SMED30016665

Overview
NameSMED30016665
Smed IDSMED30016665
Length (bp)2065
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 SMED30016665 (SMED30016665) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30016665 (SMED30016665) 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 SMED30016665 (SMED30016665) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30016665 (SMED30016665) 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



SMED30016665

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30016665SMESG000015774.1 SMESG000015763.1 SmedASXL_013780SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30016665SMESG000015774.1 SMESG000015763.1 SmedASXL_013780SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
epidermisSMED30016665SMESG000015774.1 SMESG000015763.1 dd_Smed_v4_11267_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30016665SMESG000015774.1 SMESG000015763.1 dd_Smed_v4_11267_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30016665SMESG000015774.1 SMESG000015763.1 Contig27109newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30016665SMESG000015774.1 SMESG000015763.1 Contig27109uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30016665 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.031240:501..4510 +10070
v31.009306:6442..10477 -10029
Homology
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BLAST of SMED30016665 vs. Planmine SMEST
Match: SMESG000015763.1 (SMESG000015763.1)

HSP 1 Score: 396.356 bits (1017), Expect = 1.215e-130
Identity = 187/196 (95.41%), Postives = 190/196 (96.94%), Query Frame = 1 
Query: 1366 STKGPLEFDEHEFDYIDNLCVDGENIQPYKMANRSFDHNGLLRIDRNWRFCETDSFDIKSEIKLLEKEFEINQIEPQRRTEAWVSFDSEWENSTFYGIRYRNNNFPSELPSIIVRIPEDYEQSYSADWNLNYNEYQCHPNSEAHLFLETILMSLRNEFSNLSSQSWNIVPFLDIVSIYKRSIQIGLLNYECRKSIV 1953
            + K   +  +HEFDYIDNLCVDGENIQPYKMANRSFDHNGLLRIDRNWRFCETDSFDIKSEIKLLEKEFEINQIEPQRRTEAWVSFDSEWENSTFYGIRYRNNNFPSELPSIIVRIPEDYEQSYSADWNLNYNEYQCHPNSEAHLFLETILMSLRNEFSNLSSQSWNIVPFLDIVSIYKRSIQIGLLNYECRKSIV
Sbjct:  327 TLKHVAKIQDHEFDYIDNLCVDGENIQPYKMANRSFDHNGLLRIDRNWRFCETDSFDIKSEIKLLEKEFEINQIEPQRRTEAWVSFDSEWENSTFYGIRYRNNNFPSELPSIIVRIPEDYEQSYSADWNLNYNEYQCHPNSEAHLFLETILMSLRNEFSNLSSQSWNIVPFLDIVSIYKRSIQIGLLNYECRKSIV 522
[Close]
BLAST of SMED30016665 vs. Planmine SMEST
Match: SMESG000015774.1 (SMESG000015774.1)

HSP 1 Score: 396.356 bits (1017), Expect = 1.397e-130
Identity = 187/196 (95.41%), Postives = 190/196 (96.94%), Query Frame = 1 
Query: 1366 STKGPLEFDEHEFDYIDNLCVDGENIQPYKMANRSFDHNGLLRIDRNWRFCETDSFDIKSEIKLLEKEFEINQIEPQRRTEAWVSFDSEWENSTFYGIRYRNNNFPSELPSIIVRIPEDYEQSYSADWNLNYNEYQCHPNSEAHLFLETILMSLRNEFSNLSSQSWNIVPFLDIVSIYKRSIQIGLLNYECRKSIV 1953
            + K   +  +HEFDYIDNLCVDGENIQPYKMANRSFDHNGLLRIDRNWRFCETDSFDIKSEIKLLEKEFEINQIEPQRRTEAWVSFDSEWENSTFYGIRYRNNNFPSELPSIIVRIPEDYEQSYSADWNLNYNEYQCHPNSEAHLFLETILMSLRNEFSNLSSQSWNIVPFLDIVSIYKRSIQIGLLNYECRKSIV
Sbjct:  327 TLKHVAKIQDHEFDYIDNLCVDGENIQPYKMANRSFDHNGLLRIDRNWRFCETDSFDIKSEIKLLEKEFEINQIEPQRRTEAWVSFDSEWENSTFYGIRYRNNNFPSELPSIIVRIPEDYEQSYSADWNLNYNEYQCHPNSEAHLFLETILMSLRNEFSNLSSQSWNIVPFLDIVSIYKRSIQIGLLNYECRKSIV 522
[Close]
BLAST of SMED30016665 vs. Planmine SMEST
Match: SMESG000048407.1 (SMESG000048407.1)

HSP 1 Score: 127.487 bits (319), Expect = 2.488e-30
Identity = 105/335 (31.34%), Postives = 156/335 (46.57%), Query Frame = 1 
Query: 1027 KAEQHVLKHNLNAP------------KQLVPTVQSNEEIFGKRIIPDRSKFAFNAEPLM----ENITVPNN--NNNSLDAAFDDIILKIKKHKPSHRMKVRNGLIKYIKEERKEFFRYLPKYL---------QCENEPMNSTKGPLEFDEHEFDYIDNLCVDGENIQPYKMANRSFDHNGLLRIDRNWRFCETDSFDIKSEIKLLEKEFEINQIEPQRRTEAWVSFDSEWENSTFYGIRYRNNNFPSELPSIIVRIPEDYEQSYSADWNLNYNEYQCHPNSEAHLFLETILMSLRNEFSNLSSQ-SWNIVPFLDIVSIYKRSIQIGLLNYECRKS 1947
            KAEQHVL+   N               Q+V   Q    +    +  D      +  PL     EN+ + N   N++SLD AFDD+  K+         +V+  LI + K  + ++  +LPK +           + +P +    PL  DE EF  +D    DG ++   K +    D N LL  D N+   +    D+  E+KLLEKEF++ +IE +  ++ W + DS+W +S F+   Y   + PS +P I +RI  DYE S S DWNLN   YQ  P  +   FL  +   L   F+       W+ +P L I+S+YKRSI +   NY  R S
Sbjct:  358 KAEQHVLQKCSNQTTNIHLEKLHPNTSQIVAQSQCRTTVQKPIVNYDEKSMKKSVYPLSNSSNENVDLNNGSINSSSLDIAFDDVCRKLINTDYKVVKRVQQNLIHFFKSRQTQYRHFLPKRVFIDPDDEAAADDTKPKHPKLEPLSVDE-EFGVLDKDEDDGLDLFVNKDSISLIDENRLLHTDLNFACIDMSFCDLAKELKLLEKEFQVTKIEEEHVSKDWFTHDSDWADSQFFSFLYIYKSLPSIVPPIKIRISADYEDSGSTDWNLNLELYQL-PFDD---FLNEVASLLTTNFTEAHHNYQWSGIPVLYIMSLYKRSILLAHENYLNRLS 687
[Close]
BLAST of SMED30016665 vs. Planmine SMEST
Match: SMESG000048407.1 (SMESG000048407.1)

HSP 1 Score: 127.872 bits (320), Expect = 2.626e-30
Identity = 105/335 (31.34%), Postives = 156/335 (46.57%), Query Frame = 1 
Query: 1027 KAEQHVLKHNLNAP------------KQLVPTVQSNEEIFGKRIIPDRSKFAFNAEPLM----ENITVPNN--NNNSLDAAFDDIILKIKKHKPSHRMKVRNGLIKYIKEERKEFFRYLPKYL---------QCENEPMNSTKGPLEFDEHEFDYIDNLCVDGENIQPYKMANRSFDHNGLLRIDRNWRFCETDSFDIKSEIKLLEKEFEINQIEPQRRTEAWVSFDSEWENSTFYGIRYRNNNFPSELPSIIVRIPEDYEQSYSADWNLNYNEYQCHPNSEAHLFLETILMSLRNEFSNLSSQ-SWNIVPFLDIVSIYKRSIQIGLLNYECRKS 1947
            KAEQHVL+   N               Q+V   Q    +    +  D      +  PL     EN+ + N   N++SLD AFDD+  K+         +V+  LI + K  + ++  +LPK +           + +P +    PL  DE EF  +D    DG ++   K +    D N LL  D N+   +    D+  E+KLLEKEF++ +IE +  ++ W + DS+W +S F+   Y   + PS +P I +RI  DYE S S DWNLN   YQ  P  +   FL  +   L   F+       W+ +P L I+S+YKRSI +   NY  R S
Sbjct:  433 KAEQHVLQKCSNQTTNIHLEKLHPNTSQIVAQSQCRTTVQKPIVNYDEKSMKKSVYPLSNSSNENVDLNNGSINSSSLDIAFDDVCRKLINTDYKVVKRVQQNLIHFFKSRQTQYRHFLPKRVFIDPDDEAAADDTKPKHPKLEPLSVDE-EFGVLDKDEDDGLDLFVNKDSISLIDENRLLHTDLNFACIDMSFCDLAKELKLLEKEFQVTKIEEEHVSKDWFTHDSDWADSQFFSFLYIYKSLPSIVPPIKIRISADYEDSGSTDWNLNLELYQL-PFDD---FLNEVASLLTTNFTEAHHNYQWSGIPVLYIMSLYKRSILLAHENYLNRLS 762
[Close]
BLAST of SMED30016665 vs. Planmine SMEST
Match: SMESG000015798.1 (SMESG000015798.1)

HSP 1 Score: 93.2041 bits (230), Expect = 3.314e-21
Identity = 65/199 (32.66%), Postives = 100/199 (50.25%), Query Frame = 1 
Query: 1366 STKGPLEFDEHEFDYIDNLCVDGE---NIQPYKMANRSFDHNGLLRID--RNWRFCETDSFDIKSEIKLLEKEFEINQIEPQRRTEAWVSFDSEWENSTFYGIRYRNNNFPSELPSIIVRIPEDYEQSYSADWNLNYNEYQCHPNSEAHLFLETI------LMSLRNEFSNLSSQSWNIVPFLDIVSIYKRSIQIGLLN 1929
            S K   E+ E EFD++D      +    I P+      +  +G L+ D   +W+       +++   + LE EFEI +I PQ   E W  F+S WENS FY I+Y+++  P+++  I +RI E+YE+S   D+NLN  EY     SEA  FL +I       ++L++  S            L I+  YK+S+Q  L N
Sbjct:   23 SRKPVKEYVEREFDFLDPEDDGDDDENKIVPFSGVKNRYFKDGKLKSDDFTDWKSYVIHLLEVQDIFENLESEFEITEIGPQLEPEDWTKFESNWENSRFYRIKYKHDKLPTDIIPITIRISENYERSQMVDFNLNLKEYPKKIVSEADEFLSSIKDAYLSCLTLKDGLS-----------LLAILGKYKQSVQAALGN 210
The following BLAST results are available for this feature:
BLAST of SMED30016665 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 SMED30016665 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 SMED30016665 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 SMED30016665 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 SMED30016665 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 SMED30016665 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 SMED30016665 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 SMED30016665 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 SMED30016665 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 SMED30016665 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 SMED30016665 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 SMED30016665 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 SMED30016665 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 SMED30016665 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000015763.11.215e-13095.41SMESG000015763.1[more]
SMESG000015774.11.397e-13095.41SMESG000015774.1[more]
SMESG000048407.12.488e-3031.34SMESG000048407.1[more]
SMESG000048407.12.626e-3031.34SMESG000048407.1[more]
SMESG000015798.13.314e-2132.66SMESG000015798.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30016665 ID=SMED30016665|Name=SMED30016665|organism=Schmidtea mediterranea sexual|type=transcript|length=2065bp
ATGTTAATTAATTCGTGTGCAAAACTCGTGAATTTCTATAAAATTTTAAT
ATAAAATACTTCTAATGTACGTAGTATATATTGTCGCTTATTACTGTAAT
GCTTCTAATTGTTCCAGACTATCCTTTTTTAAAAAAAGATAAAAGGATAT
TTGAGTGACATTAGTGACGCATTTTTAGAAAGGTGTAGTTACGCAATCAG
TGTTCCATGGATCCACAATGGGTAGTGAAGTTATACAAATATAGAAAGTT
GGGTTAAAATGGAATTTGTTTAAATCATAAAATACATACAACCATAGAAT
CGGAACAGCGAATAAATGGTTTGTACAGGGGAAAAGTACCCATTCGAAAG
TTGAATAATCATAATATTTTGTTACAAGGTCCAAGTGACATTTGTAATGA
ATGACAAAATTTCTATTGTAAAACAAATTGTATATATGCTCTAAAATGTT
TAATGAGGCATTTATGATATGTTTCATAAATACAATGAAATGGTAAAAGA
CAAAAATTTTATTTTGGATGAAAATGAGACAGTCTCTTTTGTGAAAACTC
GGGAATCACTCCAAAATTGATTTAAGGAATTTTCTCCGATAAAATATATT
GTTGAAAATATCACATGGATATTGAATCCATTTGTGAATCAAACCGGACT
ATAAGCTTTTCACCTACAGAAGAAGATAGGTTTTTGCTTGCGTTATTCTG
TCTATAAAAAAATAGAAATATATTTTTATTTTTGGGCATTTATACTGGTA
TTTGAATGAGGATAGGAAATGGTTAGTTCATCTTCATCAACGTTTTCTAA
TTGTTTGTTTGATTTTTACCAACTTCCCTAATAATTAAAATGATCAAAAT
TTGTTTCTAAAATATATCGATGTTCAGTGATATGACTGAAATCTTTCAAA
AGGCTTAATAATTAGTTTATTTTTAAACTAATTTTTGTTACGATTGTTGA
TTTTCAAGTATATTTATAAATCACATTGTAAAATATACATTTATGATAAT
AGTAATGATTATTTTAGTACAGCAGGAAAGCTGAACAGCATGTTCTAAAA
CATAATCTTAATGCCCCAAAACAATTAGTTCCAACGGTTCAATCTAATGA
AGAAATATTTGGTAAAAGAATCATACCTGATCGTAGTAAATTTGCCTTTA
ATGCCGAACCATTAATGGAGAACATCACTGTGCCGAATAATAATAATAAT
TCGTTAGATGCTGCTTTTGATGATATTATTCTAAAAATAAAAAAACATAA
ACCTTCACACCGAATGAAGGTAAGAAATGGACTCATAAAATATATAAAGG
AAGAGAGAAAAGAGTTTTTTCGCTACCTTCCGAAATATTTACAGTGCGAA
AATGAACCAATGAATTCCACAAAAGGACCACTTGAGTTTGATGAACACGA
ATTTGATTATATTGACAATTTGTGTGTTGATGGTGAAAATATCCAGCCTT
ATAAGATGGCAAATCGATCATTTGATCACAATGGATTATTAAGGATCGAC
AGAAATTGGAGATTTTGTGAGACGGATTCTTTCGATATCAAAAGTGAAAT
TAAACTACTTGAAAAGGAATTTGAAATCAATCAAATTGAACCCCAACGGA
GAACCGAAGCTTGGGTGAGTTTCGATAGTGAATGGGAGAATAGCACATTC
TACGGAATTAGATATCGGAATAATAATTTTCCCTCGGAGCTTCCATCGAT
AATTGTCCGTATTCCGGAAGATTATGAACAAAGTTATTCAGCAGATTGGA
ATTTGAATTACAATGAATATCAATGCCATCCCAATTCAGAAGCTCACTTA
TTTCTCGAGACTATTTTAATGTCTTTGAGAAATGAATTTTCAAATCTGAG
TTCTCAATCTTGGAATATTGTGCCGTTTCTGGATATTGTTAGTATTTATA
AACGGAGTATTCAAATCGGATTATTGAATTATGAGTGTAGAAAATCAATT
GTTTAAAATATTATGTGTAAAATCAATTGCAATCGGTTATTTTTTGATTG
CATATTTTTCTATTTTCTCAATTATTTGTTTGTAAATAAATTAAATCCAG
CATTTATTTTTCACC
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protein sequence of SMED30016665-orf-1

>SMED30016665-orf-1 ID=SMED30016665-orf-1|Name=SMED30016665-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=264bp
MENITVPNNNNNSLDAAFDDIILKIKKHKPSHRMKVRNGLIKYIKEERKE
FFRYLPKYLQCENEPMNSTKGPLEFDEHEFDYIDNLCVDGENIQPYKMAN
RSFDHNGLLRIDRNWRFCETDSFDIKSEIKLLEKEFEINQIEPQRRTEAW
VSFDSEWENSTFYGIRYRNNNFPSELPSIIVRIPEDYEQSYSADWNLNYN
EYQCHPNSEAHLFLETILMSLRNEFSNLSSQSWNIVPFLDIVSIYKRSIQ
IGLLNYECRKSIV*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell
PLANA:0002111X2 cell