SMED30005974

Overview
NameSMED30005974
Smed IDSMED30005974
Length (bp)2670
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 SMED30005974 (SMED30005974) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30005974 (SMED30005974) 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 SMED30005974 (SMED30005974) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30005974 (SMED30005974) 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



SMED30005974

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



PAGE Curations: 10

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30005974SMESG000035109.1 Contig3221newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30005974SMESG000035109.1 Contig3221uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30005974SMESG000035109.1 Contig2486newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30005974SMESG000035109.1 Contig2486uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30005974SMESG000042564.1 Contig3221newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30005974SMESG000042564.1 Contig3221uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30005974SMESG000024603.1 Contig2486newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30005974SMESG000024603.1 Contig2486uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
X1 cellSMED30005974SMESG000035109.1 SmedASXL_009548SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30005974SMESG000035109.1 SmedASXL_009548SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30005974 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004981:13098..22173 -13170
Homology
[Close]
BLAST of SMED30005974 vs. Planmine SMEST
Match: SMESG000035109.1 (SMESG000035109.1)

HSP 1 Score: 1663.66 bits (4307), Expect = 0.000e+0
Identity = 846/847 (99.88%), Postives = 847/847 (100.00%), Query Frame = 2 
Query:   41 MTTVKRDINFQGGFDELLCQKISIAIKKSNIFAHVNLSELIRKRFINANNNEVCDVPPSKKCKPINEPIPEVSNDKEIPKDNLCRSPILNDFLPNPDTLFSQSTPNPSNKSVKSECILKENSSVSRNVYLLSSSIDLSNLQPPHSIAEINVSRLSLPNNEIEVNTTLDGKDTKSISNVNFSKTNLLLENREKSPKRDGVRGKQNKDLSNLATSLLPLPTQLFGKDSMLSALESGEFFDFLNFFKEGIQIDKEISADDLTEIIEMIVKKKAFSIISGFISCLMNNNMFIEPLTNSLVKYKSELSKYKIDILKCVESMTDFKIVSSINFYIKACSVMNYWDRMWFVLSSKCPGYMIPETYFNSFMNEFDVLDKSQPMPINSETMTIIIPYISRMHPSKKVAYLTEIWLYCIYYDINNKELNSMDLEISQQSFDKIIDKLNNAKDPSFLFGMKILIKNWNLIHNYKFSEWFSKLISDKSDVRKCLFSIKDSIHALNRNVKQEIFDNFNLLVIRVMSYLNKKSLFTCSKTIYENFLKNVFSDIKRALYQVNDKFKLKWTMVECLVSSAEYEKALFIIKEFEVLKDLEVISPDYNRVKEILPNLVWHLINSSETLPVIVLFEQVISIFIFNENIDNAYTKNCNEIFDLIVIKAYESNNCEVVRKMXXXXXXXXXXXXXXXXXKDSLRYLAIAAVRTNIPFKELLDFVDVCFKFDIFENIQTAEDGFGSFVGASSNLTHEEIIILVTWMCRHVKIKLVQSVQNQGSTIRENIMKVCSIKFILHASTNSDSFCKNINSDTSFNEFLKNFTEALNNPKYLKHPIKFSTISDTSDNVMKIVCDNRIVYNTIYYSDI 2581
            MTTVKRDINFQGGFDELLCQKISIAIKKSNIFAHVNLSELIRKRFINANNNEVCDVPPSKKCKPINEPIPEVSNDKEIPKDNLCRSPILNDFLPNPDTLFSQSTPNPSNKSVKSECILKENSSVSRNVYLLSSSIDLSNLQPPHS+AEINVSRLSLPNNEIEVNTTLDGKDTKSISNVNFSKTNLLLENREKSPKRDGVRGKQNKDLSNLATSLLPLPTQLFGKDSMLSALESGEFFDFLNFFKEGIQIDKEISADDLTEIIEMIVKKKAFSIISGFISCLMNNNMFIEPLTNSLVKYKSELSKYKIDILKCVESMTDFKIVSSINFYIKACSVMNYWDRMWFVLSSKCPGYMIPETYFNSFMNEFDVLDKSQPMPINSETMTIIIPYISRMHPSKKVAYLTEIWLYCIYYDINNKELNSMDLEISQQSFDKIIDKLNNAKDPSFLFGMKILIKNWNLIHNYKFSEWFSKLISDKSDVRKCLFSIKDSIHALNRNVKQEIFDNFNLLVIRVMSYLNKKSLFTCSKTIYENFLKNVFSDIKRALYQVNDKFKLKWTMVECLVSSAEYEKALFIIKEFEVLKDLEVISPDYNRVKEILPNLVWHLINSSETLPVIVLFEQVISIFIFNENIDNAYTKNCNEIFDLIVIKAYESNNCEVVRKMISLLDLILSADIDFDISKDSLRYLAIAAVRTNIPFKELLDFVDVCFKFDIFENIQTAEDGFGSFVGASSNLTHEEIIILVTWMCRHVKIKLVQSVQNQGSTIRENIMKVCSIKFILHASTNSDSFCKNINSDTSFNEFLKNFTEALNNPKYLKHPIKFSTISDTSDNVMKIVCDNRIVYNTIYYSDI
Sbjct:    1 MTTVKRDINFQGGFDELLCQKISIAIKKSNIFAHVNLSELIRKRFINANNNEVCDVPPSKKCKPINEPIPEVSNDKEIPKDNLCRSPILNDFLPNPDTLFSQSTPNPSNKSVKSECILKENSSVSRNVYLLSSSIDLSNLQPPHSLAEINVSRLSLPNNEIEVNTTLDGKDTKSISNVNFSKTNLLLENREKSPKRDGVRGKQNKDLSNLATSLLPLPTQLFGKDSMLSALESGEFFDFLNFFKEGIQIDKEISADDLTEIIEMIVKKKAFSIISGFISCLMNNNMFIEPLTNSLVKYKSELSKYKIDILKCVESMTDFKIVSSINFYIKACSVMNYWDRMWFVLSSKCPGYMIPETYFNSFMNEFDVLDKSQPMPINSETMTIIIPYISRMHPSKKVAYLTEIWLYCIYYDINNKELNSMDLEISQQSFDKIIDKLNNAKDPSFLFGMKILIKNWNLIHNYKFSEWFSKLISDKSDVRKCLFSIKDSIHALNRNVKQEIFDNFNLLVIRVMSYLNKKSLFTCSKTIYENFLKNVFSDIKRALYQVNDKFKLKWTMVECLVSSAEYEKALFIIKEFEVLKDLEVISPDYNRVKEILPNLVWHLINSSETLPVIVLFEQVISIFIFNENIDNAYTKNCNEIFDLIVIKAYESNNCEVVRKMISLLDLILSADIDFDISKDSLRYLAIAAVRTNIPFKELLDFVDVCFKFDIFENIQTAEDGFGSFVGASSNLTHEEIIILVTWMCRHVKIKLVQSVQNQGSTIRENIMKVCSIKFILHASTNSDSFCKNINSDTSFNEFLKNFTEALNNPKYLKHPIKFSTISDTSDNVMKIVCDNRIVYNTIYYSDI 847
The following BLAST results are available for this feature:
BLAST of SMED30005974 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 SMED30005974 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 SMED30005974 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 SMED30005974 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 SMED30005974 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 SMED30005974 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 SMED30005974 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 SMED30005974 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 SMED30005974 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 SMED30005974 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 SMED30005974 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 SMED30005974 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 SMED30005974 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 SMED30005974 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000035109.10.000e+099.88SMESG000035109.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30005974 ID=SMED30005974|Name=SMED30005974|organism=Schmidtea mediterranea sexual|type=transcript|length=2670bp
GCGTCGCGCTTTTTTTGTAAATTTTACTCCATTTTAAAAAATGACAACTG
TGAAAAGAGATATAAATTTTCAAGGTGGTTTTGATGAATTATTATGCCAG
AAAATTTCAATTGCAATTAAAAAATCTAACATATTTGCACATGTTAATCT
GTCAGAATTAATTCGTAAAAGATTTATCAATGCAAATAATAATGAGGTTT
GTGATGTTCCTCCTTCCAAAAAATGCAAGCCTATAAATGAACCTATACCA
GAAGTTTCCAACGATAAAGAGATTCCTAAAGATAATTTATGCAGAAGCCC
TATTTTAAATGATTTCCTTCCTAATCCTGATACCTTATTTTCTCAAAGTA
CTCCTAACCCCTCAAATAAATCTGTAAAGTCTGAATGTATATTAAAAGAA
AATTCGTCTGTTTCACGAAATGTTTATCTTTTATCAAGCAGTATTGATTT
GTCTAATTTACAGCCACCTCATTCTATAGCTGAAATAAATGTTTCTCGTT
TGTCATTACCAAATAATGAAATTGAAGTTAATACAACATTGGACGGAAAA
GATACAAAATCAATCTCTAACGTAAATTTTTCAAAAACAAATTTGCTTTT
AGAAAACCGAGAAAAATCACCGAAAAGAGACGGAGTTAGAGGAAAACAAA
ATAAAGATCTTTCTAATTTAGCTACGTCATTACTTCCACTTCCTACTCAG
TTATTTGGGAAAGATTCAATGTTATCTGCTTTGGAAAGTGGCGAGTTCTT
TGATTTTCTTAATTTTTTTAAAGAAGGAATTCAAATTGATAAAGAAATAT
CTGCAGATGATTTGACTGAAATAATCGAAATGATTGTTAAGAAAAAGGCA
TTCTCTATTATTTCTGGATTTATTTCTTGTTTAATGAATAACAATATGTT
TATCGAGCCTCTCACAAATTCTTTGGTTAAATATAAAAGTGAACTAAGTA
AATATAAAATAGATATTTTGAAGTGTGTAGAATCTATGACAGATTTTAAA
ATCGTGTCTAGCATAAATTTTTATATTAAAGCATGTTCTGTCATGAATTA
TTGGGATAGAATGTGGTTCGTTCTTTCCAGCAAATGCCCCGGGTATATGA
TACCAGAAACATACTTTAATTCATTTATGAATGAGTTTGATGTTCTAGAT
AAGAGCCAGCCAATGCCCATCAATAGTGAAACCATGACGATAATAATTCC
ATATATTTCTCGAATGCATCCATCGAAAAAAGTAGCCTACTTGACTGAAA
TTTGGTTATATTGTATTTATTACGATATTAACAATAAGGAATTAAATTCC
ATGGACTTGGAAATTTCACAACAGTCATTTGATAAAATCATCGATAAATT
AAACAACGCTAAAGATCCGTCTTTTCTCTTTGGTATGAAGATTTTAATAA
AAAATTGGAATTTGATACATAATTACAAATTTTCTGAGTGGTTTTCAAAA
CTTATATCAGATAAAAGTGATGTTAGAAAGTGCTTATTCTCTATAAAAGA
TTCTATACATGCTTTAAATCGTAATGTTAAACAAGAAATATTTGACAATT
TCAATTTGCTGGTTATTCGCGTAATGTCATATCTTAACAAAAAGTCGTTG
TTTACATGTTCAAAAACGATTTATGAAAATTTCCTTAAAAACGTATTTTC
TGACATAAAACGGGCGCTCTATCAAGTTAATGATAAATTTAAATTAAAGT
GGACAATGGTTGAATGTCTAGTTTCATCAGCAGAATATGAAAAAGCATTA
TTTATAATCAAAGAATTTGAAGTTCTAAAAGATCTGGAAGTAATTTCACC
AGATTATAACAGAGTGAAAGAAATACTACCAAATTTAGTTTGGCATTTGA
TAAATTCATCAGAAACACTGCCAGTTATTGTTTTATTTGAGCAAGTCATA
TCCATATTCATTTTCAATGAAAATATTGATAATGCCTACACAAAAAATTG
CAACGAAATTTTCGACCTCATAGTTATTAAAGCTTACGAATCTAATAACT
GTGAAGTTGTTAGAAAGATGATATCTCTTTTGGATCTCATTTTATCCGCT
GACATTGACTTCGACATTTCCAAGGACAGCTTACGTTATTTGGCTATTGC
CGCTGTTCGTACAAATATTCCTTTCAAAGAGTTGCTTGACTTTGTAGATG
TATGCTTTAAGTTTGATATCTTTGAAAATATCCAAACAGCAGAAGACGGT
TTTGGCAGTTTTGTTGGCGCGAGTTCTAACTTAACACACGAAGAAATTAT
TATTTTGGTGACCTGGATGTGTCGCCATGTTAAAATAAAATTAGTTCAAT
CTGTACAAAATCAAGGTTCTACTATAAGAGAGAACATAATGAAAGTCTGT
TCGATTAAATTCATCTTGCACGCATCCACTAATTCAGATTCATTCTGTAA
AAATATAAATTCGGATACATCTTTTAACGAATTCTTGAAAAATTTCACAG
AAGCTCTTAATAATCCGAAATACCTTAAACATCCGATTAAGTTTTCAACT
ATCAGTGACACATCTGATAATGTAATGAAAATTGTTTGCGACAATAGAAT
AGTTTATAATACAATATATTATAGTGATATTTAAATAAATAATTTTCTAC
TGTAATTTGAAACTTATGTGTAAAATTTTCTATGTAGATATATGTTAATA
CAAATAAATCTCGTTTAAAT
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protein sequence of SMED30005974-orf-1

>SMED30005974-orf-1 ID=SMED30005974-orf-1|Name=SMED30005974-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=848bp
MTTVKRDINFQGGFDELLCQKISIAIKKSNIFAHVNLSELIRKRFINANN
NEVCDVPPSKKCKPINEPIPEVSNDKEIPKDNLCRSPILNDFLPNPDTLF
SQSTPNPSNKSVKSECILKENSSVSRNVYLLSSSIDLSNLQPPHSIAEIN
VSRLSLPNNEIEVNTTLDGKDTKSISNVNFSKTNLLLENREKSPKRDGVR
GKQNKDLSNLATSLLPLPTQLFGKDSMLSALESGEFFDFLNFFKEGIQID
KEISADDLTEIIEMIVKKKAFSIISGFISCLMNNNMFIEPLTNSLVKYKS
ELSKYKIDILKCVESMTDFKIVSSINFYIKACSVMNYWDRMWFVLSSKCP
GYMIPETYFNSFMNEFDVLDKSQPMPINSETMTIIIPYISRMHPSKKVAY
LTEIWLYCIYYDINNKELNSMDLEISQQSFDKIIDKLNNAKDPSFLFGMK
ILIKNWNLIHNYKFSEWFSKLISDKSDVRKCLFSIKDSIHALNRNVKQEI
FDNFNLLVIRVMSYLNKKSLFTCSKTIYENFLKNVFSDIKRALYQVNDKF
KLKWTMVECLVSSAEYEKALFIIKEFEVLKDLEVISPDYNRVKEILPNLV
WHLINSSETLPVIVLFEQVISIFIFNENIDNAYTKNCNEIFDLIVIKAYE
SNNCEVVRKMISLLDLILSADIDFDISKDSLRYLAIAAVRTNIPFKELLD
FVDVCFKFDIFENIQTAEDGFGSFVGASSNLTHEEIIILVTWMCRHVKIK
LVQSVQNQGSTIRENIMKVCSIKFILHASTNSDSFCKNINSDTSFNEFLK
NFTEALNNPKYLKHPIKFSTISDTSDNVMKIVCDNRIVYNTIYYSDI*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000070intestinal phagocyte
PLANA:0002109X1 cell
PLANA:0002111X2 cell