SMED30030029

Overview
NameSMED30030029
Smed IDSMED30030029
Length (bp)1639
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 SMED30030029 (SMED30030029) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30030029 (SMED30030029) 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 SMED30030029 (SMED30030029) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30030029 (SMED30030029) 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



SMED30030029

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



PAGE Curations: 8

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30030029h1SMcG0020530 SmedASXL_019445SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30030029h1SMcG0020530 dd_Smed_v4_2502_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30030029h1SMcG0020530 dd_Smed_v4_2502_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30030029h1SMcG0020530 dd_Smed_v4_2502_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult colorimetric in situ hybridization evidence
epidermisSMED30030029h1SMcG0020530 dd_Smed_v4_2502_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
whole organismSMED30030029h1SMcG0020530 dd_Smed_v4_2502_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult colorimetric in situ hybridization evidence
Category 4 cellSMED30030029h1SMcG0020530 dd_Smed_v4_2502_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
dorsal region of the epidermisSMED30030029h1SMcG0020530 dd_Smed_v4_2502_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30030029 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001392:994..6399 +7993
Homology
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BLAST of SMED30030029 vs. TrEMBL
Match: A0A183T3Z6 (Uncharacterized protein OS=Schistocephalus solidus OX=70667 GN=SSLN_LOCUS11194 PE=4 SV=1)

HSP 1 Score: 67.781 bits (164), Expect = 8.531e-9
Identity = 31/92 (33.70%), Postives = 52/92 (56.52%), Query Frame = 2 
Query:  365 TTFLHCPILDSDICYQGCTPMCKYENEN----CLVPSEMKSITK-CDHKIEEIDHVRYQFTINVEKIKKRNGEWYCSYEGINSRPITLKVFQ 625
            + +L CP + + ICY  CTP C +E E     C VP  + ++ K CD++I     +  ++T+N+E +    G W C Y+G+ SRP+ L+  +
Sbjct:  104 SVYLMCPQVQTSICYFDCTPSCTFEGEGSATVCKVPQILGNVVKSCDYRILNSATILVKYTVNMEALDS-TGIWSCEYQGVRSRPLLLQAAE 194
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BLAST of SMED30030029 vs. TrEMBL
Match: A0A0X3PM53 (Uncharacterized protein OS=Schistocephalus solidus OX=70667 GN=TR153399 PE=4 SV=1)

HSP 1 Score: 66.6254 bits (161), Expect = 8.839e-8
Identity = 31/92 (33.70%), Postives = 52/92 (56.52%), Query Frame = 2 
Query:  365 TTFLHCPILDSDICYQGCTPMCKYENEN----CLVPSEMKSITK-CDHKIEEIDHVRYQFTINVEKIKKRNGEWYCSYEGINSRPITLKVFQ 625
            + +L CP + + ICY  CTP C +E E     C VP  + ++ K CD++I     +  ++T+N+E +    G W C Y+G+ SRP+ L+  +
Sbjct:  104 SVYLMCPQVQTSICYFDCTPSCTFEGEGSATVCKVPQILGNVVKSCDYRILNSATILVKYTVNMEALDS-TGIWSCEYQGVRSRPLLLQAAE 194
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BLAST of SMED30030029 vs. TrEMBL
Match: A0A0R3TGW5 (Uncharacterized protein OS=Rodentolepis nana OX=102285 GN=HNAJ_LOCUS6302 PE=4 SV=1)

HSP 1 Score: 62.003 bits (149), Expect = 4.320e-7
Identity = 43/122 (35.25%), Postives = 63/122 (51.64%), Query Frame = 2 
Query:  266 GEATKSIFISEDIISPTLTKVTCTISDSQGIKGTTFLHCPILDSDICYQGCTPMCKY-ENENCLVPSEMKS-ITKCDHKI-EEIDHVRYQFTINVEKIKKRNGEWYCSYEGINS-RPITLKV 619
            G  T  + +S D      TK     +D+Q +    +L CP++ + ICY  CTP C Y E E C+VP  + S I  C  +I  E D +   +TI ++ +  R GEW C Y GI + RP+ L+ 
Sbjct:   66 GHLTCEVMLSTD------TKKDFDKTDNQSL-SHVYLRCPLVPAGICYVDCTPACSYDEVEGCVVPPSLSSAIEDCRFEIPPEGDKIVLDYTIAMDML-DRTGEWNCEYLGIAAPRPLKLEA 179
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BLAST of SMED30030029 vs. TrEMBL
Match: A0A3P7NK89 (Uncharacterized protein OS=Dibothriocephalus latus OX=60516 GN=DILT_LOCUS4563 PE=4 SV=1)

HSP 1 Score: 60.4622 bits (145), Expect = 5.603e-7
Identity = 28/92 (30.43%), Postives = 49/92 (53.26%), Query Frame = 2 
Query:  365 TTFLHCPILDSDICYQGCTPMCKYENEN----CLVPSEMKSIT-KCDHKIEEIDHVRYQFTINVEKIKKRNGEWYCSYEGINSRPITLKVFQ 625
            TT      + + ICY  CTP C +E E+    C VP  + ++   CD++I     +  ++T+N+E +    G W C Y+G+ +RP+ L+  +
Sbjct:   14 TTLFRIRKVPTSICYFDCTPSCTFEGESSATVCKVPETLAAVVMSCDYRILNSATILVKYTVNMEALDS-TGNWSCEYQGVRARPLLLQAAE 104
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BLAST of SMED30030029 vs. TrEMBL
Match: A0A5K3FBN5 (Uncharacterized protein OS=Mesocestoides corti OX=53468 PE=4 SV=1)

HSP 1 Score: 60.8474 bits (146), Expect = 4.880e-6
Identity = 25/79 (31.65%), Postives = 52/79 (65.82%), Query Frame = 2 
Query:  371 FLHCPILDSDICYQGCTPMCKYENEN-CLVPSEMKSITKCDHKIEEIDHVR--YQFTINVEKIKKRNGEWYCSYEGINS 598
            +L CP +D+ ICY  CTP C +++ N C+VP  + ++ +  H  +E+++ R   ++ +++E++  R G+W C Y+G+++
Sbjct:   94 YLRCPQVDTKICYVDCTPACVFDDHNGCVVPQSLSTVIEECHYEQEVENGRLILEYIVDMEEL-DRTGDWTCEYQGVSA 171
[Close]
BLAST of SMED30030029 vs. Planmine SMEST
Match: SMESG000010225.1 (SMESG000010225.1)

HSP 1 Score: 757.673 bits (1955), Expect = 0.000e+0
Identity = 421/423 (99.53%), Postives = 421/423 (99.53%), Query Frame = 2 
Query:  260 PVGEATKSIFISEDIISPTLTKVTCTISDSQGIKGTTFLHCPILDSDICYQGCTPMCKYENENCLVPSEMKSITKCDHKIEEIDHVRYQFTINVEKIKKRNGEWYCSYEGINSRPITLKVFQXXXXXXXXXXXXXXXXXXXXXXXXXXXXPIGVSRQVTTAGSAKITFRLSERVPETAVKSQVKTNDSEFNFRIFITKYEXXXXXXXXXXXXXXXXXXXCIRDSLIKQFIDNIKSNVSSNKYLLCCICQNELEGISATAKLDRILSKDPDYISTDASNCSKNDLYNNDIQRPLISPLYSNVDVNSNYTPNITRSSSIMNPEIAQNMVPVNYDQIYLTAPRGMSPYVYNPYIMTRSNIAAHERLAEYANQRHSYVLPSNFNLQSCAPVFQNPPSKKHASQNDIDLIRHCESQDQPPKVSDPINA 1528
            PVGEATKSIFISEDIISPTLTKVTCTISDSQGIKGTTFLHCPILDSDICYQGCTPMCKYENENCLVPSEMKSITKCDHKIEEIDHVRYQFTINVEKIKKRNGEWYCSYEGINSRPITLKVFQVTNNNIVTTITKTKLTSLSTKSATKKVLPIGVSRQVTTAGSAKITFRLSERVPETA KSQVKTNDSEFNFRIFITKYEVVVGIIIFLSLSIFLNFVFCIRDSLIKQFIDNIKSNVSSNKYLLCCICQNELEGISATAKLDRILSKDPDYISTDASNCSKNDLYNNDIQRPLISPLYSNVDVNSNYTPNITRSSSIMNPEIAQNMVPVNYDQIYLTAPRGMSPYVYNPYIMTRSNIAAHERLAEYANQRHSYVLPSNFNLQS APVFQNPPSKKHASQNDIDLIRHCESQDQPPKVSDPINA
Sbjct:   16 PVGEATKSIFISEDIISPTLTKVTCTISDSQGIKGTTFLHCPILDSDICYQGCTPMCKYENENCLVPSEMKSITKCDHKIEEIDHVRYQFTINVEKIKKRNGEWYCSYEGINSRPITLKVFQVTNNNIVTTITKTKLTSLSTKSATKKVLPIGVSRQVTTAGSAKITFRLSERVPETAGKSQVKTNDSEFNFRIFITKYEVVVGIIIFLSLSIFLNFVFCIRDSLIKQFIDNIKSNVSSNKYLLCCICQNELEGISATAKLDRILSKDPDYISTDASNCSKNDLYNNDIQRPLISPLYSNVDVNSNYTPNITRSSSIMNPEIAQNMVPVNYDQIYLTAPRGMSPYVYNPYIMTRSNIAAHERLAEYANQRHSYVLPSNFNLQSYAPVFQNPPSKKHASQNDIDLIRHCESQDQPPKVSDPINA 438
The following BLAST results are available for this feature:
BLAST of SMED30030029 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 SMED30030029 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 SMED30030029 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 SMED30030029 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 SMED30030029 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 SMED30030029 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 SMED30030029 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 SMED30030029 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A183T3Z68.531e-933.70Uncharacterized protein OS=Schistocephalus solidus... [more]
A0A0X3PM538.839e-833.70Uncharacterized protein OS=Schistocephalus solidus... [more]
A0A0R3TGW54.320e-735.25Uncharacterized protein OS=Rodentolepis nana OX=10... [more]
A0A3P7NK895.603e-730.43Uncharacterized protein OS=Dibothriocephalus latus... [more]
A0A5K3FBN54.880e-631.65Uncharacterized protein OS=Mesocestoides corti OX=... [more]
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BLAST of SMED30030029 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 SMED30030029 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 SMED30030029 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 SMED30030029 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 SMED30030029 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 SMED30030029 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000010225.10.000e+099.53SMESG000010225.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30030029 ID=SMED30030029|Name=SMED30030029|organism=Schmidtea mediterranea sexual|type=transcript|length=1639bp
CTAGTTTAGTTATTTAAATGATGTAAATTTAATTTTTAAAAAATTTAATA
TTATTATATTGATTGATGTAAAAAAGAAGCGCTCACTAACCTAAAATCAT
TCAAGCATGACATTAAAATACCTTTATTTTCAAACTACGCACTTGTCAAA
TCATTAATTAAAATTATGACGGCGAGACCTACATTTTCGTCAATTATTAA
ATAAATATAATTAAATGTATTTAAATTTACTTTTTATTGTTCTTATTTTT
AATTTTCTGCCTGTGGGAGAAGCCACCAAAAGCATTTTCATCAGTGAAGA
TATCATATCGCCTACTTTAACAAAAGTTACATGCACAATTTCTGACAGCC
AAGGAATAAAAGGAACAACCTTTTTACATTGTCCAATTTTGGATTCAGAC
ATCTGTTACCAAGGTTGCACTCCAATGTGCAAATATGAAAATGAAAACTG
CCTGGTTCCATCTGAAATGAAGTCAATCACAAAATGTGACCACAAAATCG
AAGAAATAGATCATGTTAGATATCAATTTACAATAAATGTAGAAAAAATC
AAAAAAAGGAATGGTGAATGGTACTGTTCATATGAAGGTATTAATTCTCG
ACCAATAACGCTGAAGGTTTTCCAAGTGACGAACAATAATATAGTAACAA
CAATAACTAAGACAAAATTAACTTCTCTTTCAACAAAAAGTGCAACTAAA
AAAGTTTTGCCAATTGGTGTATCTCGACAGGTCACGACCGCTGGTAGTGC
GAAAATCACGTTTAGACTATCAGAAAGGGTGCCGGAAACCGCCGTAAAAA
GCCAAGTTAAAACAAACGATTCAGAATTTAATTTCAGAATTTTCATCACA
AAATATGAAGTTGTGGTCGGAATAATAATTTTCCTTTCATTATCAATATT
TCTGAATTTCGTTTTTTGCATTCGGGACTCCTTGATCAAGCAGTTCATTG
ATAACATCAAAAGTAACGTCTCATCAAATAAATATCTTCTCTGTTGTATC
TGCCAAAATGAACTCGAAGGAATTTCAGCCACTGCAAAACTCGATAGAAT
ACTTTCGAAAGATCCTGATTATATCTCCACAGATGCTAGCAACTGCAGCA
AGAATGACTTGTACAACAACGATATACAGCGTCCATTGATATCTCCTTTA
TACTCCAATGTCGATGTCAACTCCAACTATACTCCCAATATCACCAGATC
ATCTTCTATAATGAATCCTGAAATAGCGCAAAATATGGTTCCTGTGAACT
ACGATCAAATATATTTAACTGCTCCACGGGGAATGTCACCATATGTATAT
AACCCATACATTATGACTAGGTCCAACATTGCCGCTCATGAACGGTTGGC
AGAATATGCTAATCAGAGACATTCATACGTGCTACCATCTAATTTTAACC
TACAAAGTTGTGCTCCCGTTTTCCAAAATCCACCGAGCAAGAAGCATGCC
AGCCAGAATGACATTGATCTGATCAGACATTGCGAAAGTCAAGATCAGCC
CCCCAAAGTCTCTGATCCTATCAATGCATAAAGATAATATAAATTTGATT
TGTTAATTTGAGAAATAATTATGATATTATTGTAAGATATTATGATAATA
ATTATAGATAAATAAAATTTTGATTTTGATGTTTTTGAG
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protein sequence of SMED30030029-orf-1

>SMED30030029-orf-1 ID=SMED30030029-orf-1|Name=SMED30030029-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=439bp
MYLNLLFIVLIFNFLPVGEATKSIFISEDIISPTLTKVTCTISDSQGIKG
TTFLHCPILDSDICYQGCTPMCKYENENCLVPSEMKSITKCDHKIEEIDH
VRYQFTINVEKIKKRNGEWYCSYEGINSRPITLKVFQVTNNNIVTTITKT
KLTSLSTKSATKKVLPIGVSRQVTTAGSAKITFRLSERVPETAVKSQVKT
NDSEFNFRIFITKYEVVVGIIIFLSLSIFLNFVFCIRDSLIKQFIDNIKS
NVSSNKYLLCCICQNELEGISATAKLDRILSKDPDYISTDASNCSKNDLY
NNDIQRPLISPLYSNVDVNSNYTPNITRSSSIMNPEIAQNMVPVNYDQIY
LTAPRGMSPYVYNPYIMTRSNIAAHERLAEYANQRHSYVLPSNFNLQSCA
PVFQNPPSKKHASQNDIDLIRHCESQDQPPKVSDPINA*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000018Category 4 cell
PLANA:0000034epidermis
PLANA:0000054dorsal region of the epidermis
PLANA:0000136whole organism
PLANA:0000418head
PLANA:0002032epidermal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..20
score: 0.896
NoneNo IPR availableTMHMMTMhelixcoord: 214..236