTAAGAAGATTTAT
GTAGCCATTGACAACGAGGTCCACCTGCTCAGCCGGCAGCCCCTGCAAGC
GGCATGAGAGATTTCCCAAGAGATTTACTGAATAAATTTTGCTATATTAT
GATTATAGATATCTATGTAACTTTTTGAGTTGTCAATGCGCAAATTGATC
TATTGTTTACACATTTATATTTCAATATTGACTTTACGC
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protein sequence of SMED30018750-orf-1

>SMED30018750-orf-1 ID=SMED30018750-orf-1|Name=SMED30018750-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=513bp
MLEKGSQELEILMNRLIECNENEKKIITKISCQQEEINKTINIIQKFQQC
LSEQYQMMSTLKENENVAKLNKKKIFQEIRNLDDEMQNVNEIDQSQLDSN
KENRFSIHECQSKTANDNNEIPSTPAEVQLQFDGNNEIEVIRESPQPKRR
KLIDYSDLNVIDLTDEGDPLAIRASQSQADNNVHNRQPLPNCKHKPVKQF
PPRKRKELTDNAKSETIDLTDEGNPNEKCDRIMKLFASEIGIFSAGTGGS
LRIHGWGNNTQSIPTGTTDDIHGFYIIKKKILLHTASQLILADWRPFWPN
GNVLERNNNNSFQIVSDFKPESIIAVHRLVNHFQIALGNGEICTFDYTRN
KLSNVFSWKLRLKSIITKLNQSVALTSDHRVYRSIDNGNPVEIKYLEGCQ
HISLSFNKQFVAIFPQTICWVNWKSCNIVKQTRIKVPIKSVFYSPLLLTV
DVKNAIVTFQQGGQIRYPTGALVKEFPHNKEVTALSNVFFKKIYVAIDNE
VHLLSRQPLQAA*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000014zeta neoblast
PLANA:0000101muscle cell
PLANA:0000429neoblast
PLANA:0002109X1 cell