SMED30019921

Overview
NameSMED30019921
Smed IDSMED30019921
Length (bp)793
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 SMED30019921 (SMED30019921) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30019921 (SMED30019921) 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 SMED30019921 (SMED30019921) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30019921 (SMED30019921) 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



SMED30019921

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
pharynxSMED30019921SMESG000058949.1 dd_Smed_v4_10877_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30019921SMESG000058949.1 dd_Smed_v4_10877_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30019921SMESG000058949.1 dd_Smed_v4_10877_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30019921SMESG000058949.1 dd_Smed_v4_10877_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30019921SMESG000058949.1 dd_Smed_v4_10877_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30019921SMESG000058949.1 dd_Smed_v6_10877_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30019921SMESG000058949.1 dd_Smed_v6_10877_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
dorsal ventral margin of the whole animalSMED30019921SMESG000058949.1 dd_Smed_v4_10877_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
SMED30019921 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001419:55797..56587 +3883
Homology
[Close]
BLAST of SMED30019921 vs. Planmine SMEST
Match: SMESG000058949.1 (SMESG000058949.1)

HSP 1 Score: 407.912 bits (1047), Expect = 3.031e-146
Identity = 200/201 (99.50%), Postives = 201/201 (100.00%), Query Frame = 3 
Query:  141 MRIILVQILHICYFFELVLSSEKSWNPEIKLLYSSCDVAVVQVRCPNNTVRRNIEFHIHRMENGKMNLWKVIVKICSKTFITIKLKYVCRSLYRMTFNLGLLNGKCDEFCQNSQSSPPWFFGSNDCYNLNENQCYFNEFLPRIGSCQATKLKCQEKTTIKNFKNNYFWIISFPFVLLIIVLFVICFFSCKRWHQRNNFVTI 743
            MRIILVQILHICYFFELVLSSEKSWNPEIKLLYSSCDVAVVQVRCPNNTVRRNIEFHIHRMENGKMNLWKVIVKICSKTFITIKLKYVCRSLYRMTFNLGLLNGKCDEFCQNSQSSPPWFFGSNDCYNLNENQCYFNEFLP+IGSCQATKLKCQEKTTIKNFKNNYFWIISFPFVLLIIVLFVICFFSCKRWHQRNNFVTI
Sbjct:    1 MRIILVQILHICYFFELVLSSEKSWNPEIKLLYSSCDVAVVQVRCPNNTVRRNIEFHIHRMENGKMNLWKVIVKICSKTFITIKLKYVCRSLYRMTFNLGLLNGKCDEFCQNSQSSPPWFFGSNDCYNLNENQCYFNEFLPQIGSCQATKLKCQEKTTIKNFKNNYFWIISFPFVLLIIVLFVICFFSCKRWHQRNNFVTI 201
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BLAST of SMED30019921 vs. Planmine SMEST
Match: SMESG000058905.1 (SMESG000058905.1)

HSP 1 Score: 70.8626 bits (172), Expect = 8.612e-14
Identity = 43/133 (32.33%), Postives = 63/133 (47.37%), Query Frame = 3 
Query:  195 LSSEKSWNPEIKLLYSSCDVAVVQVRCPNNTVRRNIEFHIHRMENGKMNLWKVIVKIC---SKTFITIKLKYVCRSLYRMTFNLGLLNGK--CDEFCQNSQSSPPWFFGSNDC------------YNLNENQC 542
            + S   W+P IKL+ + C    VQ  CP   V RN+EF + RM  G  ++   + KIC   SKT++ +  ++ CR++Y +   +  +     CDEFC    SS  W  G   C            Y +NEN C
Sbjct:  308 MQSFTQWSPNIKLITAYCTNITVQATCPFLNVSRNLEFSLLRM--GDRSISATVTKICNPLSKTYLKVSFEFECRAVYYVNIIMSPITPSMICDEFCSKQHSSEMWLLGRKLCPKVGLDYCKVRKYEINENHC 438

HSP 2 Score: 50.8322 bits (120), Expect = 4.824e-7
Identity = 39/149 (26.17%), Postives = 68/149 (45.64%), Query Frame = 3 
Query:  213 WNPEIKLLYSSCDVAVVQVRCPNNTVRRNIEFHIHRMENGKMNLWKVIVKICSKT---FITIKLKYVCRSLYRMTFNLG----LLNGKCDEFCQNSQSSPPWFFGSNDCYNLN--ENQCYFNEFLPRIGSCQATKLKCQEKTTIKNFKN 632
            W+P + L+ ++C    ++  CP     RNIEF +   E    N+  V    C  +    + + +K  C +LY++  +L     ++N  C E+C  + SSP W FG + C N     N    N+++     C A+  KC      ++ K+
Sbjct:   24 WDPNLTLISANCSNVNIEATCPKLVKERNIEFSL--FEFPTQNVQSVKTYKCPASNAKKLHVSMKLPCINLYQVNISLSPIFPMIN--CREYCLEAHSSPIWLFG-DICQNKQFLSNNGSLNKYMTPKNICPASTQKCSADLKTESQKS 167
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BLAST of SMED30019921 vs. Planmine SMEST
Match: SMESG000058883.1 (SMESG000058883.1)

HSP 1 Score: 71.2478 bits (173), Expect = 8.664e-14
Identity = 38/138 (27.54%), Postives = 72/138 (52.17%), Query Frame = 3 
Query:  213 WNPEIKLLYSSCDVAVVQVRCPNNTVRRNIEFHIHRMENGKMNLWKVI-VKICSKTFITIKLKYVCRSLYRMTFNLGLLNGKCDEFCQNSQSSPPWFFGSNDCYNLNENQCYFNEFLPRIGSCQATKLKCQEKTTIKN 623
            WNP+I+L    C+   +  +CP  + RR+IEF ++ + +   ++ + +  +I     +T      C++LYR+  +L  +   C E+C +  +S  W  G N C  +  + C FN  LPR  SC  + ++C   +T+++
Sbjct:   49 WNPDIRLTNGVCNEVTLTAKCPTLSTRRSIEFELYPLYDPTKSVIQTLQCRINQSQPLTTTFSIQCKNLYRVNISLSPI-FSCTEYCSDIHTSRIWLLGGNTCGEIALD-CAFNVHLPRENSCINSSIQCSLDSTVQS 184

HSP 2 Score: 52.373 bits (124), Expect = 1.380e-7
Identity = 40/146 (27.40%), Postives = 68/146 (46.58%), Query Frame = 3 
Query:  186 ELVLSSEKS-WNPEIKLLYSSCDVAVVQVRCPNNTVRRNIEFH-IHRMENGKMNLWKVIVKICSKTFITIKLKYVCRSLYRMTFNLGLLNG----KCDEFCQNSQSSPPWFFGSNDCYNLNENQCYFNEFLPRIGSCQATKLKCQE 605
            ++ L++  S W+P IK++ + CD   V V CP    +R IE + I    N + +    I K+ S   + I     C ++Y   FN+ +       +CD +C N  SS  +  GS  C N + + C ++ +  +   C  +  KC E
Sbjct:  325 QMSLTTPSSQWSPNIKIVKAFCDNVTVSVDCPRVNKQREIEINLIKDFRNEEFSTR--ICKLNSSETLEISFNLKCMNIYH--FNVSMKPTFSPFECDLYCSNPLSSQKYLLGSRLCRNSSFDDCKYDAYKTKNNLCPKSSKKCPE 466
[Close]
BLAST of SMED30019921 vs. Planmine SMEST
Match: SMESG000058905.1 (SMESG000058905.1)

HSP 1 Score: 70.8626 bits (172), Expect = 8.702e-14
Identity = 43/133 (32.33%), Postives = 63/133 (47.37%), Query Frame = 3 
Query:  195 LSSEKSWNPEIKLLYSSCDVAVVQVRCPNNTVRRNIEFHIHRMENGKMNLWKVIVKIC---SKTFITIKLKYVCRSLYRMTFNLGLLNGK--CDEFCQNSQSSPPWFFGSNDC------------YNLNENQC 542
            + S   W+P IKL+ + C    VQ  CP   V RN+EF + RM  G  ++   + KIC   SKT++ +  ++ CR++Y +   +  +     CDEFC    SS  W  G   C            Y +NEN C
Sbjct:  309 MQSFTQWSPNIKLITAYCTNITVQATCPFLNVSRNLEFSLLRM--GDRSISATVTKICNPLSKTYLKVSFEFECRAVYYVNIIMSPITPSMICDEFCSKQHSSEMWLLGRKLCPKVGLDYCKVRKYEINENHC 439

HSP 2 Score: 50.8322 bits (120), Expect = 4.828e-7
Identity = 39/149 (26.17%), Postives = 68/149 (45.64%), Query Frame = 3 
Query:  213 WNPEIKLLYSSCDVAVVQVRCPNNTVRRNIEFHIHRMENGKMNLWKVIVKICSKT---FITIKLKYVCRSLYRMTFNLG----LLNGKCDEFCQNSQSSPPWFFGSNDCYNLN--ENQCYFNEFLPRIGSCQATKLKCQEKTTIKNFKN 632
            W+P + L+ ++C    ++  CP     RNIEF +   E    N+  V    C  +    + + +K  C +LY++  +L     ++N  C E+C  + SSP W FG + C N     N    N+++     C A+  KC      ++ K+
Sbjct:   25 WDPNLTLISANCSNVNIEATCPKLVKERNIEFSL--FEFPTQNVQSVKTYKCPASNAKKLHVSMKLPCINLYQVNISLSPIFPMIN--CREYCLEAHSSPIWLFG-DICQNKQFLSNNGSLNKYMTPKNICPASTQKCSADLKTESQKS 168
[Close]
BLAST of SMED30019921 vs. Planmine SMEST
Match: SMESG000058905.1 (SMESG000058905.1)

HSP 1 Score: 70.8626 bits (172), Expect = 8.909e-14
Identity = 43/133 (32.33%), Postives = 63/133 (47.37%), Query Frame = 3 
Query:  195 LSSEKSWNPEIKLLYSSCDVAVVQVRCPNNTVRRNIEFHIHRMENGKMNLWKVIVKIC---SKTFITIKLKYVCRSLYRMTFNLGLLNGK--CDEFCQNSQSSPPWFFGSNDC------------YNLNENQC 542
            + S   W+P IKL+ + C    VQ  CP   V RN+EF + RM  G  ++   + KIC   SKT++ +  ++ CR++Y +   +  +     CDEFC    SS  W  G   C            Y +NEN C
Sbjct:  305 MQSFTQWSPNIKLITAYCTNITVQATCPFLNVSRNLEFSLLRM--GDRSISATVTKICNPLSKTYLKVSFEFECRAVYYVNIIMSPITPSMICDEFCSKQHSSEMWLLGRKLCPKVGLDYCKVRKYEINENHC 435

HSP 2 Score: 53.1434 bits (126), Expect = 7.915e-8
Identity = 41/160 (25.62%), Postives = 75/160 (46.88%), Query Frame = 3 
Query:  180 FFELVLSSEKSWNPEIKLLYSSCDVAVVQVRCPNNTVRRNIEFHIHRMENGKMNLWKVIVKICSKT---FITIKLKYVCRSLYRMTFNLG----LLNGKCDEFCQNSQSSPPWFFGSNDCYNLN--ENQCYFNEFLPRIGSCQATKLKCQEKTTIKNFKN 632
            F+++  ++ K W+P + L+ ++C    ++  CP     RNIEF +   E    N+  V    C  +    + + +K  C +LY++  +L     ++N  C E+C  + SSP W FG + C N     N    N+++     C A+  KC      ++ K+
Sbjct:   10 FYKVRFANIKIWDPNLTLISANCSNVNIEATCPKLVKERNIEFSL--FEFPTQNVQSVKTYKCPASNAKKLHVSMKLPCINLYQVNISLSPIFPMIN--CREYCLEAHSSPIWLFG-DICQNKQFLSNNGSLNKYMTPKNICPASTQKCSADLKTESQKS 164
The following BLAST results are available for this feature:
BLAST of SMED30019921 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 SMED30019921 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 SMED30019921 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 SMED30019921 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 SMED30019921 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 SMED30019921 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 SMED30019921 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 SMED30019921 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 SMED30019921 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 SMED30019921 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 SMED30019921 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 SMED30019921 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 SMED30019921 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 SMED30019921 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000058949.13.031e-14699.50SMESG000058949.1[more]
SMESG000058905.18.612e-1432.33SMESG000058905.1[more]
SMESG000058883.18.664e-1427.54SMESG000058883.1[more]
SMESG000058905.18.702e-1432.33SMESG000058905.1[more]
SMESG000058905.18.909e-1432.33SMESG000058905.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30019921 ID=SMED30019921|Name=SMED30019921|organism=Schmidtea mediterranea sexual|type=transcript|length=793bp
CATCGCAGAATTGCATGACTAAACATGTTTTATATCCGTTTCGCACAATA
AAAATCAGATTAATCATTTCTGTATAAATATAACAAGAACTTTCTATATT
TGTACAAATATTTTGAAATTTATCTGCTCTTATTGGAACAATGAGAATTA
TTTTAGTGCAAATACTCCACATTTGTTATTTCTTTGAGCTTGTCTTGAGT
TCTGAAAAAAGTTGGAATCCGGAAATCAAACTCCTTTACTCTTCTTGCGA
TGTTGCAGTTGTCCAAGTTCGGTGTCCAAACAATACTGTAAGAAGAAACA
TTGAATTCCATATCCATCGAATGGAAAACGGTAAAATGAATCTGTGGAAG
GTCATTGTGAAAATTTGTTCAAAAACGTTTATCACAATCAAGCTGAAATA
CGTTTGTAGGTCTTTGTACAGAATGACATTTAATCTTGGTTTACTCAATG
GAAAATGCGATGAATTTTGTCAAAATTCGCAATCCAGTCCTCCATGGTTT
TTTGGATCAAATGACTGTTATAATTTGAATGAAAACCAGTGTTACTTCAA
TGAATTCCTTCCCCGAATTGGTTCATGTCAGGCAACCAAATTGAAATGTC
AAGAAAAAACTACAATAAAAAACTTTAAGAATAATTATTTTTGGATAATT
TCTTTCCCTTTTGTGTTGTTAATCATTGTCCTCTTTGTCATATGCTTTTT
CTCCTGTAAACGGTGGCATCAACGTAATAACTTTGTAACTATTTAGTATT
TGTTACTTTATTTTAATAATAAAATGTTGATTTTGCTAACTCT
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protein sequence of SMED30019921-orf-1

>SMED30019921-orf-1 ID=SMED30019921-orf-1|Name=SMED30019921-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=202bp
MRIILVQILHICYFFELVLSSEKSWNPEIKLLYSSCDVAVVQVRCPNNTV
RRNIEFHIHRMENGKMNLWKVIVKICSKTFITIKLKYVCRSLYRMTFNLG
LLNGKCDEFCQNSQSSPPWFFGSNDCYNLNENQCYFNEFLPRIGSCQATK
LKCQEKTTIKNFKNNYFWIISFPFVLLIIVLFVICFFSCKRWHQRNNFVT
I*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000034epidermis
PLANA:0000043dorsal ventral margin of the whole animal
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: 0.713
NoneNo IPR availableTMHMMTMhelixcoord: 166..188