SMED30020972

Overview
NameSMED30020972
Smed IDSMED30020972
Length (bp)948
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




SMED30020972

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 primordiumSMED30020972SMESG000038439.1 Contig265_SE3GPL10652PMID:20844018
Wang et al., 2010
whole organism juvenile cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30020972 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002731:13432..14379 +4713
Homology
BLAST of SMED30020972 vs. TrEMBL
Match: A0A550CH28 (Mob1/phocein OS=Auriculariopsis ampla OX=97359 GN=BD626DRAFT_493759 PE=4 SV=1)

HSP 1 Score: 63.5438 bits (153), Expect = 5.463e-8
Identity = 46/181 (25.41%), Postives = 74/181 (40.88%), Query Frame = 2
Query:  296 EWIAYTIFHLHDRLINYWNVLMYFCLDCNSEKRLQKARSVKYYGVPAAGPLPRELKDQLSKSVNYCMFDKEWSQTKYDSGNCSAIQTYPEYIEKYIGHLADVRIDPELMPG-IEEEFHPDFMESIAPTYKNIIPFFAHVYRKHYRGLCGMGILYHFNSLFMNIIHQGIAYKMINESDINDE 835
            EW+A  IF  +  L  ++ VL   C   +                 +AGP           S+NY      W+       N SA    P YI+  +  +  +  D  + P    + FHP F  ++   Y+ ++  FAH+Y  HY  +  +    HFNSLF + +  G  Y+++  +DI  E
Sbjct:   78 EWVAVNIFDFYTNLNEFYGVLTEVCTQQSCPTM-------------SAGP-----------SLNYL-----WTNQDKKQINLSA----PNYIDSVMSSVQTILDDENIFPTKSSQNFHPSFPHTVKLVYRQLLRVFAHLYHAHYEAILHLRSEPHFNSLFAHFLAFGKEYELLEVADIRGE 225          
BLAST of SMED30020972 vs. TrEMBL
Match: D8PX78 (Uncharacterized protein OS=Schizophyllum commune (strain H4-8 / FGSC 9210) OX=578458 GN=SCHCODRAFT_256573 PE=4 SV=1)

HSP 1 Score: 63.5438 bits (153), Expect = 6.674e-8
Identity = 46/181 (25.41%), Postives = 74/181 (40.88%), Query Frame = 2
Query:  296 EWIAYTIFHLHDRLINYWNVLMYFCLDCNSEKRLQKARSVKYYGVPAAGPLPRELKDQLSKSVNYCMFDKEWSQTKYDSGNCSAIQTYPEYIEKYIGHLADVRIDPELMPG-IEEEFHPDFMESIAPTYKNIIPFFAHVYRKHYRGLCGMGILYHFNSLFMNIIHQGIAYKMINESDINDE 835
            EW+A  IF  +  L  ++ VL   C   +                 +AGP           S+NY      W+       N SA    P YI+  +  +  +  D  + P    + FHP F  ++   Y+ ++  FAH+Y  HY  +  +    HFNSLF + +  G  Y+++  +DI  E
Sbjct:   78 EWVAVNIFDFYTNLNEFYGVLTEVCTQQSCPNM-------------SAGP-----------SLNYL-----WTNQDKKQINLSA----PNYIDSVMSSVQTILDDENIFPTKSSQNFHPSFPHTVKLVYRQLLRVFAHLYHAHYEAILHLRSEPHFNSLFAHFLAFGKEYELLEVADIRGE 225          
BLAST of SMED30020972 vs. TrEMBL
Match: A0A0C9XSX9 (Unplaced genomic scaffold K443scaffold_9, whole genome shotgun sequence OS=Laccaria amethystina LaAM-08-1 OX=1095629 GN=K443DRAFT_608015 PE=4 SV=1)

HSP 1 Score: 60.8474 bits (146), Expect = 6.017e-7
Identity = 49/188 (26.06%), Postives = 80/188 (42.55%), Query Frame = 2
Query:  296 EWIAYTIFHLHDRLINYWNVLMYFCLDCNSEKRLQKARSVKYYGVPAAGPLPRELKDQLSKSVNYCMFDKEWSQTKYDSGNC--SAIQTYP----EYIEKYIGHLADVRIDPELMPGIEEEFHPDFMESIAPTYKNIIPFFAHVYRKHYRGLCGMGILYHFNSLFMNIIHQGIAYKMINESDINDEYV 841
            EW+A  +F  +  L  ++ V+   C   ++   +    ++ Y     +GP  R+L       ++Y M      Q   D  N   S   T+P    + +   I H AD            + FHP F  +I   Y+ ++  FAHVY  HY+ +  +    HFNSLF + +  G  Y+++   DI  E V
Sbjct:   82 EWVAVNMFDFYTNLNEFYGVINETCTQ-HTCPTMSAGPTLNYIWT-TSGPGGRQLTLPAPTYIDYVMTSI---QNLIDDENVFPSKSSTFPVTSAQVLLPNINHFAD------------QSFHPSFPATIRTVYRQLLRVFAHVYHAHYQQILHLRSEPHFNSLFAHFLAFGREYELLEVRDIKGEPV 252          
BLAST of SMED30020972 vs. TrEMBL
Match: A0A5C3M636 (Protein kinase activator OS=Crucibulum laeve OX=68775 GN=BDQ12DRAFT_680217 PE=4 SV=1)

HSP 1 Score: 59.3066 bits (142), Expect = 1.699e-6
Identity = 46/183 (25.14%), Postives = 76/183 (41.53%), Query Frame = 2
Query:  296 EWIAYTIFHLHDRLINYWNVLMYFCL--DCNSEKRLQKARSVKYYGVPAAGPLPRELKDQLSKSVNYCMFDKEWSQTKYDSGNCSAIQTYPEYIEKYIGHLADVRIDPELMPG-IEEEFHPDFMESIAPTYKNIIPFFAHVYRKHYRGLCGMGILYHFNSLFMNIIHQGIAYKMINESDINDE 835
            EW+A  +F  +  L  ++ V+   C    C S                +AGP           S+NY      W+    + G   A    P YI+  +  + ++  D  + P    + FHP F  +I   Y+ ++  FAH+Y  HY+ +  +    HFNSLF + +  G  Y+++   DI  E
Sbjct:   71 EWVAVNMFDFYTNLNEFYGVINEACTQHSCPSM---------------SAGP-----------SLNYL-----WT----NQGGKQAALPAPTYIDYVMSSIQNLLDDENVFPTKTNQAFHPSFPATIRTVYRQLLRVFAHIYHAHYQQILHLRSEPHFNSLFAHFLAFGREYELLEVKDIRGE 218          
BLAST of SMED30020972 vs. TrEMBL
Match: A0A383VR74 (Uncharacterized protein OS=Tetradesmus obliquus OX=3088 GN=BQ4739_LOCUS8345 PE=4 SV=1)

HSP 1 Score: 58.9214 bits (141), Expect = 2.082e-6
Identity = 27/90 (30.00%), Postives = 48/90 (53.33%), Query Frame = 2
Query:  560 PEYIEKYIGHLADVRIDPELMPG-IEEEFHPDFMESIAPTYKNIIPFFAHVYRKHYRGLCGMGILYHFNSLFMNIIHQGIAYKMINESDI 826
            PEY++K    + D   DP + PG   E F P+FME +   +K +   +AH+Y  H++ +C +G   H N+ F + I     + ++ E ++
Sbjct:  113 PEYVDKLFDWIEDQIDDPSVFPGQFGEPFPPNFMEVVRTIFKRLFRVYAHIYHSHFKQVCSLGEEAHLNTCFKHFIFFVRHFDLVEEKEL 202          
BLAST of SMED30020972 vs. Ensembl Cavefish
Match: si:dkey-266m15.5 (si:dkey-266m15.5 [Source:ZFIN;Acc:ZDB-GENE-070705-442])

HSP 1 Score: 48.521 bits (114), Expect = 2.637e-6
Identity = 28/107 (26.17%), Postives = 50/107 (46.73%), Query Frame = 2
Query:  506 EWSQTKYDSGNCSAIQTYPEYIEKYIGHLADVRIDPELMPG-IEEEFHPDFMESIAPTYKNIIPFFAHVYRKHYRGLCGMGILYHFNSLFMNIIHQGIAYKMINESD 823
            EW+  +     CSA    P Y +  + ++ ++  D  + P   + +F P FM  +   +  +   FAH+Y  HYR    M I  H N+LF + I     ++++  S+
Sbjct:  116 EWTDDQGKRLKCSA----PLYTDYAMSYIQELLTDENVFPSRADAQFPPGFMFLVQKVFLLLFRTFAHLYSAHYRDAITMEIHPHLNTLFTHFITFSHTFRLLEPSE 218          
BLAST of SMED30020972 vs. Planmine SMEST
Match: SMESG000038439.1 (SMESG000038439.1)

HSP 1 Score: 586.26 bits (1510), Expect = 0.000e+0
Identity = 278/278 (100.00%), Postives = 278/278 (100.00%), Query Frame = 2
Query:   65 MACRRNKGIPGSQLQLAQGQDYDSPIKRCRLAHMQTEHIKHKDIAELEGGEGPMPDTLRIGIRTRYFAIAPNDSSHNEWIAYTIFHLHDRLINYWNVLMYFCLDCNSEKRLQKARSVKYYGVPAAGPLPRELKDQLSKSVNYCMFDKEWSQTKYDSGNCSAIQTYPEYIEKYIGHLADVRIDPELMPGIEEEFHPDFMESIAPTYKNIIPFFAHVYRKHYRGLCGMGILYHFNSLFMNIIHQGIAYKMINESDINDEYVFNHYKRIYQEEEMRVKGGI 898
            MACRRNKGIPGSQLQLAQGQDYDSPIKRCRLAHMQTEHIKHKDIAELEGGEGPMPDTLRIGIRTRYFAIAPNDSSHNEWIAYTIFHLHDRLINYWNVLMYFCLDCNSEKRLQKARSVKYYGVPAAGPLPRELKDQLSKSVNYCMFDKEWSQTKYDSGNCSAIQTYPEYIEKYIGHLADVRIDPELMPGIEEEFHPDFMESIAPTYKNIIPFFAHVYRKHYRGLCGMGILYHFNSLFMNIIHQGIAYKMINESDINDEYVFNHYKRIYQEEEMRVKGGI
Sbjct:    1 MACRRNKGIPGSQLQLAQGQDYDSPIKRCRLAHMQTEHIKHKDIAELEGGEGPMPDTLRIGIRTRYFAIAPNDSSHNEWIAYTIFHLHDRLINYWNVLMYFCLDCNSEKRLQKARSVKYYGVPAAGPLPRELKDQLSKSVNYCMFDKEWSQTKYDSGNCSAIQTYPEYIEKYIGHLADVRIDPELMPGIEEEFHPDFMESIAPTYKNIIPFFAHVYRKHYRGLCGMGILYHFNSLFMNIIHQGIAYKMINESDINDEYVFNHYKRIYQEEEMRVKGGI 278          
BLAST of SMED30020972 vs. Planmine SMEST
Match: SMESG000022865.1 (SMESG000022865.1)

HSP 1 Score: 177.563 bits (449), Expect = 6.134e-54
Identity = 96/264 (36.36%), Postives = 147/264 (55.68%), Query Frame = 2
Query:  125 DYDSPIKRCRLAHMQTEHIKHKDIAELEGGEGPMPDTLRIGIRTRYFAIAPNDSSHNEWIAYTIFHLHDRLINYWNVLMYFCLDCNSEKRLQKARSVKYYGVPAAGPLPRELKDQLSKSVNYC---MFDKEWSQTKYDSGNCSAIQTYPEYIEKYIGHLADVRIDPELMPGIEEEFHP-DFMESIAPTYKNIIPFFAHVYRKHYRGLCGMGILYHFNSLFMNIIHQGIAYKMI---NESDINDEYVFNHYKRIYQEEEMRVKGG 895
            DY SP+KR R+  +Q  H  +  I+     +G MPDTLRIG++ + F +AP     NEWIAY ++H+ DR+ N WN+ MYFCLD  S  R+  +RS++YYG+P  G L +  +   +   ++C   M DK + Q  Y + N   I+T+  +I+  +    +++ D + M  +E +  P +F + + P + N    F H Y  HY  +C MG+L HFNSLF NI+     Y ++   NES   + + F  Y++I QEE   VK  
Sbjct:    8 DYSSPVKRQRMEEIQKTHQTYYGISS--APQGGMPDTLRIGMQMKDFVVAPPKVDENEWIAYMVYHISDRMKNLWNLFMYFCLDDRSVNRINASRSIQYYGLPQPGTLTQSEESFYTNEKSFCKLTMNDKIY-QNTYLTTNNGPIRTWAVFIDVLMVDFENLKTDEKTMGKMENDVLPENFRKMLTPFFTNAFSMFEHFYNHHYGDICSMGVLLHFNSLFTNIVALSDTYGILSANNESLGANLFAF--YQKILQEELEHVKTA 266          
The following BLAST results are available for this feature:
BLAST of SMED30020972 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 SMED30020972 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 SMED30020972 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 SMED30020972 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 SMED30020972 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 SMED30020972 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 SMED30020972 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 SMED30020972 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A550CH285.463e-825.41Mob1/phocein OS=Auriculariopsis ampla OX=97359 GN=... [more]
D8PX786.674e-825.41Uncharacterized protein OS=Schizophyllum commune (... [more]
A0A0C9XSX96.017e-726.06Unplaced genomic scaffold K443scaffold_9, whole ge... [more]
A0A5C3M6361.699e-625.14Protein kinase activator OS=Crucibulum laeve OX=68... [more]
A0A383VR742.082e-630.00Uncharacterized protein OS=Tetradesmus obliquus OX... [more]
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BLAST of SMED30020972 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 1
Match NameE-valueIdentityDescription
si:dkey-266m15.52.637e-626.17si:dkey-266m15.5 [Source:ZFIN;Acc:ZDB-GENE-070705-... [more]
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BLAST of SMED30020972 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 SMED30020972 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 SMED30020972 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 SMED30020972 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 SMED30020972 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000038439.10.000e+0100.00SMESG000038439.1[more]
SMESG000022865.16.134e-5436.36SMESG000022865.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30020972 ID=SMED30020972|Name=SMED30020972|organism=Schmidtea mediterranea sexual|type=transcript|length=948bp
TGATTTCAAATTTAAGTCAATTATAGGAATCACGATAATTAAATTAAAAT
AATTATCATCAATAATGGCTTGTAGAAGAAATAAAGGAATTCCAGGCTCA
CAGTTACAATTAGCACAAGGCCAAGATTATGATTCTCCAATCAAAAGATG
TAGGTTAGCGCATATGCAGACCGAGCATATAAAACATAAAGATATTGCCG
AACTTGAAGGGGGCGAAGGACCAATGCCAGACACTCTGAGAATAGGTATA
AGAACTCGCTATTTTGCGATCGCTCCCAATGATTCATCTCACAACGAATG
GATCGCCTATACTATATTTCATCTTCATGATCGCTTAATAAATTACTGGA
ATGTATTAATGTATTTCTGCTTGGATTGTAACTCAGAAAAACGACTTCAG
AAAGCTAGGTCAGTAAAATACTATGGTGTACCGGCAGCTGGTCCTTTACC
CAGAGAATTAAAAGACCAGTTAAGTAAATCGGTAAATTACTGTATGTTTG
ATAAAGAATGGTCTCAAACAAAATATGATTCCGGAAACTGCAGTGCTATT
CAGACATATCCTGAATACATAGAGAAATATATTGGACATTTGGCAGATGT
TAGAATAGACCCAGAACTTATGCCAGGAATTGAAGAAGAATTTCATCCTG
ACTTTATGGAATCCATAGCACCAACTTATAAAAACATTATCCCATTTTTT
GCACATGTTTATCGAAAACATTACAGAGGTCTTTGTGGAATGGGGATTTT
ATATCACTTTAATTCACTTTTCATGAATATTATACATCAAGGAATAGCAT
ATAAAATGATAAATGAATCTGATATTAATGATGAATATGTATTTAATCAT
TATAAAAGAATTTATCAAGAAGAAGAAATGAGAGTAAAGGGAGGTATTTA
AGTATTAAACGAAACAAAAATGTTTCAATTGAAATTATAATTTATGCA
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protein sequence of SMED30020972-orf-1

>SMED30020972-orf-1 ID=SMED30020972-orf-1|Name=SMED30020972-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=279bp
MACRRNKGIPGSQLQLAQGQDYDSPIKRCRLAHMQTEHIKHKDIAELEGG
EGPMPDTLRIGIRTRYFAIAPNDSSHNEWIAYTIFHLHDRLINYWNVLMY
FCLDCNSEKRLQKARSVKYYGVPAAGPLPRELKDQLSKSVNYCMFDKEWS
QTKYDSGNCSAIQTYPEYIEKYIGHLADVRIDPELMPGIEEEFHPDFMES
IAPTYKNIIPFFAHVYRKHYRGLCGMGILYHFNSLFMNIIHQGIAYKMIN
ESDINDEYVFNHYKRIYQEEEMRVKGGI*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0003304testis primordium
Vocabulary: INTERPRO
TermDefinition
IPR036703MOB_kinase_act_sf
IPR005301MOB_kinase_act_fam
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR036703MOB kinase activator superfamilyGENE3DG3DSA:1.20.140.30coord: 67..266
e-value: 4.5E-11
score: 44.7
IPR036703MOB kinase activator superfamilySUPERFAMILYSSF101152Mob1/phoceincoord: 158..254
IPR005301MOB kinase activator familyPFAMPF03637Mob1_phoceincoord: 70..255
e-value: 8.5E-10
score: 38.9
IPR005301MOB kinase activator familyPANTHERPTHR22599MPS ONE BINDER KINASE ACTIVATOR-LIKE MOBcoord: 159..255
NoneNo IPR availablePANTHERPTHR22599:SF20CBK1 KINASE ACTIVATOR PROTEIN MOB2coord: 159..255