Tspan1

Overview
NameTspan1
Smed IDSMED30011277
Length (bp)781
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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 Tspan1 (SMED30011277) t-SNE clustered cells

Violin plots show distribution of expression levels for Tspan1 (SMED30011277) in cells (dots) of each of the 12 neoblast clusters.

 

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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.
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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



SMED30011277

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
neoblastSMED30011277SMESG000066703.1 SMED30011277smed_20140614PMID:29906446
Zeng et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
X1 cellSMED30011277SMESG000066703.1 SmedASXL_007816SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
neoblastSMED30011277SMESG000066703.1 SMED_12608_V2_1GPL14150PMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30011277SMESG000066703.1 SMED_12608_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30011277SMESG000066703.1 SMED_28390_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30011277SMESG000066703.1 SMED_28390_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
Homology
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BLAST of Tspan1 vs. TrEMBL
Match: A0A2Z4EM42 (Tspan1 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 409.838 bits (1052), Expect = 5.856e-143
Identity = 244/244 (100.00%), Postives = 244/244 (100.00%), Query Frame = 3 
Query:    3 MGKILKFLLGXXXXXXXXXXXXXXXXXXXXXXTLGLSNQIELSSYLVIFTFILLGCGTYIVIYSSLVFHGLRKRNSRYLKTFSALVVXXXXXXXXXXXXXXXXRKSMIEKLDFLMDDAVTDEIEYKYTKHIRYMDLIQYSLSCCGRISYREYSLNIKDLPKSCCRTFDACNNAVLNATVYDWNTGCMEQIKSGISPTMICLIVLIFVVEILMALLGWLIEFNFISIGKFIHQNARGMNTMMSMH 734
            MGKILKFLLGFINVFNLIIGLFIIFSSSYFIVTLGLSNQIELSSYLVIFTFILLGCGTYIVIYSSLVFHGLRKRNSRYLKTFSALVVLFLILQIGSLSLGILFRKSMIEKLDFLMDDAVTDEIEYKYTKHIRYMDLIQYSLSCCGRISYREYSLNIKDLPKSCCRTFDACNNAVLNATVYDWNTGCMEQIKSGISPTMICLIVLIFVVEILMALLGWLIEFNFISIGKFIHQNARGMNTMMSMH
Sbjct:    1 MGKILKFLLGFINVFNLIIGLFIIFSSSYFIVTLGLSNQIELSSYLVIFTFILLGCGTYIVIYSSLVFHGLRKRNSRYLKTFSALVVLFLILQIGSLSLGILFRKSMIEKLDFLMDDAVTDEIEYKYTKHIRYMDLIQYSLSCCGRISYREYSLNIKDLPKSCCRTFDACNNAVLNATVYDWNTGCMEQIKSGISPTMICLIVLIFVVEILMALLGWLIEFNFISIGKFIHQNARGMNTMMSMH 244
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BLAST of Tspan1 vs. Planmine SMEST
Match: SMESG000066703.1 (SMESG000066703.1)

HSP 1 Score: 409.838 bits (1052), Expect = 1.628e-146
Identity = 244/244 (100.00%), Postives = 244/244 (100.00%), Query Frame = 3 
Query:    3 MGKILKFLLGXXXXXXXXXXXXXXXXXXXXXXTLGLSNQIELSSYLVIFTFILLGCGTYIVIYSSLVFHGLRKRNSRYLKTFSALVVXXXXXXXXXXXXXXXXRKSMIEKLDFLMDDAVTDEIEYKYTKHIRYMDLIQYSLSCCGRISYREYSLNIKDLPKSCCRTFDACNNAVLNATVYDWNTGCMEQIKSGISPTMICLIVLIFVVEILMALLGWLIEFNFISIGKFIHQNARGMNTMMSMH 734
            MGKILKFLLGFINVFNLIIGLFIIFSSSYFIVTLGLSNQIELSSYLVIFTFILLGCGTYIVIYSSLVFHGLRKRNSRYLKTFSALVVLFLILQIGSLSLGILFRKSMIEKLDFLMDDAVTDEIEYKYTKHIRYMDLIQYSLSCCGRISYREYSLNIKDLPKSCCRTFDACNNAVLNATVYDWNTGCMEQIKSGISPTMICLIVLIFVVEILMALLGWLIEFNFISIGKFIHQNARGMNTMMSMH
Sbjct:    1 MGKILKFLLGFINVFNLIIGLFIIFSSSYFIVTLGLSNQIELSSYLVIFTFILLGCGTYIVIYSSLVFHGLRKRNSRYLKTFSALVVLFLILQIGSLSLGILFRKSMIEKLDFLMDDAVTDEIEYKYTKHIRYMDLIQYSLSCCGRISYREYSLNIKDLPKSCCRTFDACNNAVLNATVYDWNTGCMEQIKSGISPTMICLIVLIFVVEILMALLGWLIEFNFISIGKFIHQNARGMNTMMSMH 244
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BLAST of Tspan1 vs. Planmine SMEST
Match: SMESG000070572.1 (SMESG000070572.1)

HSP 1 Score: 63.5438 bits (153), Expect = 1.919e-12
Identity = 39/141 (27.66%), Postives = 70/141 (49.65%), Query Frame = 3 
Query:  321 MIEKLDFLMDDAVTDEIEYKYTKHIRYMDLIQYSLSCCGRISYREYSLNIKDLPKSCCRTFDACNNAVLNATVYDWNTGCMEQIKSGI--SPTMICLIVLIF--VVEILMALLGWLIEFNFISIGKFIHQNARGMNTMMSM 731
            M   ++  + D++ D   Y+    IR +D++Q    CCG+I+Y +Y +   DLP SCCR  ++C +++      D  TGC++ I   I   P    LI L+   V+E ++  +   + F +    +   QN + +N +  M
Sbjct:    1 MKPNIESFLHDSIIDRTSYRGYSIIRPIDIVQNMYQCCGKINYNDYKVLESDLPTSCCRAMNSCQHSI-EFIHKDKKTGCVDPIYQNIFQKPNKWILIGLLLNVVLETIVLAVSLALRFRY---NRIQDQNFQDINMLNGM 137
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BLAST of Tspan1 vs. Planmine SMEST
Match: SMESG000011084.1 (SMESG000011084.1)

HSP 1 Score: 63.5438 bits (153), Expect = 1.919e-12
Identity = 39/141 (27.66%), Postives = 70/141 (49.65%), Query Frame = 3 
Query:  321 MIEKLDFLMDDAVTDEIEYKYTKHIRYMDLIQYSLSCCGRISYREYSLNIKDLPKSCCRTFDACNNAVLNATVYDWNTGCMEQIKSGI--SPTMICLIVLIF--VVEILMALLGWLIEFNFISIGKFIHQNARGMNTMMSM 731
            M   ++  + D++ D   Y+    IR +D++Q    CCG+I+Y +Y +   DLP SCCR  ++C +++      D  TGC++ I   I   P    LI L+   V+E ++  +   + F +    +   QN + +N +  M
Sbjct:    1 MKPNIESFLHDSIIDRTSYRGYSIIRPIDIVQNMYQCCGKINYNDYKVLESDLPTSCCRAMNSCQHSI-EFIHKDKKTGCVDPIYQNIFQKPNKWILIGLLLNVVLETIVLAVSLALRFRY---NRIQDQNFQDINMLNGM 137
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BLAST of Tspan1 vs. Planmine SMEST
Match: SMESG000009559.1 (SMESG000009559.1)

HSP 1 Score: 50.8322 bits (120), Expect = 1.769e-7
Identity = 34/131 (25.95%), Postives = 58/131 (44.27%), Query Frame = 3 
Query:  312 RKSMIEKLDFLMDDAVTDEIEYKYTKHIR--YMDLIQYSLSCCGRISYREYSLNIKDLPKSCCRTFDACNNAVLNATVYDWNTGCMEQIKSGISPTMICLIVL--------IFVVEILMALLGWLIEFNFI 674
            R  M   +  L++ A+      + T  +   + D IQ  L CCG  S  +Y +  K +P+SCC    +CNN         +N GC   +KS I   ++ + V         IF + ++ +LL  +  +N +
Sbjct:   78 RSKMESSIKGLLEKALKKAYTKEKTGKVNTLFFDRIQDDLKCCGVTSVHDYEMIQKPIPESCCPNKISCNNNTA------YNNGCSNSMKSAIGRHLLSIAVAEIVFCISTIFQIILVFSLLSRVRHYNQV 202
The following BLAST results are available for this feature:
BLAST of Tspan1 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 Tspan1 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 Tspan1 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 Tspan1 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 Tspan1 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 Tspan1 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 Tspan1 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 Tspan1 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A2Z4EM425.856e-143100.00Tspan1 OS=Schmidtea mediterranea OX=79327 PE=2 SV=... [more]
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BLAST of Tspan1 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 Tspan1 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 Tspan1 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 Tspan1 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 Tspan1 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 Tspan1 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000066703.11.628e-146100.00SMESG000066703.1[more]
SMESG000070572.11.919e-1227.66SMESG000070572.1[more]
SMESG000011084.11.919e-1227.66SMESG000011084.1[more]
SMESG000009559.11.769e-725.95SMESG000009559.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30011277 ID=SMED30011277|Name=Tspan1|organism=Schmidtea mediterranea sexual|type=transcript|length=781bp
AAATGGGAAAAATTCTCAAATTTCTCCTCGGGTTTATAAATGTGTTCAAT
TTAATTATTGGATTATTTATTATATTTTCCTCGTCATATTTTATTGTGAC
GCTTGGACTGTCAAATCAGATTGAGCTATCGAGCTATTTGGTGATTTTCA
CCTTCATCCTTCTAGGTTGTGGAACCTATATCGTTATCTACTCGTCTCTC
GTATTCCATGGTTTGCGAAAACGAAACTCTCGATACCTGAAAACGTTTTC
AGCTTTAGTTGTATTGTTTTTGATTTTACAAATCGGTAGCCTGTCGTTGG
GAATTCTGTTTAGGAAATCAATGATCGAGAAACTCGATTTCCTGATGGAT
GATGCTGTAACAGACGAGATAGAATACAAATACACCAAGCACATTCGATA
TATGGATTTGATTCAATATTCTCTAAGCTGCTGCGGACGAATCAGTTATC
GAGAATACTCTCTCAACATAAAGGATCTTCCGAAATCTTGTTGTCGAACA
TTTGATGCTTGTAACAATGCCGTTCTAAACGCGACTGTGTACGATTGGAA
CACCGGCTGCATGGAACAGATAAAATCTGGAATTAGCCCGACAATGATTT
GTCTGATAGTGCTAATTTTTGTTGTTGAGATATTAATGGCATTATTGGGA
TGGCTGATTGAATTCAACTTCATCTCGATCGGGAAATTTATCCATCAAAA
TGCCCGAGGAATGAATACAATGATGTCGATGCACTGATTTATTGACCGCG
AATTGTAAATATAAAAATAAATGTATTATGA
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protein sequence of SMED30011277-orf-1

>SMED30011277-orf-1 ID=SMED30011277-orf-1|Name=SMED30011277-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=245bp
MGKILKFLLGFINVFNLIIGLFIIFSSSYFIVTLGLSNQIELSSYLVIFT
FILLGCGTYIVIYSSLVFHGLRKRNSRYLKTFSALVVLFLILQIGSLSLG
ILFRKSMIEKLDFLMDDAVTDEIEYKYTKHIRYMDLIQYSLSCCGRISYR
EYSLNIKDLPKSCCRTFDACNNAVLNATVYDWNTGCMEQIKSGISPTMIC
LIVLIFVVEILMALLGWLIEFNFISIGKFIHQNARGMNTMMSMH*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000429neoblast
PLANA:0002109X1 cell
Vocabulary: INTERPRO
TermDefinition
IPR018499Tetraspanin/Peripherin
IPR008952Tetraspanin_EC2_sf
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR008952Tetraspanin, EC2 domain superfamilyGENE3DG3DSA:1.10.1450.10coord: 104..191
e-value: 4.1E-8
score: 34.9
IPR008952Tetraspanin, EC2 domain superfamilySUPERFAMILYSSF48652Tetraspanincoord: 113..195
IPR018499Tetraspanin/PeripherinPFAMPF00335Tetraspanincoord: 5..216
e-value: 6.8E-24
score: 84.8
NoneNo IPR availablePANTHERPTHR19282TETRASPANINcoord: 11..208
NoneNo IPR availablePANTHERPTHR19282:SF379TETRASPANIN-17coord: 11..208
NoneNo IPR availableCDDcd03127tetraspanin_LELcoord: 107..192
e-value: 5.01386E-11
score: 55.5883
NoneNo IPR availableTMHMMTMhelixcoord: 81..103
NoneNo IPR availableTMHMMTMhelixcoord: 9..31
NoneNo IPR availableTMHMMTMhelixcoord: 46..68
NoneNo IPR availableTMHMMTMhelixcoord: 197..219