SMED30013289

Overview
NameSMED30013289
Smed IDSMED30013289
Length (bp)8051
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 SMED30013289 (SMED30013289) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30013289 (SMED30013289) 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 SMED30013289 (SMED30013289) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30013289 (SMED30013289) 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




SMED30013289

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parenchymal cellSMED30013289 dd_Smed_v4_10565_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
SMED30013289 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000855:42644..50691 +39799
Homology
The following BLAST results are available for this feature:
BLAST of SMED30013289 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 SMED30013289 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 SMED30013289 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 SMED30013289 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 SMED30013289 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 SMED30013289 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 SMED30013289 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 SMED30013289 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 SMED30013289 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 SMED30013289 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 SMED30013289 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 SMED30013289 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 SMED30013289 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 SMED30013289 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30013289 ID=SMED30013289|Name=SMED30013289|organism=Schmidtea mediterranea sexual|type=transcript|length=8051bp
TAAACCTAGCAGAGGTTTTAACACTTAATTTGTTTATGGCTTACTTGTTT
TTTGTACAGATTGCAAATTTGACTCAGTTTATGATTATCACGTCAAGGTT
CTGAGAAGAGATTTTTTTAGCAAATTTTGAATTACATGTTACTTTTTAGC
AACCATTGCTCATCATTTAACGTTTTCAACAGGGCTCATGGTCTGTTGAA
ACCTTTCACCATGTTCATCTCTGGATTTCCTCAAATTACGGATAAAAAAA
TAAAGGTGAATTTTCAATTACAGACGAGAGAAATTAATTATTTTATTATT
TCCATTGAACCTCATTTTCCTGAAATATTAAACGATAAAAGTTTTGTACA
AAAAAATATGCAATTCTTCCATATTTGTACTTGTCCAAATAGGTTTTTGA
GAGCTAACGATACTTAGCAGCCAACCACAGCCTTGTATGCTCGCTTTTCA
TCATTTTAAGAATGTTTGAAACTGAAAATCTTGGAAAGGCCTTTACAAAG
TTCTTAAATAATATCAGCGTTTTGTGCAAGATGAGCAATAATATTTTATC
AACAGGAACAAGTGCTTCATGTTTGATATATGCTCTTCTTGGTAATTGTC
ACACGACTATCTCATAAGCACGCGAAACAACAATATTTCGTGTAACCACC
CTGCAATCATGTAATCTTAATCCCCACCAAACCATTTGAACTTTTTGTAA
TGCACTAACTCCAGAATAAATTGCATAATCTTACTAAATTCTTTGATGTG
TCTTAAATAGACAAAGTAGCTGAAAACTGCTTAACATGAAAAAGAGCAGC
CCTTACATTCACTATCATTAATGAAGAGCCACCAATATTTTTTTCACATC
AGATTATATACTCAGCTTTGTGAACAGACCTAGAACATTGCAACAGTAAA
TAAAACCATGATGTTCATTTCTGTAAAAATGCTGATTGTAAATTCTGTTT
CTTTATTATTTTGTTTCAGCTACCATAATACTTAATCTATTCAGCATCGA
GTAGACATCTCCCTTCGATAACCTAAGCTTTCTAACAAAATGATTTAATT
GCTCTTGACTGATTTCAAGCTGCGATATATACTGCGATATATTCATTTGC
CATTACTCAATCTCATGTGACGTGGTTTTCTTCTCAAAGCTGTTGGCTGA
GTTAGAAGTGTATGATGAATTTTCATGTTTTTATTCATATGATTTATCGC
AAACCAAATCTGGATGCAGAATATGCTTTACTAGCATTTTCTTTAAGGCA
GTTATTCTTGTCGTACTAAATAGCAGTCGTAATGGTTTCTTTGTTCTCAA
GGCCATAAATGTACTGATTAACACATTTTTCAACTTTCCTACAACCCGCA
TTGAAAGGTTTGAGTAGTGAGAAGCAAACGACTTTTCTTGGTAACCGATT
TTTATTTCGAATTATTTCTGGAACTTGATTTCGACGAGGAAGTTAGTAAG
GATCTTTAAATAAATATTCTAGACAAATATAAAAAATTGCTTTCCTTTGT
GAGAAAACAATGGGAATTGTGAGTTGAATAACAATGCGTAATATTTAATA
AACAGCAGAAAATTTTCGATTTACAAAAATAGTAGCACGTGTAATAGTAA
TAAATAGTTATGTACCAATGCTCATTTGATTCCTGTTTAGCGGTTGTTTT
CAACATTCCGTCAAATTCTACTTTCATGTTTACTGTCTAGTATTTCTTCT
GCAACAGGTATTTTAAAAGAAATTAAAGCTGTTAAAATGAAATTTTCCGC
TTCAAAGACTTTTTAATTAACTCTGACCTAAAAAAATACTAGGTGGCGTA
CATTTTCGTAATTCCTATCAAAGTATAACGGTGGAAATTTGGGCTTCAAT
TTTTGTTTGAGGGTGTAATCAGGGGTTACATTGCACAAACATTATTTCAT
TGGCATATAACGCTATTTTAGAATTAGAATGTGACGTGTCAGTTGTTATC
CATTAACAACATAATATATACAGACCTAATATTACGCTTTTTGTATCAAA
TAAAGACTCATGGCTGGATAAGTTTAACAGAACGTTTGAAATCTGAGCCA
TATTCAGAATATATCAATACTATTACGATAAATTAAAAAAAAATTTAAGT
ATTATTTATAATATGAACAATGAACTATTTTTGTAAATCTTGTCAATGCA
TAACTTGTCAATGCATAATTTGACATTACTATAATTAAGTCCTTAAAATT
GGTCATTTTTTACTAAACTTATTTCATAAACTATAACAAATTAAAACAAT
AAGACTCTTCTATTTCTAAAAATATTAAAATATGCTACATAATTCTATTT
TATTGAGCTTTATTATTGAAAATTAAATGAATTGCTAACTTATTTCGACT
TGAATTACAAATGTGAAATTTTATGAATAAAAATGTATGTTATTTAAAAT
AACATTAAATGATAATTATTGTCAAATTATAATATAATTTAATTATAATA
AATGCCATTTTGATAAATCAAATTGACATTAAAACGACAATATTATTGAA
GAAATTTGTTACTAAAGCTACAAATTATTAAAACACTAAATCTTTATAAA
TATGCGCGTAATTCAAAATTTAAAGTTAGTAAATTTTAATATTCGAGATC
AATTGATGACTAAAATAATATATTTTGAAGTAAAAATTATCTTTCATTTC
AAAACTAAAATATAGAAGTGGAACATTTTGAATTTAAAAAAAGGAATGAA
ACAAATAAAGAATATTTAAGATTGGTGAAAATCAAGTATAATTTGTAAGA
GTTGAATGTAAGCGGATAAAATCAGATAAAAAAAATAACTTTCTAAATAG
ACTTTCCAAATAAATTAAGGTTTAACTTAAATAAATTAACAATTTATAAA
TTTTATATAATGACTTTTATAGGAATATTACAATTATCTTTTAAAAATAT
GCATTATTGGATAGCATTCACTACAAATAACTCATTATGTCGTATATTAC
AAAGAATAAATGATTCTCGCCAAAGTTTCGGAGGATATCTACAAGAAGGT
CGACGGTAAAAGGAATGTTTAGAGAAAGCAAATGAAGATTATTATAATTT
TCTAGCGATAAACATAATTTGCATAAGTCTTAGAGGTGGTATTAGGGTTT
AAAAATGTTTATAAATTTATGCTGATTTTTTAAAATCTTAGAATGAATGC
AAAAATTTGAAAGATATTGGAATATGAGAAAATAAGATTATGTTAATTTA
ATCGCGAAGAAAGTTTCATGATAGTGTTAAATAGTGTTGAGGTAAAAATA
AAATTAGACTTAGTATTTTTTTATCTTAGTGTTGTTTTTATTGTTTTTTG
CAAAAATGTATGTTTTTCATTAATTAAAAATTAAATATAAGCACTAAACA
ATTACTTAAATAGGGTTATATTTGATAAATCTATAAATGCAATATGAATT
TCAATTTATTTTTTGTTTAAAATAATTGTAATTTTTTTGATTTAACTAAA
TTTATTAACATTTCAAGATCATCTAATTTTTAATTCTAAACATTTTTAAC
CATCCAAATTCAACAAAATAGGATGAGTTTACTTAATTCGCGTTAATAAT
TTAATGAAGTTGTTAAATTTTTAGTACTTAACAGATTTCTCCATTAACAT
ACATTTAAACATAAAAAGGCAAAATTTATTAAAAATTTAAACCCCAAAAA
GGTTGTACTTATTCTTATTTCAGATATTTATGGAATTAGAATTTTTAAGC
TGCGACAATATTTAATGAAGGTTATTTTTATTAACAATAAATTACGGCAA
AACGAGTGTTTAAAGTACTTATTTGTCAAGCCTGATAAATATCATAGAAC
ACATAATGAAAATCATTAATGGATTTAAGAAACCATTATAAAACAAAGAA
ACCACCCAATAAGGACTAAAAGTGCTTAGGACATCCCACATTACTCATTA
CAAGTCAATTTTTGCAATTAAATGATAAATGTAAAATACTTAAAAAGTTT
ATCGATTAACCAAATAATTGATAATTTAAAAAGGTTTTCAAGTTAATCGA
TTCATAAATTTGAATAACATAATTTTGTAAGTGGACATTCTTCAAGCAAC
TTCATTAATTACAATAACTTGACAATAAATTTCTATTTGTAGTTATTTAA
ATTTTAATGGTAAACCATTTCCAAAATATTTCAATAAATACATATTTTTC
ATATATGCAATTACTTATTTAATATTATTCTAGTTACTTTACTATAAAAC
ATCGAAAATTTCTTACACAACAAAGTTATTTATTTATATTCATTTTATAG
AAATAAATGCCTTCAATTCTTTTGTATTATAATTATTCATTTTATTTGCA
TTCCATGAATTTCTATTAGATATTTTGACTAGTGAATATTTCGCTAATTA
TTTCTCATTTAAAGCGTTAAAATTTTGTTATTTTCGCAAATACAATTAAA
TCAAATATTTATTTATAACATAATTTTTAATTTTCTGACCAATGTAAGTT
TAAAGCTAGATTTCAAGTGAATTCATTTATATTTTAAATTTCATTAATTA
AATGGTAATTTTTTACGTAAATATTAAATAAACTTAAAATAATTTGATTT
TGCTAAAAATTATCACTTGCTTAAAATTAATCTTCTTGATTATCTCGATT
TTTGAATAAATAAATTTGATATTAACTTTCATTTTTTTGAATGTACTTTT
ATTATAAAAAATACTTTATATATCATTGCGCAGGTACGATGCGTATCCGT
GTTTTTAGTAATACGTGTTTTGGCTTGACATGACTAAAAATTTCCTTTCT
ATCAATGCAAAGATTGGTTCTTAATTTATCGTTAAGTTTTCCGTTAAATA
ATTTTTCCTATTTATGGATTCCAAGAATCATTAGTAATTCTTTATTTGCT
TCACGACATTACATCACATATTATCAAATTGTCACCGCTTATACTATCTA
TCATTTCAATCACGAACCGTTCTGCAGTCAATCATTTCAAATTTAACGCT
TCTATACCAAACTTTCCGATTCTCAATAATACAATTACAATTAAAATATG
ATTATTTAAATAATGTTCTAGACGAGGGTTCTAATGTTGAATTGAGTAGA
ATTCTTACAACTATCACGTTATCTTAATAGAATAACACTCCACTTACTTT
TTTTCGATAAATTTTAGTACAATTATTCTGCTTTATTAATTATTTGCTTT
TTAACTCGTCAATATTTTATTACTCACGATTTGGTAAACTTTTTTTGTTT
AATACCTTTTTAAAAATTGATTAATTACCATTAACATAATTATCATAAAT
TATGTTTAACAGAATAGAAATTGATATTTAAATTATTGATGACGTAGAAA
TAATAACGTATAAATTACTGACAGAAGAAATTGGAGGAAGAAAGTAGTAA
TTACTTGTTTTAATTATTTAATATAAAAAGAAACGAGAAACAATATTGGG
CACACAAATTATTGAAAACAACGCAGTTATTAGTCATTGTGGTAAAAGCA
ATTAACGAATAAATTTATAATTAAATTACATAAATAGTTTCCCTGACGAA
ATAAAAAACATTGATAATAAATTTTGAAAACAAGAAGAAATAAAGTAGAG
AAAATGGAAAATTATATTCACAGCGAAGAAAATTCAAACCAGCTCGTAAG
ATTTTGAATCTAACAGAAGTCTGTGGATATTGCTTTATTCTAGTTATGAC
TGTATATTTATTCAAAAATTTTTCTTGAACAAATCACCGTATATACTATT
TTATAAATCGACTCAAGTATAAGTCGAATTGAAAATTTAAAGCCAGTTTT
TAGTCCAAAATTGAAAGCCCATGCATAAGTGGAAGTAAAAAAACAGGTAA
ACAACAAAACCAAACAAAAAATCTTCCAAAAAAAATAACAAAAATAGATA
GACGAAAAACAGACTTGGAAAAAAACACATACAAGTTGTCAAATCTAGAA
AAACCGTTTTAAAAAGCAATCTCGTACTAACTTTTCGTCAACGTCTCTGG
TAACATATGATTTGCCATTAATTTCAGCAATCTCAACAACTCGTAATTCA
TCTTTAAAAAATTTATCGACAAAACTATACTAAAAATATTATTTTAAAAA
TTTTATCATGTAATTTTGTCGAATTTAACTTTCAAAATTGTCAACTTTTA
AAATTTTTCTTTGAATAATTGCAGATTACTAGTTTTATTTCTTTGCAAAT
ATTGGTTATTGGATTTAATTTTATTAATAATTTAATTTAAATGTCTTTAA
TAATTAACAAATCCGTTGTTCGAATTCCATATTTTATTTGAAATTAATTA
ATTAGATTAAAAGCGGCATAATTAAAGATCTCATTTTTCAAAGGTATTTT
TGAAAAAAATATATAATTTTTGTACAAGTCGAATTGAAAAAAAGTCATCA
AATTTAATACAAAATTTATCGACTTATACACGAGTATATTCGGTTCATTT
CTTACAACAGTAAAATTAGTTTAAACCATGTCAATAATTATTAATAATAT
CTATTTAAATATTTATTGCAGCACTGTTAATTTTCCTTAACAAACTTAGT
TTTTGCACTTTATTTTTAAACATTGATTAAAATTGAAATTTCTATAAAAT
TTCTTTTACAAAAATGAATTAGGCACTGTCTTTGGTATTTTGCATAAATA
TTTTTATCTCAAATTAAAGCTGCATTTTCATGGTTTGAAACAAACAATAT
AGTGTATTTTTACTGGAGTTTTTAAACTGCAATGACGGCGAGCTAAATAA
AAAAGTTTTTTATTTTTAATATAGAAAAATCTCACAAAACAATATTATCA
AAATATTTAATAAATGTAAATTTCTTTTTATAAAATAATGGCGTTTTTCA
AATGGTGAAAATGAAAATCAGATATTTTAAAGCATAATTTCACCAGTAAA
TTATATTTTCAATTATGTTTTATGATTTTTATTTATCTTTAATTTAAAAA
AATGAAAATTAATATTTAAAACTTTAAAGACCGCATTGAAAAATCGTATT
TCTCACATATGAACCGTCATTTTTTTTATTTTTCATTACATATTATTTTT
AAAATATTTTTTAGTGTACAATAATTTAACCCCTAGATTTATTTCAATTA
AAAGGCACCCGCCCGGTCCCAAAATGTAAACAAGCGGTCCCCAAGTAAAA
CATGTCGTGTGCCCACCCGTGAGCCGCTGTCCGTTAATGTTGTTTCGGAG
TGACCCACCAGTTAATTTAACGTGTTAATTAAAGATCAATAAGTTTGTTA
GGAAATGAAAAAATACAGATTTTGAATTATTCGTTTTATCTCTTGATTGG
CTTTTTATTCCAAATATTTTAAGTTCATGTATAAACTTAATATATTAATA
TATTAACTTTTGCCAAAACCATCTCACTATTTACAGGTAATAATTTTTGA
TATTTTAATAATTTTGTTTCAGTCAGTATTATTGTAATGGATACTTTATG
ATTGAATTATTATTAAACATGAATCGAATGTGTGTTTTAAAATATAATTT
TGTTATTTTTGATGTTCGTTATTAAATGCTGTTCTCTATGCTTATTTCCT
GTATTTTAATAGAATCTAAATTCAAAAATTTACTTAAACTTTATAAAATT
TTAAACAGAGGATATTTATGTATCAATTTTTTAATATTTAGAAATTTCTA
CCATTTGCTATCTTTTTATAAATCTAAAGTTATTTAAATACTAAGAATTC
AAGGAAATAGGTATATCATAATTGATCATATTATTTATGATCATAAGAAT
TCAAAAATCCCTAGAAGTCAGCAACAAGGTTGAACTGTTACAGAAGCATA
ATAAATGAGTTGTTTAAAACGTTTTCCATTAACAAGATTTTCCTTTCAGT
CCAAGTTGACGTATACGGCCCATATTTAAAAAGGTTGTTTTCAATGCTAC
AAAGCTATAATTAGCAGGAAAATTTTTAATATGAATTAGACAACAAATCA
GCGTTTCAAATCAATTTTATATTTTAAATAAATTTACATTTAAATTTTAT
ATTAATTTAAATAGTAATACTAAATTTTTCATATTTAGCTTTTCGATTTA
ATTTTACCCCTTAAAACGTCCACTGATATCAGTGTTGAATGTTGATATTT
G
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000070intestinal phagocyte
PLANA:0003116parenchymal cell