SMED30017226

Overview
NameSMED30017226
Smed IDSMED30017226
Length (bp)1634
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 SMED30017226 (SMED30017226) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30017226 (SMED30017226) 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 SMED30017226 (SMED30017226) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30017226 (SMED30017226) 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



SMED30017226

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
epidermisSMED30017226SMESG000026752.1 dd_Smed_v4_6791_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30017226SMESG000026752.1 dd_Smed_v4_6791_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30017226SMESG000026752.1 Contig53840newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30017226SMESG000026752.1 Contig53840uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
epidermisSMED30017226SMESG000026752.1 dd_Smed_v4_6791_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
dorsal region of the epidermisSMED30017226SMESG000026752.1 dd_Smed_v4_6791_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
ciliated epithelial cellSMED30017226SMESG000026752.1 dd_Smed_v4_6791_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
SMED30017226 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.020499:1246..2872 +7916
Homology
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BLAST of SMED30017226 vs. Planmine SMEST
Match: SMESG000026752.1 (SMESG000026752.1)

HSP 1 Score: 905.59 bits (2339), Expect = 0.000e+0
Identity = 477/477 (100.00%), Postives = 477/477 (100.00%), Query Frame = 3 
Query:  189 KPQVSKNMNIFQTIVVGLSIAAVLGNLYLFCKNQVLFEKSEFKNKIILCSTYVIGLVGVVNAIYEINYETYRDITYFIDKLVXXXXXXXXXXXXXXSDWMPHIQRPQVDDNDYKKRVFRINYLISLFGTICLVGCFIIFGRIIAIKERKILTMTENINSSSLSCLSFKDHIKIEVTEILDYFLENYFIISSVFIFVYLRFISRQIRDIHEELAYQQNVDPDVGRVLPNDNERPHLETNDPIRSDQTNESLNERTPLVNITDPPRKCCNKQIILSAIVSGXXXXXXXXXXXXXXXXYDFIHIAYQAINIVVHLLLIGAISMCWHQILYWNNKKSSILQLDNLFLKIGTFGQVLNGCLVLISAFYVESYGNCGGSAVSINALWATSNFLQIFQSIFQMYLIHEISKRSVIENALEHLKPLTLFLCVTNLSFALENLTMKPMTMTVYDKAWIVADMLINPMKFINRLHAFAFFANILAKQ 1619
            KPQVSKNMNIFQTIVVGLSIAAVLGNLYLFCKNQVLFEKSEFKNKIILCSTYVIGLVGVVNAIYEINYETYRDITYFIDKLVIIIFAILLAIYLYISDWMPHIQRPQVDDNDYKKRVFRINYLISLFGTICLVGCFIIFGRIIAIKERKILTMTENINSSSLSCLSFKDHIKIEVTEILDYFLENYFIISSVFIFVYLRFISRQIRDIHEELAYQQNVDPDVGRVLPNDNERPHLETNDPIRSDQTNESLNERTPLVNITDPPRKCCNKQIILSAIVSGFFLIFLNNLNFLKILKYDFIHIAYQAINIVVHLLLIGAISMCWHQILYWNNKKSSILQLDNLFLKIGTFGQVLNGCLVLISAFYVESYGNCGGSAVSINALWATSNFLQIFQSIFQMYLIHEISKRSVIENALEHLKPLTLFLCVTNLSFALENLTMKPMTMTVYDKAWIVADMLINPMKFINRLHAFAFFANILAKQ
Sbjct:   36 KPQVSKNMNIFQTIVVGLSIAAVLGNLYLFCKNQVLFEKSEFKNKIILCSTYVIGLVGVVNAIYEINYETYRDITYFIDKLVIIIFAILLAIYLYISDWMPHIQRPQVDDNDYKKRVFRINYLISLFGTICLVGCFIIFGRIIAIKERKILTMTENINSSSLSCLSFKDHIKIEVTEILDYFLENYFIISSVFIFVYLRFISRQIRDIHEELAYQQNVDPDVGRVLPNDNERPHLETNDPIRSDQTNESLNERTPLVNITDPPRKCCNKQIILSAIVSGFFLIFLNNLNFLKILKYDFIHIAYQAINIVVHLLLIGAISMCWHQILYWNNKKSSILQLDNLFLKIGTFGQVLNGCLVLISAFYVESYGNCGGSAVSINALWATSNFLQIFQSIFQMYLIHEISKRSVIENALEHLKPLTLFLCVTNLSFALENLTMKPMTMTVYDKAWIVADMLINPMKFINRLHAFAFFANILAKQ 512
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BLAST of SMED30017226 vs. Planmine SMEST
Match: SMESG000027067.1 (SMESG000027067.1)

HSP 1 Score: 501.901 bits (1291), Expect = 2.908e-174
Identity = 312/518 (60.23%), Postives = 380/518 (73.36%), Query Frame = 3 
Query:   78 MAIHIEDHLIPVXXXXXXXXXXXXXXXXXXXXXXXXXKPQVSKNMNIFQTIVVGLSIAAVLGNLYLFCKNQVLFEKSEFKNKIILCSTYVIGLVGVVNAIYEINYETYRDI-TYFIDKLVXXXXXXXXXXXXXXSDWMPHIQRPQVDDNDYKKRVFRINYLISLFGTICLVGCFIIFGRIIAIKERKILTMTENINSSSLSCLSFKDHIKIEVTEILDYFLENYFIISSVFIFVYLRFISRQIRDIHEELAYQQNVDPDVGRVLPNDNERPHLETNDPIRSDQTNESLNE-RTPLV-NITDPPRKCCNKQIILSAIVSGXXXXXXXXXXXXXXXXYDF--IHIAYQAINIVVHLLLIGAISMCWHQILYWNNKKSSILQLDNLFLKIGTFGQVLNGCLVLISAFYVESYGNCGGSAVSINALWATSNFLQIFQSIFQMYLIHEISKRSVIENALEHLKPLTLFLCVTNLSFALENLTMKPMTMTVYDKAWIVADMLINPMKFINRLHAFAFFANILAK 1616
            MAIHIEDHLIPVELIKSLKYFLLLLIFSS+ YE F S+P+V   MNIFQT++V +SI+A+LGN  L  +N+  F     KNK++LCS  VIGL GVV ++YE++ E    I ++F+D++ II FAILLA+YLY SDW+P IQRP +D+N      +RINY   LFGTICL+GCF+IFGRIIAIKER+ L MT N N    SC S+KD  K++V +I + FL NYFIIS V +++YLRFISRQIRD+HEE A                    HLE + PIR DQ NE  N+ R+PL+ N  +P ++CCNKQIILSA++S  FLI LN LN   I   D   IHIAYQA+ I+++LL IG   + W Q+L W  + + +LQ+DNLFLKIGTFGQ LNGCLVLISAFYV  + +C  +   IN LWATSNF+QIFQSIFQMYLI EIS RSV   A  H KPL LFLCV NLSFALENL MKPMT+ +Y+KAW+VADMLINP++FINRLHAFAFFANILA+
Sbjct:    1 MAIHIEDHLIPVELIKSLKYFLLLLIFSSAFYEFFFSQPKVELTMNIFQTVIVAISISAILGNFVLLRQNRDQFYYKGCKNKVVLCSNCVIGLSGVVYSMYELHKENNNLINSHFVDQIFIIAFAILLALYLYSSDWIPDIQRPLLDNNFSGICTYRINYWSCLFGTICLIGCFVIFGRIIAIKERQTLNMTVNRNRDFFSCPSYKDPKKLDVKKIFENFLLNYFIISFVLVYIYLRFISRQIRDLHEEWA--------------------HLEADHPIRFDQPNEDPNDVRSPLITNNRNPFKRCCNKQIILSAVISISFLISLNTLNIFLIYSDDKVKIHIAYQAVKIIIYLLFIGTFILLWCQLLKWRIEITPLLQIDNLFLKIGTFGQALNGCLVLISAFYVIVHKDCDRTVKYINVLWATSNFMQIFQSIFQMYLIREISNRSVTRVASVHWKPLALFLCVMNLSFALENLIMKPMTIQMYNKAWVVADMLINPLRFINRLHAFAFFANILAE 498
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BLAST of SMED30017226 vs. Planmine SMEST
Match: SMESG000071516.1 (SMESG000071516.1)

HSP 1 Score: 56.9954 bits (136), Expect = 2.492e-8
Identity = 57/191 (29.84%), Postives = 89/191 (46.60%), Query Frame = 3 
Query: 1083 IHIAYQAINIVVHLLLIGAISMCW-HQILYWNNKKSSILQLDNLFLKIGTFGQVLNGCLVLISAFYVESYGNCGGSAVSINALWATSNFLQIFQSIFQMYLIHEISKRSVIE-----NALEHLKPLTL----FLCVTNLSFALENL-----TMKPMTMTVYDKAWIVADMLINPMKFINRLHAFAFFANIL 1610
            I + Y    I V+++LI  ISM + H+I  W  +K+     D   + IGTFGQV+      I+  YV          +    L    N LQI Q + Q ++I EI +R V +           + +T+     LC+ NL F L N+      M  + M+   + WI+   ++  +  +NRLH FAFF ++L
Sbjct:  293 ILVFYNECQISVYVILI-IISMLYLHKIFQWKFEKNIRSNNDCWIVNIGTFGQVMEA----ITISYVSFIKLSDDCHLKFLYLSIVLNILQIIQIVGQRFVILEILQRKVKKLRSRNYETNFFRRITINHCAVLCIANLGFVLINILHYSQAMDKIQMS-KGRTWILIRCILVLISTLNRLHGFAFFLDVL 477
The following BLAST results are available for this feature:
BLAST of SMED30017226 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 SMED30017226 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 SMED30017226 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 SMED30017226 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 SMED30017226 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 SMED30017226 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 SMED30017226 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 SMED30017226 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 SMED30017226 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 SMED30017226 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 SMED30017226 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 SMED30017226 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 SMED30017226 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 SMED30017226 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000026752.10.000e+0100.00SMESG000026752.1[more]
SMESG000027067.12.908e-17460.23SMESG000027067.1[more]
SMESG000071516.12.492e-829.84SMESG000071516.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30017226 ID=SMED30017226|Name=SMED30017226|organism=Schmidtea mediterranea sexual|type=transcript|length=1634bp
CTGAATCACGCGCACTCAATGTGACTACATTTAAACAAAAGCGCTTATTA
ATTATTAAACTCTTGCAAAACTTTGAAATGGCAATTCATATAGAGGATCA
TCTGATTCCCGTGGAACTGATTAAGAGTTTGAAATATTTTCTTTTATTGT
TAATATTCTCATCGTCCCTTTATGAACTGTTCATTTCCAAGCCTCAAGTC
TCGAAAAACATGAACATATTTCAAACGATAGTTGTTGGACTTTCGATTGC
CGCCGTTTTGGGAAATCTCTATCTTTTCTGCAAGAACCAAGTTCTATTCG
AAAAGAGCGAATTTAAAAATAAAATTATTTTGTGTTCTACCTATGTGATA
GGGTTGGTTGGGGTTGTCAACGCAATCTATGAAATAAATTATGAAACATA
TAGAGATATCACTTATTTTATTGATAAACTTGTTATAATAATATTTGCAA
TATTGCTAGCGATATATTTATACATTTCTGATTGGATGCCGCACATTCAA
AGGCCTCAAGTGGATGATAATGATTACAAGAAACGCGTCTTCCGCATTAA
TTATTTGATAAGCCTATTTGGTACGATTTGTCTAGTTGGCTGTTTTATCA
TTTTTGGGAGAATAATCGCCATTAAAGAAAGAAAAATTTTGACCATGACT
GAAAATATAAATTCCAGTTCCTTATCTTGTTTGTCCTTTAAGGATCATAT
TAAAATAGAAGTTACGGAAATTTTGGATTACTTTCTGGAAAATTATTTTA
TTATTTCGTCTGTATTTATCTTTGTTTATTTGAGATTTATTTCTAGACAA
ATCCGAGATATCCACGAAGAATTGGCATATCAACAAAATGTAGATCCGGA
TGTTGGCCGAGTTCTACCCAACGACAATGAAAGGCCACATCTGGAAACGA
ACGATCCGATACGTTCTGATCAAACAAATGAAAGCCTGAATGAGCGAACG
CCACTCGTCAATATCACGGACCCTCCACGGAAATGTTGTAATAAACAAAT
TATTCTTTCTGCTATCGTTTCGGGTTTCTTTTTAATTTTTTTGAATAATT
TGAATTTTTTGAAAATTTTGAAATATGATTTCATACATATTGCGTATCAA
GCCATAAACATAGTTGTTCATTTGCTTCTCATTGGGGCTATTAGTATGTG
TTGGCATCAAATCTTGTATTGGAACAATAAAAAATCTTCAATTTTACAAC
TAGACAATTTATTTTTGAAAATTGGAACATTTGGCCAAGTACTGAACGGA
TGCCTGGTGCTCATATCCGCATTCTACGTGGAATCTTATGGGAATTGTGG
AGGGTCTGCGGTTTCTATAAACGCGTTATGGGCAACTTCTAATTTCTTGC
AAATATTTCAGAGTATTTTCCAAATGTATCTTATCCATGAAATCTCGAAA
CGATCAGTTATTGAAAATGCTTTGGAACATTTGAAACCCCTTACATTATT
TCTCTGTGTGACGAACCTCAGTTTTGCGCTGGAAAATCTCACAATGAAGC
CAATGACAATGACAGTGTATGACAAAGCTTGGATTGTGGCAGACATGCTG
ATCAACCCAATGAAATTCATTAATAGGCTTCACGCTTTTGCATTTTTTGC
AAATATTTTAGCTAAACAATGATAGAAATTCCAT
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protein sequence of SMED30017226-orf-1

>SMED30017226-orf-1 ID=SMED30017226-orf-1|Name=SMED30017226-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=540bp
ESRALNVTTFKQKRLLIIKLLQNFEMAIHIEDHLIPVELIKSLKYFLLLL
IFSSSLYELFISKPQVSKNMNIFQTIVVGLSIAAVLGNLYLFCKNQVLFE
KSEFKNKIILCSTYVIGLVGVVNAIYEINYETYRDITYFIDKLVIIIFAI
LLAIYLYISDWMPHIQRPQVDDNDYKKRVFRINYLISLFGTICLVGCFII
FGRIIAIKERKILTMTENINSSSLSCLSFKDHIKIEVTEILDYFLENYFI
ISSVFIFVYLRFISRQIRDIHEELAYQQNVDPDVGRVLPNDNERPHLETN
DPIRSDQTNESLNERTPLVNITDPPRKCCNKQIILSAIVSGFFLIFLNNL
NFLKILKYDFIHIAYQAINIVVHLLLIGAISMCWHQILYWNNKKSSILQL
DNLFLKIGTFGQVLNGCLVLISAFYVESYGNCGGSAVSINALWATSNFLQ
IFQSIFQMYLIHEISKRSVIENALEHLKPLTLFLCVTNLSFALENLTMKP
MTMTVYDKAWIVADMLINPMKFINRLHAFAFFANILAKQ*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000054dorsal region of the epidermis
PLANA:0000106ciliated epithelial cell
PLANA:0002032epidermal cell
Vocabulary: INTERPRO
TermDefinition
IPR004878Otopetrin
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR004878OtopetrinPFAMPF03189Otopetrincoord: 181..479
e-value: 3.6E-8
score: 32.6
NoneNo IPR availableSIGNALP_EUKSignalP-TMSignalP-TMcoord: 1..19
score: 0.524
NoneNo IPR availableTMHMMTMhelixcoord: 401..423
NoneNo IPR availableTMHMMTMhelixcoord: 34..53
NoneNo IPR availableTMHMMTMhelixcoord: 202..224
NoneNo IPR availableTMHMMTMhelixcoord: 329..351
NoneNo IPR availableTMHMMTMhelixcoord: 98..120
NoneNo IPR availableTMHMMTMhelixcoord: 66..88
NoneNo IPR availableTMHMMTMhelixcoord: 7..24
NoneNo IPR availableTMHMMTMhelixcoord: 364..386
NoneNo IPR availableTMHMMTMhelixcoord: 147..169
NoneNo IPR availableTMHMMTMhelixcoord: 295..314