SMED30029640

Overview
NameSMED30029640
Smed IDSMED30029640
Length (bp)1573
Neoblast Clusters

Zeng et. al., 2018



 

 

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

 

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Anatomical Expression

PAGE et. al., 2020



SMED30029640

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30029640SMESG000050293.1 dd_Smed_v4_19713_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30029640SMESG000050293.1 dd_Smed_v4_19713_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30029640SMESG000050293.1 dd_Smed_v4_19713_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30029640SMESG000050293.1 dd_Smed_v4_19713_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30029640 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.012543:15221..17707 -6341
Homology
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BLAST of SMED30029640 vs. Planmine SMEST
Match: SMESG000050293.1 (SMESG000050293.1)

HSP 1 Score: 345.125 bits (884), Expect = 3.902e-117
Identity = 211/214 (98.60%), Postives = 212/214 (99.07%), Query Frame = 1 
Query:  877 KTFPTPSKMALLEIKLKDESFFLVYINEHNECVVNFRRIESNFYEHIISRKVFYKSRNILLIYSDRENIILKIFDGFNITTFQTRVRSEFVLMNVGFFDHSNLFTEFNGKMGFKYNPSYWMRTSDVLVLSTEVSPVKNYKTKXXXXXXXXXXXXXXXXXXXHAKTKYNKKRNFPRXXXXXXXXXXXXXXXXRPPSDENVKKSFQPTDDETINSN 1518
            KTFPTPSKMALLEIKLKDESFFLVYINEHNECVVNFRRIESNFYEHIISRK+FYKSRNILLIYSDRENIILKIFDGFNITTFQTRVRSEFVLMNVGFFDHSNLFTEFNGKM FKYNPSYWMRTSDVLVLSTEVSPVKNYKTKIYLLLGLFLIIIIILVIFI AKTKYNKKRNFPRKSLNKSSLNSNEYELERPPSDENVKKSFQPTDDETINSN
Sbjct:    8 KTFPTPSKMALLEIKLKDESFFLVYINEHNECVVNFRRIESNFYEHIISRKIFYKSRNILLIYSDRENIILKIFDGFNITTFQTRVRSEFVLMNVGFFDHSNLFTEFNGKMSFKYNPSYWMRTSDVLVLSTEVSPVKNYKTKIYLLLGLFLIIIIILVIFILAKTKYNKKRNFPRKSLNKSSLNSNEYELERPPSDENVKKSFQPTDDETINSN 221
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BLAST of SMED30029640 vs. Planmine SMEST
Match: SMESG000050289.1 (SMESG000050289.1)

HSP 1 Score: 220.705 bits (561), Expect = 2.215e-65
Identity = 144/406 (35.47%), Postives = 217/406 (53.45%), Query Frame = 1 
Query:   73 KYIILLSVLNYKIPLYCTNYIYGQFDGKLHSTKELTFSMYILSINGTIFYTVDGISRFLLAAYHDQMGHYFNIKFNYFKNYVASKTQXXXXXXXXXXF-NQYIKFILLLDKLQVKIICNNISTTIRLNYEINNEELFNYPMPPINIKKENQTTFWMGNIGPYTG--DKIYEPLNAQLIGCLDKYNFTEQNVIFSQIGNKFLPSCDIKYNERVCNRTYCANKKIFYKMYDCSPESMNGIYCQQELENYSKYLNSYKKFRSDDGILCLKLEW-IKTFPTPSKMALLEIKLKDESFFLVYINEHNECVVNFRRIESNFYEHIISRKVFYKSRNILLIYSDRENIILKIFDGFNITTFQTRVRSEFVLMNVGFFDHSNLFTEFNGKMGFKYNPSYWMRT---SDVLVLST 1269
            KY + LSVL  K     + YIY +FDG + S K + FS++I +  G +FY VD  +R L+             KFN   +YV S+   +          N Y++  +LL +L++ I CN  +  ++ N E +++E   YP PP     + +T FWMGNIGP+TG  +KIY  L +QL GCLDK+ F  +N+ F + G  F   C++ Y E+VCN + C+N +  YKMYDCSP SMNG +C+  L +Y+    SY + +    ++  +L+W ++      + +L+EIKLKDE+  L YI+     V++   I +N      S K     R  LLI        +K+ D  NI T+  +   EFVL+N+G       F+ F GK+ F++NP YW  +   SD  + ST
Sbjct:    6 KYFLFLSVLLSKFNGMFSEYIYEKFDGNMVSDKGMNFSVFIKNFKGVLFYCVDSKNRLLIQINKKSTETIITFKFN---SYVTSEDMTSKRLCKCSNCSNVYLQLSILLQQLEILINCNKQANVVKFNKETDSDEFSEYPTPPDYNNNQTKTYFWMGNIGPFTGSKNKIYLALTSQLSGCLDKFYFNGKNIKFKKSGKIFQSFCEVLYKEKVCNESRCSNNETHYKMYDCSPLSMNGKHCETILSDYAIVQKSYIRKQRWKEVIYFRLDWQMEVNSKIKRFSLMEIKLKDETLLLFYIDSTRNIVMSTLNISANTDIVDFSMKSDLNHRFTLLIILGESETTIKLNDCSNILTYIKKNIFEFVLINIGTIQSDPSFSLFEGKINFQFNPKYWKISNGNSDFFLTST 408
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BLAST of SMED30029640 vs. Planmine SMEST
Match: SMESG000050289.1 (SMESG000050289.1)

HSP 1 Score: 201.445 bits (511), Expect = 1.861e-58
Identity = 127/364 (34.89%), Postives = 195/364 (53.57%), Query Frame = 1 
Query:  157 LHSTKELTFSMYILSINGTIFYTVDGISRFLLAAYHDQMGHYFNIKFNYFKNYVASKTQXXXXXXXXXXF-NQYIKFILLLDKLQVKIICNNISTTIRLNYEINNEELFNYPMPPINIKKENQTTFWMGNIGPYTG--DKIYEPLNAQLIGCLDKYNFTEQNVIFSQIGNKFLPSCDIKYNERVCNRTYCANKKIFYKMYDCSPESMNGIYCQQELENYSKYLNSYKKFRSDDGILCLKLEW-IKTFPTPSKMALLEIKLKDESFFLVYINEHNECVVNFRRIESNFYEHIISRKVFYKSRNILLIYSDRENIILKIFDGFNITTFQTRVRSEFVLMNVGFFDHSNLFTEFNGKMGFKYNPSYW 1236
            + S K + FS++I +  G +FY VD  +R L+             KFN   +YV S+   +          N Y++  +LL +L++ I CN  +  ++ N E +++E   YP PP     + +T FWMGNIGP+TG  +KIY  L +QL GCLDK+ F  +N+ F + G  F   C++ Y E+VCN + C+N +  YKMYDCSP SMNG +C+  L +Y+    SY + +    ++  +L+W ++      + +L+EIKLKDE+  L YI+     V++   I +N      S K     R  LLI        +K+ D  NI T+  +   EFVL+N+G       F+ F GK+ F++NP YW
Sbjct:    1 MVSDKGMNFSVFIKNFKGVLFYCVDSKNRLLIQINKKSTETIITFKFN---SYVTSEDMTSKRLCKCSNCSNVYLQLSILLQQLEILINCNKQANVVKFNKETDSDEFSEYPTPPDYNNNQTKTYFWMGNIGPFTGSKNKIYLALTSQLSGCLDKFYFNGKNIKFKKSGKIFQSFCEVLYKEKVCNESRCSNNETHYKMYDCSPLSMNGKHCETILSDYAIVQKSYIRKQRWKEVIYFRLDWQMEVNSKIKRFSLMEIKLKDETLLLFYIDSTRNIVMSTLNISANTDIVDFSMKSDLNHRFTLLIILGESETTIKLNDCSNILTYIKKNIFEFVLINIGTIQSDPSFSLFEGKINFQFNPKYW 361
[Close]
BLAST of SMED30029640 vs. Planmine SMEST
Match: SMESG000050292.1 (SMESG000050292.1)

HSP 1 Score: 152.525 bits (384), Expect = 2.859e-40
Identity = 119/389 (30.59%), Postives = 187/389 (48.07%), Query Frame = 1 
Query:   85 LLSVLNYKIPLYCTNYIYGQFDGKLHSTKELTFSMYILSINGTIFYTVDGISRFLLAAYHDQMGHYFNIKFNYFKNYVASKTQXXXXXXXXXXFNQYIKFILLLDKLQVKIICNNISTTIRLNYEINNEELFNYPMPPINIKKENQTTFWMGNIGPYTG--DKIYEPLNAQLIGCLDKYNFTEQNVIFSQIGNKFLPSCDIKYNERVCNRTYCANKKIFYKMYDCSPESMNGIYCQQELENYSKYLNSYKKFRSDDGILCLKLEWIKTFPTPS-KMALLEIKLKDESFFLVYINEHNECVVNFRRIESNFYEHIISRKVFYKS--RNILLIYSDRENIILKIFDGFNITTFQTRVRSEFVLMNVGFFDHSNLFTEFNGKMGFKYNPSYW 1236
            LL+  N    +    YIY +FD        L F++Y+ +  G + Y +D  ++ L+    +      +I FN     +  K   TT+  C++  + Y+ F L L + ++ I C N++ + +L      +E   YP P  + KK+ +   WMGNIGPY G     Y+PL  QL GC DK             GN+F+  CDI Y E          +    KMY+C+  SMN +YCQ    ++S+  +SY K      I   ++EW  +    S    LLE+K  +E   L+++++  +  V+     SN     I+ K+F  +  RN+LLI++   ++I+K++DG  I T    + S   L+NVGF  H N    F GKM F+YN   W
Sbjct:    8 LLTSFNNLFNIILATYIYQEFDNVSLKRDNLIFNVYLQTFKGVLLYGLDSENKLLIKVNREMEFRTIHIIFN--SEEIGIKLTKTTLKFCSLNEDVYLDFTLRLSRSELTIKCRNMTWSYKLRQNTFKDEFDLYPQPNHDFKKKKKLFIWMGNIGPYIGRDSAHYKPLQNQLYGCTDKS------------GNQFIFPCDINYQETEYKGKNVTKRLSTIKMYNCTHYSMNPLYCQTNPLDFSEKTHSYHKQSMSSEIDYFRIEWKNSASKNSINYCLLEMKYNNEMIILLFLDQ--DGYVSVESKNSNDPNIQINLKIFMPNFKRNVLLIFTTNIDLIIKVYDGQQIQTHIYHINSLLSLINVGFC-HVNYLRNFAGKMRFRYNSLDW 379
[Close]
BLAST of SMED30029640 vs. Planmine SMEST
Match: SMESG000050295.1 (SMESG000050295.1)

HSP 1 Score: 145.976 bits (367), Expect = 6.362e-38
Identity = 118/385 (30.65%), Postives = 187/385 (48.57%), Query Frame = 1 
Query:   79 IILLSVLNYKIPLYC-TNYIYGQFDGKLHSTKELTFSMYILSINGTIFYTVDGISRFLLAAYHDQMGHYFNIKFNYFKNYVASK-TQXXXXXXXXXXFNQYIKFILLLDKLQVKIICNNISTTIRLNYEINNEELFNYPMPPINIKKENQTTFWMGNIGPYTG--DKIYEPLNAQLIGCLDKYNFTEQNV-IFSQIGNKFLPSCDIKYNERVCNRTYCANKKIFYKMYDCSPESMNGIYCQQELENYSKYLNSYKKFRSDDGILCLKLEWIKTFPTPSKMALLEIKLKDESFFLVYINEHNECVVNFRRIESNFYEHIISRKVFYKSRNILLIYSDRENIILKIFDGFNITTFQTRVRSEFVLMNVGFFDHSNLFTEFNGKMGFK 1218
            +ILL +    I L+   +YIY +  G +     L F +YIL+ +G IFY+ D  +   +    D+      + +N     + SK + +  IC C+ CFN ++ F   LD   + I C N S  I L    + +    +P P      E     WMGNIG Y G     Y PL AQ+ GCLD     ++ V +  Q G  FL SCDI YNE+VC ++ C   K  YKMYDCS  S+N  YC      +  Y   +   ++ + I  ++++WI+         LLEI LK+ +  +++I+ HN   +N +  ++    +    K+     N LL+  D  N  +K+  G     ++  + SE+V++ VG + HSN++ EF G +  +
Sbjct:    6 LILLFITYLNIFLWLNASYIYKELAGTIADHLGLEFRIYILNGSGIIFYSFDVENDIFVKIDVDRPKPELIVAYN---QKIPSKISTMNEICGCSACFNIFMTFKFHLDLSLIDIECANKSNIILLKNTTDKDSFKFFPRPKSYKSSEKILFIWMGNIGKYIGYSGMKYLPLKAQIFGCLDYIKVDKKYVKLERQEGVSFLNSCDILYNEKVCYKSNCWQNKNSYKMYDCSVASLNTKYCNITFSRH--YEKEFDSRKNSERIKLMRIDWIRDQHIMKNYCLLEIILKNGTILMLHIDRHNHLRMNIKHSKTKLLINTNLNKI----SNSLLVNLDPSNFSVKVSFGEGRVEYRDEMTSEYVIITVGKWQHSNIYPEFLGNISIR 381
The following BLAST results are available for this feature:
BLAST of SMED30029640 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 SMED30029640 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 SMED30029640 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 SMED30029640 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 SMED30029640 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 SMED30029640 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 SMED30029640 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 SMED30029640 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 SMED30029640 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 SMED30029640 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 SMED30029640 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 SMED30029640 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 SMED30029640 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 SMED30029640 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000050293.13.902e-11798.60SMESG000050293.1[more]
SMESG000050289.12.215e-6535.47SMESG000050289.1[more]
SMESG000050289.11.861e-5834.89SMESG000050289.1[more]
SMESG000050292.12.859e-4030.59SMESG000050292.1[more]
SMESG000050295.16.362e-3830.65SMESG000050295.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30029640 ID=SMED30029640|Name=SMED30029640|organism=Schmidtea mediterranea sexual|type=transcript|length=1573bp
TTTATAAATGTCTATGATCCTTGCAGTTATTAATTAATAAATAATGCAAT
AATGATTATATTAAGAATTTGGAAATATATAATATTGTTGTCAGTATTGA
ATTATAAAATTCCACTATATTGTACAAATTATATTTACGGTCAATTCGAT
GGAAAATTACACAGTACCAAAGAACTCACATTTTCAATGTATATTCTGTC
TATAAATGGAACAATATTTTATACAGTTGATGGAATCAGTCGGTTTTTGC
TAGCAGCCTATCATGACCAAATGGGGCATTATTTTAATATAAAATTTAAT
TATTTCAAAAATTATGTGGCAAGCAAAACTCAAATTACAACTATTTGTAA
ATGTACGATTTGTTTTAATCAATACATCAAATTTATATTATTACTCGACA
AATTGCAAGTCAAAATTATTTGTAACAATATTTCGACGACAATTCGTCTA
AATTATGAAATAAATAATGAAGAATTATTCAATTATCCAATGCCACCAAT
AAACATTAAAAAAGAAAATCAAACTACATTTTGGATGGGCAACATTGGTC
CATACACGGGAGATAAAATTTATGAACCTTTGAATGCTCAGCTGATAGGA
TGTTTGGATAAATATAATTTCACTGAGCAAAATGTAATATTTTCACAAAT
CGGGAACAAATTTCTGCCTTCGTGTGACATCAAGTACAATGAAAGGGTTT
GCAATCGAACATATTGTGCAAATAAGAAAATTTTTTATAAAATGTATGAT
TGCTCCCCTGAGTCAATGAATGGAATTTATTGTCAACAAGAACTGGAAAA
TTATTCTAAATATCTAAATTCTTACAAAAAATTCAGATCTGATGACGGAA
TTCTATGTTTGAAACTGGAGTGGATAAAAACCTTTCCCACTCCCTCGAAA
ATGGCGTTATTGGAGATAAAACTGAAAGATGAGTCTTTTTTCTTGGTGTA
CATCAATGAGCATAACGAATGCGTCGTTAACTTTCGACGAATAGAGTCGA
ACTTTTATGAGCATATTATCTCAAGGAAAGTCTTTTACAAATCAAGAAAT
ATTTTATTAATATATTCCGACAGGGAAAATATTATTCTTAAAATATTCGA
TGGATTTAATATTACAACCTTCCAAACAAGGGTGAGAAGTGAATTCGTTC
TTATGAATGTTGGGTTCTTTGATCACAGCAATTTGTTCACAGAATTTAAT
GGAAAAATGGGTTTTAAATACAATCCGTCGTATTGGATGAGAACATCGGA
TGTCCTGGTATTGAGCACAGAGGTTTCCCCGGTTAAAAATTATAAAACAA
AAATATATCTCTTACTGGGACTATTTCTAATCATAATAATTATATTGGTA
ATATTCATTCATGCCAAGACAAAATATAATAAAAAAAGAAACTTTCCTCG
TAAATCTCTAAATAAGTCATCATTAAATTCTAACGAATATGAATTAGAAC
GGCCTCCGTCGGATGAAAATGTCAAAAAGAGTTTTCAACCAACAGACGAC
GAAACTATTAATTCCAATTATGATTATATTATATAAATTTTACATTTATA
TATTAATTTAAAAATATAAGATC
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protein sequence of SMED30029640-orf-1

>SMED30029640-orf-1 ID=SMED30029640-orf-1|Name=SMED30029640-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=495bp
MIILRIWKYIILLSVLNYKIPLYCTNYIYGQFDGKLHSTKELTFSMYILS
INGTIFYTVDGISRFLLAAYHDQMGHYFNIKFNYFKNYVASKTQITTICK
CTICFNQYIKFILLLDKLQVKIICNNISTTIRLNYEINNEELFNYPMPPI
NIKKENQTTFWMGNIGPYTGDKIYEPLNAQLIGCLDKYNFTEQNVIFSQI
GNKFLPSCDIKYNERVCNRTYCANKKIFYKMYDCSPESMNGIYCQQELEN
YSKYLNSYKKFRSDDGILCLKLEWIKTFPTPSKMALLEIKLKDESFFLVY
INEHNECVVNFRRIESNFYEHIISRKVFYKSRNILLIYSDRENIILKIFD
GFNITTFQTRVRSEFVLMNVGFFDHSNLFTEFNGKMGFKYNPSYWMRTSD
VLVLSTEVSPVKNYKTKIYLLLGLFLIIIIILVIFIHAKTKYNKKRNFPR
KSLNKSSLNSNEYELERPPSDENVKKSFQPTDDETINSNYDYII*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0003116parenchymal cell