SMED30033565

Overview
NameSMED30033565
Smed IDSMED30033565
Length (bp)916
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 SMED30033565 (SMED30033565) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30033565 (SMED30033565) 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 SMED30033565 (SMED30033565) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30033565 (SMED30033565) 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



SMED30033565

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



PAGE Curations: 18

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pigment cellSMED30033565SMESG000050427.1 SmedASXL_017550SmedAsxl_ww_GCZZ01PMID:29158443
He et al., 2017		whole organism asexual adult RNA-sequencing evidence
X1 cellSMED30033565SMESG000050427.1 SmedASXL_017550SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30033565SMESG000050427.1 SmedASXL_017550SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
nervous systemSMED30033565SMESG000050427.1 dd_Smed_v4_3777_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30033565SMESG000050427.1 dd_Smed_v4_3777_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30033565SMESG000050427.1 dd_Smed_v4_3777_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30033565SMESG000050427.1 dd_Smed_v4_3777_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30033565SMESG000050427.1 dd_Smed_v4_3777_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30033565SMESG000050427.1 dd_Smed_v4_3777_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30033565SMESG000050427.1 Contig20539newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30033565SMESG000050427.1 Contig20539uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30033565SMESG000050427.1 Contig37647newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30033565SMESG000050427.1 Contig37647uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
parapharyngeal regionSMED30033565SMESG000050427.1 dd_Smed_v6_3777_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
neoblastSMED30033565SMESG000050427.1 dd_Smed_v6_3777_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
zeta neoblastSMED30033565SMESG000050427.1 dd_Smed_v4_3777_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
neoblastSMED30033565SMESG000050427.1 SMED_29717_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30033565SMESG000050427.1 SMED_29717_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
SMED30033565 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002089:105648..106563 +4562
Homology
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BLAST of SMED30033565 vs. Planmine SMEST
Match: SMESG000050427.1 (SMESG000050427.1)

HSP 1 Score: 359.377 bits (921), Expect = 6.135e-113
Identity = 196/201 (97.51%), Postives = 197/201 (98.01%), Query Frame = 3 
Query:    3 ALESETN-GYGDKNSVLEKDNSAVIIKKTRGRQKKPIIENLTETLEPVSITVGDNQHTTKILGRKKEKVFGNMGQSSANTIENVNSLTLRSTRARTNTVKSDNSKLITDENKSENEIPKISTGQQKKLIENEISGDEVVGVLASXXXXXXXXXXXXVDEFKKPHATIKRNYKKKINQTNIISTESSSIAQSTTFESTQEDT 602
             LESETN GYGDKNSVLEKDNSAVIIKKTRGRQKKPIIENLTETLEPVSITVGDNQHTTKILGRKKEKVFGNMGQSSANTIENVNSLTLRSTRARTNTVKSDNSKLITDENKSENEIPKISTGQQKKLIENEISGDEVVGVLASEITEN+ILENNEVDEFKKPHATIKRNYKKKINQTNI STESSSIAQS TFESTQEDT
Sbjct: 2982 VLESETNDGYGDKNSVLEKDNSAVIIKKTRGRQKKPIIENLTETLEPVSITVGDNQHTTKILGRKKEKVFGNMGQSSANTIENVNSLTLRSTRARTNTVKSDNSKLITDENKSENEIPKISTGQQKKLIENEISGDEVVGVLASEITENMILENNEVDEFKKPHATIKRNYKKKINQTNITSTESSSIAQSATFESTQEDT 3182

HSP 2 Score: 50.8322 bits (120), Expect = 8.440e-7
Identity = 28/41 (68.29%), Postives = 32/41 (78.05%), Query Frame = 3 
Query:    3 ALESETN-GYGDKNSVLEKDNSAVIIKKTRGRQKKPIIENL 122
            ALESETN G GDKNS++EK NS V  K TRGRQKK I E++
Sbjct: 2802 ALESETNDGNGDKNSIVEKKNSVVFTKNTRGRQKKQINESV 2842
[Close]
BLAST of SMED30033565 vs. Planmine SMEST
Match: SMESG000050427.1 (SMESG000050427.1)

HSP 1 Score: 359.377 bits (921), Expect = 6.315e-113
Identity = 196/201 (97.51%), Postives = 197/201 (98.01%), Query Frame = 3 
Query:    3 ALESETN-GYGDKNSVLEKDNSAVIIKKTRGRQKKPIIENLTETLEPVSITVGDNQHTTKILGRKKEKVFGNMGQSSANTIENVNSLTLRSTRARTNTVKSDNSKLITDENKSENEIPKISTGQQKKLIENEISGDEVVGVLASXXXXXXXXXXXXVDEFKKPHATIKRNYKKKINQTNIISTESSSIAQSTTFESTQEDT 602
             LESETN GYGDKNSVLEKDNSAVIIKKTRGRQKKPIIENLTETLEPVSITVGDNQHTTKILGRKKEKVFGNMGQSSANTIENVNSLTLRSTRARTNTVKSDNSKLITDENKSENEIPKISTGQQKKLIENEISGDEVVGVLASEITEN+ILENNEVDEFKKPHATIKRNYKKKINQTNI STESSSIAQS TFESTQEDT
Sbjct: 2977 VLESETNDGYGDKNSVLEKDNSAVIIKKTRGRQKKPIIENLTETLEPVSITVGDNQHTTKILGRKKEKVFGNMGQSSANTIENVNSLTLRSTRARTNTVKSDNSKLITDENKSENEIPKISTGQQKKLIENEISGDEVVGVLASEITENMILENNEVDEFKKPHATIKRNYKKKINQTNITSTESSSIAQSATFESTQEDT 3177

HSP 2 Score: 50.8322 bits (120), Expect = 8.514e-7
Identity = 28/41 (68.29%), Postives = 32/41 (78.05%), Query Frame = 3 
Query:    3 ALESETN-GYGDKNSVLEKDNSAVIIKKTRGRQKKPIIENL 122
            ALESETN G GDKNS++EK NS V  K TRGRQKK I E++
Sbjct: 2797 ALESETNDGNGDKNSIVEKKNSVVFTKNTRGRQKKQINESV 2837
[Close]
BLAST of SMED30033565 vs. Planmine SMEST
Match: SMESG000050427.1 (SMESG000050427.1)

HSP 1 Score: 359.377 bits (921), Expect = 6.377e-113
Identity = 196/201 (97.51%), Postives = 197/201 (98.01%), Query Frame = 3 
Query:    3 ALESETN-GYGDKNSVLEKDNSAVIIKKTRGRQKKPIIENLTETLEPVSITVGDNQHTTKILGRKKEKVFGNMGQSSANTIENVNSLTLRSTRARTNTVKSDNSKLITDENKSENEIPKISTGQQKKLIENEISGDEVVGVLASXXXXXXXXXXXXVDEFKKPHATIKRNYKKKINQTNIISTESSSIAQSTTFESTQEDT 602
             LESETN GYGDKNSVLEKDNSAVIIKKTRGRQKKPIIENLTETLEPVSITVGDNQHTTKILGRKKEKVFGNMGQSSANTIENVNSLTLRSTRARTNTVKSDNSKLITDENKSENEIPKISTGQQKKLIENEISGDEVVGVLASEITEN+ILENNEVDEFKKPHATIKRNYKKKINQTNI STESSSIAQS TFESTQEDT
Sbjct: 2984 VLESETNDGYGDKNSVLEKDNSAVIIKKTRGRQKKPIIENLTETLEPVSITVGDNQHTTKILGRKKEKVFGNMGQSSANTIENVNSLTLRSTRARTNTVKSDNSKLITDENKSENEIPKISTGQQKKLIENEISGDEVVGVLASEITENMILENNEVDEFKKPHATIKRNYKKKINQTNITSTESSSIAQSATFESTQEDT 3184

HSP 2 Score: 50.8322 bits (120), Expect = 8.515e-7
Identity = 28/41 (68.29%), Postives = 32/41 (78.05%), Query Frame = 3 
Query:    3 ALESETN-GYGDKNSVLEKDNSAVIIKKTRGRQKKPIIENL 122
            ALESETN G GDKNS++EK NS V  K TRGRQKK I E++
Sbjct: 2804 ALESETNDGNGDKNSIVEKKNSVVFTKNTRGRQKKQINESV 2844
[Close]
BLAST of SMED30033565 vs. Planmine SMEST
Match: SMESG000050427.1 (SMESG000050427.1)

HSP 1 Score: 359.377 bits (921), Expect = 6.691e-113
Identity = 196/201 (97.51%), Postives = 197/201 (98.01%), Query Frame = 3 
Query:    3 ALESETN-GYGDKNSVLEKDNSAVIIKKTRGRQKKPIIENLTETLEPVSITVGDNQHTTKILGRKKEKVFGNMGQSSANTIENVNSLTLRSTRARTNTVKSDNSKLITDENKSENEIPKISTGQQKKLIENEISGDEVVGVLASXXXXXXXXXXXXVDEFKKPHATIKRNYKKKINQTNIISTESSSIAQSTTFESTQEDT 602
             LESETN GYGDKNSVLEKDNSAVIIKKTRGRQKKPIIENLTETLEPVSITVGDNQHTTKILGRKKEKVFGNMGQSSANTIENVNSLTLRSTRARTNTVKSDNSKLITDENKSENEIPKISTGQQKKLIENEISGDEVVGVLASEITEN+ILENNEVDEFKKPHATIKRNYKKKINQTNI STESSSIAQS TFESTQEDT
Sbjct: 2974 VLESETNDGYGDKNSVLEKDNSAVIIKKTRGRQKKPIIENLTETLEPVSITVGDNQHTTKILGRKKEKVFGNMGQSSANTIENVNSLTLRSTRARTNTVKSDNSKLITDENKSENEIPKISTGQQKKLIENEISGDEVVGVLASEITENMILENNEVDEFKKPHATIKRNYKKKINQTNITSTESSSIAQSATFESTQEDT 3174

HSP 2 Score: 50.8322 bits (120), Expect = 8.666e-7
Identity = 28/41 (68.29%), Postives = 32/41 (78.05%), Query Frame = 3 
Query:    3 ALESETN-GYGDKNSVLEKDNSAVIIKKTRGRQKKPIIENL 122
            ALESETN G GDKNS++EK NS V  K TRGRQKK I E++
Sbjct: 2794 ALESETNDGNGDKNSIVEKKNSVVFTKNTRGRQKKQINESV 2834
The following BLAST results are available for this feature:
BLAST of SMED30033565 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 SMED30033565 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 SMED30033565 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 SMED30033565 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 SMED30033565 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 SMED30033565 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 SMED30033565 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 SMED30033565 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 SMED30033565 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 SMED30033565 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 SMED30033565 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 SMED30033565 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 SMED30033565 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 SMED30033565 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000050427.16.135e-11397.51SMESG000050427.1[more]
SMESG000050427.16.315e-11397.51SMESG000050427.1[more]
SMESG000050427.16.377e-11397.51SMESG000050427.1[more]
SMESG000050427.16.691e-11397.51SMESG000050427.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30033565 ID=SMED30033565|Name=SMED30033565|organism=Schmidtea mediterranea sexual|type=transcript|length=916bp
GTGCTTTGGAAAGTGAAACTAATGGATATGGGGACAAAAATAGCGTTTTG
GAAAAAGACAATTCGGCTGTTATTATAAAGAAAACTCGTGGAAGACAAAA
GAAACCCATAATCGAAAATCTTACAGAAACCCTTGAACCTGTTTCAATTA
CGGTTGGAGACAATCAACACACCACAAAAATACTTGGTCGAAAAAAGGAA
AAAGTATTTGGAAATATGGGCCAAAGTAGCGCAAATACTATTGAAAATGT
AAATTCTTTAACTCTACGCTCAACTCGTGCTCGAACAAATACAGTTAAAT
CAGATAACTCTAAATTGATTACCGATGAAAATAAAAGTGAAAATGAGATT
CCCAAAATATCAACAGGACAACAAAAGAAATTGATTGAAAACGAGATTAG
TGGTGATGAAGTTGTCGGAGTTTTGGCTAGTGAAATCACAGAAAATATTA
TTTTAGAAAATAATGAAGTAGATGAATTCAAAAAGCCACATGCAACCATC
AAAAGAAATTATAAGAAAAAAATTAACCAAACAAATATCATAAGTACGGA
AAGTTCTTCAATTGCACAGAGTACCACATTTGAATCGACTCAAGAAGACA
CTGTTGATAAAGATAAAAATAGAAAAAAAAATGTTGAAAATGTAAAAAAT
TCTAATAAAGAGAATGTTTTTAATACTGGAACACAGAAAAAAACTCGATC
GGCAGCGAAACTTTTAGAAAATCAGCCTAAATTGAGTGATAGTGAGACAT
TGGTTTTGAGATCGAAAAAAAGAGGTCATTGTAAAAGTTCTAATAACAGT
GACATTCAGTTAAATATTTTAACTGAGAATAAAAACACAGAAAATTCTGA
ATTTTCAGGTGTTAAAACCAGAACAAGAAGCAAAAAGATGTATATTTGAT
GTTTTATTATGATTTA
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protein sequence of SMED30033565-orf-1

>SMED30033565-orf-1 ID=SMED30033565-orf-1|Name=SMED30033565-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=299bp
ALESETNGYGDKNSVLEKDNSAVIIKKTRGRQKKPIIENLTETLEPVSIT
VGDNQHTTKILGRKKEKVFGNMGQSSANTIENVNSLTLRSTRARTNTVKS
DNSKLITDENKSENEIPKISTGQQKKLIENEISGDEVVGVLASEITENII
LENNEVDEFKKPHATIKRNYKKKINQTNIISTESSSIAQSTTFESTQEDT
VDKDKNRKKNVENVKNSNKENVFNTGTQKKTRSAAKLLENQPKLSDSETL
VLRSKKRGHCKSSNNSDIQLNILTENKNTENSEFSGVKTRTRSKKMYI*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000014zeta neoblast
PLANA:0000420parapharyngeal region
PLANA:0000429neoblast
PLANA:0002075pigment cell
PLANA:0002109X1 cell
PLANA:0002111X2 cell