SMED30020877

Overview
NameSMED30020877
Smed IDSMED30020877
Length (bp)757
Neoblast Clusters

Zeng et. al., 2018



 

 

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



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



SMED30020877

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
testisSMED30020877SMESG000039101.1 Contig42_SE3GPL10652PMID:20844018
Wang et al., 2010		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
early male germ cellSMED30020877SMESG000039101.1 Contig42_SE3GPL10652PMID:20844018
Wang et al., 2010		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30020877SMESG000039101.1 SMED_12294_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30020877SMESG000039101.1 SMED_12294_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
SMED30020877 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000645:77979..81739 -3693
Homology
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BLAST of SMED30020877 vs. TrEMBL
Match: A0A0X3PLB0 (Uncharacterized protein (Fragment) OS=Schistocephalus solidus OX=70667 GN=TR85681 PE=4 SV=1)

HSP 1 Score: 74.7146 bits (182), Expect = 1.310e-12
Identity = 60/176 (34.09%), Postives = 83/176 (47.16%), Query Frame = 1 
Query:  199 KWNCFHGPHNPEYFNNLKNEGDVARTL-----EPDKDTVERNLPQVRNYLKEPWREFRIDNGGIRKMDWHPSKYYDYNAKPKLKITSPPYYQPNNFNLLKYYQKLMEWQAGHPADLLEMYLYRK----IIFPPINTENCVKMEEVDDCDRNILKNEMSPIDINRMRFLSGNYKSFD 699
            KW C  GPH+P YF N   + D AR       EP K  +E + P       EP+R +  D  G+RK DWH     D     + +     YY  N+  LLK   +L +W A HPA LL+ ++YRK    +       ENC K            K  MS   ++R+RF++GNY++ D
Sbjct:   31 KWICLPGPHHPGYFQNSCMKEDPARIFRTREPEPWKHYIEPHGPI------EPYRLWLHDKRGLRKDDWH-RVLEDCAESKQPRKFHIRYYHENHHGLLKTQNELNDWWARHPARLLKDFVYRKPDYYLKHDKETRENCEKGTVPPYTPPPTRK--MSDRCLHRLRFVTGNYQALD 197
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BLAST of SMED30020877 vs. TrEMBL
Match: A0A0R3U1H8 (Uncharacterized protein OS=Mesocestoides corti OX=53468 PE=4 SV=1)

HSP 1 Score: 60.077 bits (144), Expect = 3.948e-7
Identity = 54/194 (27.84%), Postives = 89/194 (45.88%), Query Frame = 1 
Query:  196 NKWNCFHGPHNPEYFNNLKNEGDVARTLEPDKDTVERNLPQVRNYLK-----EPWREFRIDNGGIRKMDWH--PSKYYDYNAKPK-----LKIT---SPPYYQPNNFNLLKYYQKLMEWQAGHPADLLEMYLYRKIIFPPINTENCVKMEEVDDCDRNILKNEMSPID-----------INRMRFLSGNYKSFD 699
            NKW C  GPH+PEYF N     D +R  E       R     + Y+      +P+R ++ID  G R  DW+  P+  ++ N K +     +K T      YY+ N+ NL+   ++L ++   HPA LL  ++YRK  +   +TE         +  +N L  ++ P             + R++F + NY++ D
Sbjct:   31 NKWICLPGPHHPEYFENYCVTEDPSRIFE------NRPKEHWKFYMPNRGPIDPYRIWKIDKRGFRHDDWYNAPNDCFEKNEKARHTFIIVKYTWRFYTAYYRENHHNLIPRSEQLTDFWERHPARLLNDFVYRKPDYYIKHTE---------ETQKNCLNKQVPPFKAPSRKKISERCLMRLQFATNNYRTID 209
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BLAST of SMED30020877 vs. TrEMBL
Match: A0A3P6H4G5 (Uncharacterized protein OS=Mesocestoides corti OX=53468 GN=MCOS_LOCUS218 PE=4 SV=1)

HSP 1 Score: 60.077 bits (144), Expect = 3.987e-7
Identity = 54/194 (27.84%), Postives = 89/194 (45.88%), Query Frame = 1 
Query:  196 NKWNCFHGPHNPEYFNNLKNEGDVARTLEPDKDTVERNLPQVRNYLK-----EPWREFRIDNGGIRKMDWH--PSKYYDYNAKPK-----LKIT---SPPYYQPNNFNLLKYYQKLMEWQAGHPADLLEMYLYRKIIFPPINTENCVKMEEVDDCDRNILKNEMSPID-----------INRMRFLSGNYKSFD 699
            NKW C  GPH+PEYF N     D +R  E       R     + Y+      +P+R ++ID  G R  DW+  P+  ++ N K +     +K T      YY+ N+ NL+   ++L ++   HPA LL  ++YRK  +   +TE         +  +N L  ++ P             + R++F + NY++ D
Sbjct:   31 NKWICLPGPHHPEYFENYCVTEDPSRIFE------NRPKEHWKFYMPNRGPIDPYRIWKIDKRGFRHDDWYNAPNDCFEKNEKARHTFIIVKYTWRFYTAYYRENHHNLIPRSEQLTDFWERHPARLLNDFVYRKPDYYIKHTE---------ETQKNCLNKQVPPFKAPSRKKISERCLMRLQFATNNYRTID 209
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BLAST of SMED30020877 vs. TrEMBL
Match: A0A2H1C1F4 (Uncharacterized protein OS=Fasciola hepatica OX=6192 GN=D915_007865 PE=4 SV=1)

HSP 1 Score: 58.5362 bits (140), Expect = 1.261e-6
Identity = 58/181 (32.04%), Postives = 83/181 (45.86%), Query Frame = 1 
Query:  187 LTDNKWNCFHGPHNPEYFNNLKNEGDVARTLEPD-KDTVERNLPQVRNYLKEPWREFRIDNGGIRKMDWHPSKYYDYNAKPKLK-ITSPPYYQPNNFNLLKYYQKLMEWQAGHPADLLEMYLYRKIIFPP---INTENCVKMEEVDDCDRNILKNEMSPI---DINRMRFLSGNYKSFDSW 705
            +T +KW C  G H  EYF+      +V    +P+ +     N+ +V+N + EPWR +  D  G R  DW+ S+      KPKL      P        L +Y+ +L    A HP  LLE Y+YR     P   + +E   K+     CD    + E+ P    +I RMRF   NY +FD W
Sbjct:   23 VTRSKWICSPGIHPSEYFHCADWTPEVEAINKPEPRIRWNENVSRVKNCM-EPWRPWVYDQSGWRLSDWNASEID--CKKPKLGNFEYKPVCLTEPAPLNRYFNQLDNLDALHPRYLLEHYVYRD----PDEYLPSEEQGKLACTFGCDARPFR-ELKPASQREIMRMRFAKNNYMTFDDW 195
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BLAST of SMED30020877 vs. Planmine SMEST
Match: SMESG000039101.1 (SMESG000039101.1)

HSP 1 Score: 422.165 bits (1084), Expect = 6.397e-152
Identity = 218/219 (99.54%), Postives = 218/219 (99.54%), Query Frame = 1 
Query:   70 MISVXXXXXXXXXXXXTYPCLRACPINCESTDYSLLAPYLTDNKWNCFHGPHNPEYFNNLKNEGDVARTLEPDKDTVERNLPQVRNYLKEPWREFRIDNGGIRKMDWHPSKYYDYNAKPKLKITSPPYYQPNNFNLLKYYQKLMEWQAGHPADLLEMYLYRKIIFPPINTENCVKMEEVDDCDRNILKNEMSPIDINRMRFLSGNYKSFDSWNSKFYPK 726
            MISVEEKLEKEKESLKTYPCLRACPINCESTDYSLLAPYLTDNKWNCFHGPHNPEYFNNLKNEGDVARTLEPDKDTVERNLPQVRNYLKEPWREFRIDNGGIRKMDWHPSKYY YNAKPKLKITSPPYYQPNNFNLLKYYQKLMEWQAGHPADLLEMYLYRKIIFPPINTENCVKMEEVDDCDRNILKNEMSPIDINRMRFLSGNYKSFDSWNSKFYPK
Sbjct:    1 MISVEEKLEKEKESLKTYPCLRACPINCESTDYSLLAPYLTDNKWNCFHGPHNPEYFNNLKNEGDVARTLEPDKDTVERNLPQVRNYLKEPWREFRIDNGGIRKMDWHPSKYYVYNAKPKLKITSPPYYQPNNFNLLKYYQKLMEWQAGHPADLLEMYLYRKIIFPPINTENCVKMEEVDDCDRNILKNEMSPIDINRMRFLSGNYKSFDSWNSKFYPK 219
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BLAST of SMED30020877 vs. Planmine SMEST
Match: SMESG000047743.1 (SMESG000047743.1)

HSP 1 Score: 181.415 bits (459), Expect = 5.406e-57
Identity = 94/203 (46.31%), Postives = 127/203 (62.56%), Query Frame = 1 
Query:  124 PCLRACPINC-ESTDYSLLAPYLTDNKWNCFHGPHNPEYFNNLKNEGDVARTLEPDKDTVERNLPQVRNYLKEPWREFRIDNGGIRKMDWHPSKYYDYN-AKPKLKITSPPYYQPNNFNLLKYYQKLMEWQAGHPADLLEMYLYRKIIFPPINTENC------VKMEEVDDCDRNILKNEMSPIDINRMRFLSGNYKSFDSWN 708
            PC+R     C ++ DY  L PY+  NKWNCFHGPHNP YFNNL N GDV  ++   +   ++NLP +R++ KEPWR F  D GGIRKMD  PS YY YN A+ + K  + PY + N  +LL+Y+Q LM+++  HP+ LL  YLYRK+I P    E C       K EE     +++L + MS +D+ R+RFL  NY +FD W+
Sbjct:   10 PCIRTTQDICYDTIDYEALDPYIKCNKWNCFHGPHNPAYFNNLTNTGDVQNSINSGEPKKKKNLPGIRHFTKEPWRPFHWDRGGIRKMDAKPSPYYQYNSAQYQEKAPTEPYVKTNIHSLLRYHQGLMDFEPNHPSKLLNTYLYRKVILPHEGAEKCDDELELEKNEEDKFKSKDLLGSTMSNLDVWRLRFLGNNYMTFDDWS 212
[Close]
BLAST of SMED30020877 vs. Planmine SMEST
Match: SMESG000047743.1 (SMESG000047743.1)

HSP 1 Score: 181.415 bits (459), Expect = 6.334e-57
Identity = 94/203 (46.31%), Postives = 127/203 (62.56%), Query Frame = 1 
Query:  124 PCLRACPINC-ESTDYSLLAPYLTDNKWNCFHGPHNPEYFNNLKNEGDVARTLEPDKDTVERNLPQVRNYLKEPWREFRIDNGGIRKMDWHPSKYYDYN-AKPKLKITSPPYYQPNNFNLLKYYQKLMEWQAGHPADLLEMYLYRKIIFPPINTENC------VKMEEVDDCDRNILKNEMSPIDINRMRFLSGNYKSFDSWN 708
            PC+R     C ++ DY  L PY+  NKWNCFHGPHNP YFNNL N GDV  ++   +   ++NLP +R++ KEPWR F  D GGIRKMD  PS YY YN A+ + K  + PY + N  +LL+Y+Q LM+++  HP+ LL  YLYRK+I P    E C       K EE     +++L + MS +D+ R+RFL  NY +FD W+
Sbjct:   18 PCIRTTQDICYDTIDYEALDPYIKCNKWNCFHGPHNPAYFNNLTNTGDVQNSINSGEPKKKKNLPGIRHFTKEPWRPFHWDRGGIRKMDAKPSPYYQYNSAQYQEKAPTEPYVKTNIHSLLRYHQGLMDFEPNHPSKLLNTYLYRKVILPHEGAEKCDDELELEKNEEDKFKSKDLLGSTMSNLDVWRLRFLGNNYMTFDDWS 220
The following BLAST results are available for this feature:
BLAST of SMED30020877 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 SMED30020877 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 SMED30020877 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 SMED30020877 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 SMED30020877 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 SMED30020877 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 SMED30020877 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 SMED30020877 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 4
Match NameE-valueIdentityDescription
A0A0X3PLB01.310e-1234.09Uncharacterized protein (Fragment) OS=Schistocepha... [more]
A0A0R3U1H83.948e-727.84Uncharacterized protein OS=Mesocestoides corti OX=... [more]
A0A3P6H4G53.987e-727.84Uncharacterized protein OS=Mesocestoides corti OX=... [more]
A0A2H1C1F41.261e-632.04Uncharacterized protein OS=Fasciola hepatica OX=61... [more]
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BLAST of SMED30020877 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 SMED30020877 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 SMED30020877 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 SMED30020877 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 SMED30020877 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 SMED30020877 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000039101.16.397e-15299.54SMESG000039101.1[more]
SMESG000047743.15.406e-5746.31SMESG000047743.1[more]
SMESG000047743.16.334e-5746.31SMESG000047743.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30020877 ID=SMED30020877|Name=SMED30020877|organism=Schmidtea mediterranea sexual|type=transcript|length=757bp
ATTGAAATAAAATATACATACAATTTTAAATAAAATCAATTGTATTTTTA
ACACCAAATATATCCAGTGATGATAAGTGTGGAAGAGAAGTTGGAAAAAG
AAAAAGAGTCTCTTAAAACGTACCCGTGTCTAAGAGCTTGTCCAATTAAT
TGTGAATCCACTGATTATAGTTTGCTGGCTCCATACCTGACAGATAACAA
ATGGAATTGCTTTCATGGGCCACATAATCCGGAGTACTTTAATAATCTTA
AAAATGAAGGAGACGTAGCTAGAACGTTGGAACCGGATAAAGATACAGTG
GAACGAAACTTACCTCAAGTTAGAAATTATTTAAAAGAGCCCTGGAGGGA
ATTCAGAATAGATAATGGAGGGATCAGAAAGATGGACTGGCATCCTAGTA
AATATTATGACTATAATGCAAAACCAAAACTAAAAATAACTTCTCCGCCA
TATTATCAACCAAATAATTTCAATTTATTGAAATATTATCAGAAATTGAT
GGAATGGCAAGCCGGACATCCGGCTGATTTATTAGAAATGTATCTGTATC
GAAAAATTATATTTCCTCCGATCAACACAGAAAATTGCGTCAAAATGGAG
GAAGTTGACGACTGCGATAGAAACATACTCAAAAATGAAATGTCCCCCAT
AGACATAAACCGAATGAGATTCCTCAGTGGAAACTACAAATCGTTTGATA
GTTGGAATAGCAAATTTTATCCAAAATAGTGATAAAATTGACATTATTTA
TCAGATC
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protein sequence of SMED30020877-orf-1

>SMED30020877-orf-1 ID=SMED30020877-orf-1|Name=SMED30020877-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=220bp
MISVEEKLEKEKESLKTYPCLRACPINCESTDYSLLAPYLTDNKWNCFHG
PHNPEYFNNLKNEGDVARTLEPDKDTVERNLPQVRNYLKEPWREFRIDNG
GIRKMDWHPSKYYDYNAKPKLKITSPPYYQPNNFNLLKYYQKLMEWQAGH
PADLLEMYLYRKIIFPPINTENCVKMEEVDDCDRNILKNEMSPIDINRMR
FLSGNYKSFDSWNSKFYPK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000208testis
PLANA:0000429neoblast
PLANA:0002030early male germ cell