SMED30003555

Overview
NameSMED30003555
Smed IDSMED30003555
Length (bp)1245
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




SMED30003555

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
testis primordiumSMED30003555SMESG000071919.1 PL030002A10C06_SE3GPL10652PMID:20844018
Wang et al., 2010
whole organism juvenile cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30003555 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.005045:5715..8989 +5437
Homology
BLAST of SMED30003555 vs. TrEMBL
Match: A7M6E0 (Uncharacterized protein OS=Dugesia ryukyuensis OX=79738 PE=2 SV=1)

HSP 1 Score: 81.6481 bits (200), Expect = 7.169e-13
Identity = 41/90 (45.56%), Postives = 58/90 (64.44%), Query Frame = 3
Query:  888 RVFELKKFDEIIKSHQARSDRRLKAISNRMLCKLDIIGP---YQSTNSQQNSRTAVDWYNLIVYASNKLRLEKSINCIQLSFPSSCFNEK 1148
            R+FEL  +D++IKS+Q+ SDRR+KA+ N+M CK+ I GP   Y STN+  N R  +  Y   +    K  +EK + C+Q +FP SC NEK
Sbjct:  483 RIFELNPYDDLIKSYQSHSDRRIKAVGNKMKCKIVIEGPIRIYDSTNACWNMRNKI-AYRCSLNGPTKEAVEKCLKCLQDTFPQSCLNEK 571          
BLAST of SMED30003555 vs. TrEMBL
Match: A0A0R3WQH8 (Uncharacterized protein OS=Hydatigena taeniaeformis OX=6205 GN=TTAC_LOCUS3003 PE=4 SV=1)

HSP 1 Score: 72.4034 bits (176), Expect = 8.128e-10
Identity = 33/94 (35.11%), Postives = 56/94 (59.57%), Query Frame = 3
Query:  882 YYRVFELKKFDEIIKSHQARSDRRLKAISNRMLCKLDIIGPYQSTNSQQNSRTAVDWYNLIVYASNKLRLEKSINCIQLSFPSSCFNEKLYKTS 1163
            Y ++ E+   DE++ SHQ   DRR+KA+S +  C LDI GP +      N R   + Y LI+ A NK + ++ IN ++ +FP +   +K++++S
Sbjct:  972 YEQIIEVAPHDELVHSHQNAHDRRIKAVSMKTGCHLDIKGPIKRPPIDGNMRREREVYELIIGAPNKEKADRCINYLRDTFPRAVLTKKMHRSS 1065          
BLAST of SMED30003555 vs. TrEMBL
Match: A0A0R3W5U4 (Uncharacterized protein OS=Taenia asiatica OX=60517 GN=TASK_LOCUS5515 PE=4 SV=1)

HSP 1 Score: 64.3142 bits (155), Expect = 3.206e-7
Identity = 29/93 (31.18%), Postives = 55/93 (59.14%), Query Frame = 3
Query:  882 YYRVFELKKFDEIIKSHQARSDRRLKAISNRMLCKLDIIGPYQSTNSQQNSRTAVDWYNLIVYASNKLRLEKSINCIQLSFPSSCFNEKLYKT 1160
            Y ++ E+   DE++ S+Q   DRR+KA+  +  C LDI GP + +    N R   + Y L + AS+K + ++ IN ++ +FP +   +K++++
Sbjct: 1003 YEQIIEIAPHDELVHSYQNVHDRRIKAVGMKTGCFLDIKGPIKRSPVDGNMRREREVYELTIGASSKEKADRCINYLRDTFPRAVLTKKMHRS 1095          
BLAST of SMED30003555 vs. TrEMBL
Match: A0A183NYC0 (Uncharacterized protein OS=Schistosoma mattheei OX=31246 GN=SMTD_LOCUS7106 PE=4 SV=1)

HSP 1 Score: 60.8474 bits (146), Expect = 3.329e-6
Identity = 36/109 (33.03%), Postives = 65/109 (59.63%), Query Frame = 3
Query:  819 VSYIPAE--MISSISHFTNDLWDYYRVFELKKFDEIIKSHQARSDRRLKAISNRMLCKLDIIGPYQSTNSQQNSRTAVD--WYNLIVYASNKLRLEKSINCIQLSFPSS 1133
            ++Y+ A+   I++  H+ ND   +  +FEL  +D+++KS+   +DRR+KAI+ +  C + + GP+  +   +N R  +    Y   VYA N+  L+K IN I+ +FP+S
Sbjct:  535 LTYMNADSFTINNNEHYNND---FKEIFELSPYDDLVKSYLTTTDRRIKAIATKNNCIIKLHGPFTLSKHVKNDRVILSKIKYECHVYAVNEKMLKKCINYIKETFPNS 640          
BLAST of SMED30003555 vs. TrEMBL
Match: A0A0R3SPS1 (Uncharacterized protein OS=Hymenolepis diminuta OX=6216 GN=HDID_LOCUS6985 PE=4 SV=1)

HSP 1 Score: 60.8474 bits (146), Expect = 4.291e-6
Identity = 28/93 (30.11%), Postives = 54/93 (58.06%), Query Frame = 3
Query:  870 DLWDYYRVFELKKFDEIIKSHQARSDRRLKAISNRMLCKLDIIGPYQSTNSQQNSRTAVDWYNLIVYASNKLRLEKSINCIQLSFPSSCFNEK 1148
            +L ++  VFE+   D+I+KSH    DRR+K++S +  C L++ GP +  +     +   + Y L + A NK++ ++ +N ++ +FP + F  K
Sbjct:  781 NLHEFEEVFEIDPHDDIVKSHLNSHDRRIKSVSMKTGCYLNMKGPVKVPSLDGTLKRDKEVYELTIGAPNKVKADRCVNFLRETFPHTAFLRK 873          
BLAST of SMED30003555 vs. Planmine SMEST
Match: SMESG000071919.1 (SMESG000071919.1)

HSP 1 Score: 489.189 bits (1258), Expect = 1.010e-174
Identity = 254/255 (99.61%), Postives = 254/255 (99.61%), Query Frame = 3
Query:  414 QTSNNHLSEDCLSNCSDPYTQTFEIPVANNKIIGYAKKIVDVVRAKASVGNDEEPSSKESPVQTYSLNKPDKSVNESDNNETYYSQXXXXXXXXXXXXXXVIEDEESEKSVNIFSPDSGIINILNNETHVEECVSVSYIPAEMISSISHFTNDLWDYYRVFELKKFDEIIKSHQARSDRRLKAISNRMLCKLDIIGPYQSTNSQQNSRTAVDWYNLIVYASNKLRLEKSINCIQLSFPSSCFNEKLYKTSQSLNR 1178
            QTSNNHLSEDCLSNCSDPYTQTFEIPVANNKIIGYAKKIVDVVRAKASVGNDEEPS KESPVQTYSLNKPDKSVNESDNNETYYSQSISNSLEDLSENSNVIEDEESEKSVNIFSPDSGIINILNNETHVEECVSVSYIPAEMISSISHFTNDLWDYYRVFELKKFDEIIKSHQARSDRRLKAISNRMLCKLDIIGPYQSTNSQQNSRTAVDWYNLIVYASNKLRLEKSINCIQLSFPSSCFNEKLYKTSQSLNR
Sbjct:   27 QTSNNHLSEDCLSNCSDPYTQTFEIPVANNKIIGYAKKIVDVVRAKASVGNDEEPSGKESPVQTYSLNKPDKSVNESDNNETYYSQSISNSLEDLSENSNVIEDEESEKSVNIFSPDSGIINILNNETHVEECVSVSYIPAEMISSISHFTNDLWDYYRVFELKKFDEIIKSHQARSDRRLKAISNRMLCKLDIIGPYQSTNSQQNSRTAVDWYNLIVYASNKLRLEKSINCIQLSFPSSCFNEKLYKTSQSLNR 281          
BLAST of SMED30003555 vs. Planmine SMEST
Match: SMESG000012235.1 (SMESG000012235.1)

HSP 1 Score: 80.8777 bits (198), Expect = 2.903e-16
Identity = 34/97 (35.05%), Postives = 66/97 (68.04%), Query Frame = 3
Query:  882 YYRVFELKKFDEIIKSHQARSDRRLKAISNRMLCKLDIIGPYQSTNSQQNSRTAVDW-------YNLIVYASNKLRLEKSINCIQLSFPSSCFNEKL 1151
            Y + F++++FDEI+KS    SDRR++A+ +R+ C++ + GP  ++ SQ +S++ + +       Y+L+++   K +L+KS+ CIQ +FP +C NE++
Sbjct:  427 YRKCFQVQQFDEIVKSFNTPSDRRMRAVCSRVNCQIKLFGP--TSRSQVDSKSHISFVNHEQPLYHLLIFTKTKEQLDKSLKCIQETFPKACLNERM 521          
BLAST of SMED30003555 vs. Planmine SMEST
Match: SMESG000024364.1 (SMESG000024364.1)

HSP 1 Score: 74.3294 bits (181), Expect = 3.516e-14
Identity = 35/94 (37.23%), Postives = 61/94 (64.89%), Query Frame = 3
Query:  858 HFTNDLWDYYRVFELKKFDEIIKSHQARSDRRLKAISNRMLCKLDIIGPYQSTNSQQNSRTAVD--WYNLIVYASNKLRLEKSINCIQLSFPSS 1133
            H ++D  ++ +VF L  FDEIIKSH   +DRRL+A++N+M CK+DI GP + ++   +  T  +   ++ ++   +K  LEK + CI+ +FP++
Sbjct:  324 HLSSDPNNFQKVFVLSPFDEIIKSHTCPNDRRLRAVANKMRCKIDIFGPMKVSHFTPSFYTTREKIIFHCVLSGDSKYNLEKCLKCIKDTFPTT 417          
BLAST of SMED30003555 vs. Planmine SMEST
Match: SMESG000076818.1 (SMESG000076818.1)

HSP 1 Score: 53.1434 bits (126), Expect = 3.097e-7
Identity = 31/88 (35.23%), Postives = 51/88 (57.95%), Query Frame = 3
Query:  876 WDYYRVFELKKFDEIIKSHQARSDRRLKAISNRMLCKLDIIGPYQSTN--SQQNSRTAVDWYNLIVYASNKLRLEKSINCIQLSFPSS 1133
            +  +R FEL  +D+IIK+H    DRR+K+++ +  C++ I GP  S +  S Q  R  V  Y   V   NK  L+K +N ++ +FP++
Sbjct:  688 FKVFRSFELSPYDDIIKAHLNPIDRRVKSVAAKNGCRIAIDGPINSYDPLSCQAFRNKV-TYRCTVAGPNKENLDKCMNYLKETFPNT 774          
The following BLAST results are available for this feature:
BLAST of SMED30003555 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 SMED30003555 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 SMED30003555 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 SMED30003555 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 SMED30003555 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 SMED30003555 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 SMED30003555 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 SMED30003555 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A7M6E07.169e-1345.56Uncharacterized protein OS=Dugesia ryukyuensis OX=... [more]
A0A0R3WQH88.128e-1035.11Uncharacterized protein OS=Hydatigena taeniaeformi... [more]
A0A0R3W5U43.206e-731.18Uncharacterized protein OS=Taenia asiatica OX=6051... [more]
A0A183NYC03.329e-633.03Uncharacterized protein OS=Schistosoma mattheei OX... [more]
A0A0R3SPS14.291e-630.11Uncharacterized protein OS=Hymenolepis diminuta OX... [more]
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BLAST of SMED30003555 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 SMED30003555 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 SMED30003555 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 SMED30003555 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 SMED30003555 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 SMED30003555 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000071919.11.010e-17499.61SMESG000071919.1[more]
SMESG000012235.12.903e-1635.05SMESG000012235.1[more]
SMESG000024364.13.516e-1437.23SMESG000024364.1[more]
SMESG000076818.13.097e-735.23SMESG000076818.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30003555 ID=SMED30003555|Name=SMED30003555|organism=Schmidtea mediterranea sexual|type=transcript|length=1245bp
CTCTTCCGATCTGTCATTGATTGAAAGTATTTTCTTCCTACATGGAATTT
TTCAGCTGGACAAATAAATCCCAAATGAACAGACAATACGTTGTTACTAC
AGATGACGAAAGTCCGAATCTTTCCTCTACTAAAAAAGGCTATCAAATTC
ATGAACTAATTTTAACGATTCCTCAAGACGACCAAGACAACATTTATACA
TCAAAGGAATCTTTTTCACATCTTTTTATGGAGAATGATTATTTTATGCC
AAATGAGTTTTGTTCTAATAGCATAACAATAAACCTTCCCATGGAAAACG
GAGACGTCTCAAGCGTGGAGTTGGCGAATCAATTGTCGAAAATGACGCAA
ACATTGCATAAAAATCAAGATCAGTCAGTTAATACGTCAATCGCTTTGGT
TTGTGCGTCAACGCAAACCTCAAATAATCATTTATCGGAAGATTGCCTAT
CGAATTGCTCTGATCCCTATACTCAGACCTTTGAAATCCCAGTGGCAAAT
AACAAAATAATAGGCTATGCTAAAAAGATAGTTGATGTCGTCCGAGCGAA
GGCATCAGTGGGCAATGACGAGGAACCTTCTAGCAAGGAATCGCCAGTGC
AAACTTATTCATTAAACAAACCAGACAAATCGGTAAACGAATCTGATAAC
AATGAGACATATTATTCACAAAGCATTTCAAATTCTCTCGAAGACCTCAG
CGAAAATTCCAATGTGATTGAAGACGAAGAGTCGGAAAAAAGCGTAAACA
TATTTTCACCGGACTCTGGAATCATCAATATTCTGAATAATGAAACCCAC
GTTGAAGAATGCGTTTCAGTGTCTTATATTCCTGCAGAAATGATCTCAAG
TATCAGTCATTTTACAAACGACTTGTGGGACTATTATCGAGTATTTGAGT
TGAAGAAATTTGATGAAATAATCAAATCCCACCAAGCCCGGTCGGACAGG
CGATTGAAAGCCATTTCCAATAGAATGCTTTGTAAACTAGACATAATTGG
ACCTTACCAGTCGACGAATTCTCAACAGAATTCTCGAACGGCCGTTGATT
GGTATAATCTGATTGTCTACGCAAGCAACAAGTTGCGATTGGAGAAGTCC
ATCAATTGCATTCAGCTGTCGTTTCCAAGTTCTTGTTTCAATGAAAAACT
TTACAAAACTTCTCAGTCATTAAATAGATGAGAAAATCTATGTAAATTAT
TTTCTATGTATTTTCTCTTAGATCTCTCTAACTAATTGAAAAGAA
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protein sequence of SMED30003555-orf-1

>SMED30003555-orf-1 ID=SMED30003555-orf-1|Name=SMED30003555-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=380bp
MEFFSWTNKSQMNRQYVVTTDDESPNLSSTKKGYQIHELILTIPQDDQDN
IYTSKESFSHLFMENDYFMPNEFCSNSITINLPMENGDVSSVELANQLSK
MTQTLHKNQDQSVNTSIALVCASTQTSNNHLSEDCLSNCSDPYTQTFEIP
VANNKIIGYAKKIVDVVRAKASVGNDEEPSSKESPVQTYSLNKPDKSVNE
SDNNETYYSQSISNSLEDLSENSNVIEDEESEKSVNIFSPDSGIINILNN
ETHVEECVSVSYIPAEMISSISHFTNDLWDYYRVFELKKFDEIIKSHQAR
SDRRLKAISNRMLCKLDIIGPYQSTNSQQNSRTAVDWYNLIVYASNKLRL
EKSINCIQLSFPSSCFNEKLYKTSQSLNR*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0003304testis primordium
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 57..79
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 48..79