SMED30027970

Overview
NameSMED30027970
Smed IDSMED30027970
Length (bp)1114
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 SMED30027970 (SMED30027970) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30027970 (SMED30027970) 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




SMED30027970

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parapharyngeal regionSMED30027970h1SMcG0012966 dd_Smed_v4_8806_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30027970h1SMcG0012966 dd_Smed_v6_8806_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
head regionSMED30027970h1SMcG0012966 OX_Smed_1.0.11088ox_Smed_v2PMID:24238224
Kao et al., 2013
whole organism asexual adult RNA-sequencing evidence
head regionSMED30027970h1SMcG0021131 OX_Smed_1.0.11088ox_Smed_v2PMID:24238224
Kao et al., 2013
whole organism asexual adult RNA-sequencing evidence
zeta neoblastSMED30027970h1SMcG0012966 dd_Smed_v4_8806_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
SMED30027970 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001949:4619..5731 -5454
Homology
BLAST of SMED30027970 vs. TrEMBL
Match: A0A1A8A9P5 (DUF4371 domain-containing protein (Fragment) OS=Nothobranchius furzeri OX=105023 GN=Nfu_g_1_023723 PE=4 SV=1)

HSP 1 Score: 82.0333 bits (201), Expect = 2.430e-13
Identity = 76/284 (26.76%), Postives = 124/284 (43.66%), Query Frame = 3
Query:   90 GTSTVTMCAKSVTYFVIV*SMRNFAPASTKMWA*L--HNIFKINSPVVKSPSKTRFSSCSDTSHAIVENYHDIRDFLMVILKDQNEPSIDVQEAVSFDNIMYC*KEASIVILWNGILM*I*KTFVAKQMSDITLNTVVLVY--------DLRNRLNIYENLDKKLTGNDEYPGWK--------VFHDVNHKEMRRFEVRVINSDHRRSSYLLTD-LQPALSECSRSYSNAPKNFNFLTSFWIVEVTEIR-STEQLVNLYSKNLDSGLPDEFLLLVHFVASEENV 881
            G      C ++V++F  + ++ NF  AS++ W  L  H         +KS S TR+S+ +D + A+   Y  I+D L  I  D   P     EA     +M   + A + +LW+ +L  I  T  A Q     + TV ++Y          RN  ++YE   K LT  + Y            +F +    E+RR        D   + Y++ D L   L +   +Y N  + F FLT    + + +IR +TE+L  +Y ++L+     EF   +  V  EE+V
Sbjct:  166 GACAAECCIEAVSFFGFIQNLYNFFSASSRRWEILTAHLTKCEQGLTLKSLSSTRWSARADATKALRFGYKAIQDALNEIKVDHGTPRAAQYEASQLITVMETLETAVMTVLWDELLRRINVTSKALQQVHTDVCTVPILYSSLIEYIGQARNDFDVYEAEAKTLTATEGYKADSQRRRVKKVMFDESAGPEVRRSGREAFLID---THYVICDCLSQELKKRKDAYKNVEEKFGFLTKRKSMNIEQIRAATEKLKKIYPQDLEEDFTAEFCQFMSMVKDEESV 446          
BLAST of SMED30027970 vs. TrEMBL
Match: A0A151I6I1 (Zinc finger MYM-type protein 1 (Fragment) OS=Cyphomyrmex costatus OX=456900 GN=ALC62_15981 PE=4 SV=1)

HSP 1 Score: 78.5666 bits (192), Expect = 4.667e-12
Identity = 81/302 (26.82%), Postives = 139/302 (46.03%), Query Frame = 3
Query:   36 QNGIEIYFLISINFLYLFGTSTVTMCAKSVTYFVIV*SMRNFAPASTKMWA*LHNIFKINSPVV---KSPSKTRFSSCSDTSHAIVENYHDIRDFLMVILKDQNEPSIDVQEAVSFDNIMYC*KEASIVILWNGILM*I*KTFVAKQMSDITLNTVVLVYD--------LRNRLNIYENLDKKLTGNDEYP--------GWKVFHDVNHKEMRRFEVRVINSDHRRSSYL--LTDLQPALSECSRSYSNAPKNFNFLTSFWIVEVTE-IRSTEQLVNLYSKNLDSGLPDEFLLLVHFVASEE 875
            +N + IY   + + L L G +    C ++  +F+ V  +  F  AST  WA + +  + N P +   KS S TR+S+ ++   A+V ++  +RD L  I++D +E      EA          + A +V++W+ IL    KT  + Q  +I L TVV +Y+        LRNR + YE   K+L+  ++Y             F +VN  ++    +    ++ R +++L  L  L   L + S +Y      F FLT    +   E I   E+L  +YS +L +   +E L   +F+   E
Sbjct:  332 RNPLAIYVPCAAHSLNLVGQAAAECCLEATKFFMFVQHIYTFLSASTSRWAKIKSKVE-NQPGMLLPKSLSNTRWSARAEACRALVNSWGSLRDALDDIVEDASEKPTTKAEAEGLLQQFGSLETAIMVVVWSDILERFDKTNKSLQRVNIDLTTVVQLYNALHTYIVSLRNRFDHYEIQAKELSQCNDYARENQRRRRRTAKFDEVNDNDV----ILDTKANMRVNTFLVILDRLAGELEKRSIAYKVVDTRFGFLTCLLFLTDAEIITKCEELQAIYSTDLGNDFGEECLYFRNFIREME 628          
BLAST of SMED30027970 vs. TrEMBL
Match: A0A151IMG2 (Zinc finger MYM-type protein 1 (Fragment) OS=Cyphomyrmex costatus OX=456900 GN=ALC62_03006 PE=4 SV=1)

HSP 1 Score: 77.0258 bits (188), Expect = 1.607e-11
Identity = 81/302 (26.82%), Postives = 138/302 (45.70%), Query Frame = 3
Query:   36 QNGIEIYFLISINFLYLFGTSTVTMCAKSVTYFVIV*SMRNFAPASTKMWA*LHNIFKINSPVV---KSPSKTRFSSCSDTSHAIVENYHDIRDFLMVILKDQNEPSIDVQEAVSFDNIMYC*KEASIVILWNGILM*I*KTFVAKQMSDITLNTVVLVYD--------LRNRLNIYENLDKKLTGNDEYP--------GWKVFHDVNHKEMRRFEVRVINSDHRRSSYL--LTDLQPALSECSRSYSNAPKNFNFLTSFWIVEVTE-IRSTEQLVNLYSKNLDSGLPDEFLLLVHFVASEE 875
            +N + IY   + + L L G +    C ++  +F+ V  +  F  AST  WA + +  + N P +   KS S TR+S+ ++   A+V ++  +RD L  I++D +E      EA          + A +V++W+ IL    KT  + Q  +I L TVV +Y+        LRNR + YE   K+L+  ++Y             F +VN  ++    +    ++ R +++L  L  L   L + S  Y      F FLT    +   E I   E+L  +YS +L +   +E L   +F+   E
Sbjct:  339 RNPLAIYVPCAAHSLNLVGQAAAECCLEATKFFMFVQHIYTFLSASTSRWAKIKSKVE-NQPGMLLPKSLSNTRWSARAEACRALVNSWGSLRDALDDIVEDASEKPTTKAEAEGLLQQFGSLETAIMVVVWSDILERFDKTNKSLQRVNIDLTTVVQLYNALHTYIVSLRNRFDHYEIQAKELSQCNDYARENQRRRRRTAKFDEVNDNDV----ILDTKANMRVNTFLVILDRLAGELEKRSIVYKVVDTRFGFLTCLLFLTDAEIITKCEELQAIYSTDLGNDFGEECLYFRNFIREME 635          
BLAST of SMED30027970 vs. TrEMBL
Match: A0A151ICP7 (Zinc finger MYM-type protein 1 OS=Cyphomyrmex costatus OX=456900 GN=ALC62_11195 PE=4 SV=1)

HSP 1 Score: 77.0258 bits (188), Expect = 1.689e-11
Identity = 81/302 (26.82%), Postives = 138/302 (45.70%), Query Frame = 3
Query:   36 QNGIEIYFLISINFLYLFGTSTVTMCAKSVTYFVIV*SMRNFAPASTKMWA*LHNIFKINSPVV---KSPSKTRFSSCSDTSHAIVENYHDIRDFLMVILKDQNEPSIDVQEAVSFDNIMYC*KEASIVILWNGILM*I*KTFVAKQMSDITLNTVVLVYD--------LRNRLNIYENLDKKLTGNDEYP--------GWKVFHDVNHKEMRRFEVRVINSDHRRSSYL--LTDLQPALSECSRSYSNAPKNFNFLTSFWIVEVTE-IRSTEQLVNLYSKNLDSGLPDEFLLLVHFVASEE 875
            +N + IY   + + L L G +    C ++  +F+ V  +  F  AST  WA + +  + N P +   KS S TR+S+ ++   A+V ++  +RD L  I++D +E      EA          + A +V++W+ IL    KT  + Q  +I L TVV +Y+        LRNR + YE   K+L+  ++Y             F +VN  ++    +    ++ R +++L  L  L   L + S  Y      F FLT    +   E I   E+L  +YS +L +   +E L   +F+   E
Sbjct:  320 RNPLAIYVPCAAHSLNLVGQAAAECCLEATKFFMFVQHIYTFLSASTSRWAKIKSKVE-NQPGMLLPKSLSNTRWSARAEACRALVNSWGSLRDALDDIVEDASEKPTTKAEAEGLLQQFGSLETAIMVVVWSDILERFDKTNKSLQRVNIDLTTVVQLYNALHTYIVSLRNRFDHYEIQAKELSQCNDYARENQRRRRRTAKFDEVNDNDV----ILDTKANMRVNTFLVILDRLAGELKKRSIVYKVVDTRFGFLTCLLFLTDAEIITKCEELQAIYSTDLGNDFGEECLYFRNFIREME 616          
BLAST of SMED30027970 vs. TrEMBL
Match: X1XM97 (Uncharacterized protein OS=Acyrthosiphon pisum OX=7029 PE=4 SV=1)

HSP 1 Score: 71.633 bits (174), Expect = 9.674e-10
Identity = 84/332 (25.30%), Postives = 149/332 (44.88%), Query Frame = 3
Query:   39 NGIEIYFLISINFLYLFGTSTVTMCAKSVTYFVIV*SMRNFAPASTKMWA*LHNIFKINSPVVKSPSKTRFSSCSDTSHAIVENYHDIRDFLMVILKDQNEPSIDVQEAVSFDNIMYC*KEASIVILWNGILM*I*KTFVAKQMSDITLNTVVLVYD--------LRNRLNIYENLDKKLTGNDEYPGWKVFHDVNHKEMRRFEVRVINSDHRRSS----------------YLLTD-LQPALSECSRSYSNAPKNFNFLTSFWIVEVT-EIRST-EQLVNLYSKNLDSG--LPDEFLLLVHFVASEENVFPEI-LYKTLKTQHLESTFQML 944
            N    Y   S + L L GT     C  + ++F+++  + NF  +ST  W  L    K N  V K+ S TR+S+  D  HA+  +Y  I + L  I+ +Q E ++   EA      +   +   ++ +WN IL     T    Q +DI L+TV  +Y+        +R+  +++EN   ++TG  EY       D   K+  R+ +    +D  RS                 Y++ D L+  LS   ++Y      +  + + +    +  IR+T E L   +  ++++   L DE +L    +++++NV   + +YK +KT+ LE  F  L
Sbjct:  241 NSFAEYVPCSAHSLNLVGTCEAESCNSATSFFMLLQELYNFFSSSTARWDILKTYLKKNLSV-KNLSVTRWSARFDACHALFNSYAFIIEALHSIVDNQKEKAVYKVEANGLLARLKTLETGLMICIWNSILNSFNATNKKLQSTDIDLHTVSELYNGLENYLVQIRDDFDVFENKAVEITGCSEYA-----KDSKRKKRERYAM----ADESRSQPLTEITGKIDFIRNVYYVIIDTLKCQLSSRRQAYEKISDIYGCIPTLYKTPSSIVIRNTCETLAKYFIDDVENSSLLIDECILFSKLISTDKNVKSVLSMYKLIKTKELECMFPNL 562          
The following BLAST results are available for this feature:
BLAST of SMED30027970 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 SMED30027970 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 SMED30027970 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 SMED30027970 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 SMED30027970 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 SMED30027970 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 SMED30027970 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 SMED30027970 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A1A8A9P52.430e-1326.76DUF4371 domain-containing protein (Fragment) OS=No... [more]
A0A151I6I14.667e-1226.82Zinc finger MYM-type protein 1 (Fragment) OS=Cypho... [more]
A0A151IMG21.607e-1126.82Zinc finger MYM-type protein 1 (Fragment) OS=Cypho... [more]
A0A151ICP71.689e-1126.82Zinc finger MYM-type protein 1 OS=Cyphomyrmex cost... [more]
X1XM979.674e-1025.30Uncharacterized protein OS=Acyrthosiphon pisum OX=... [more]
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BLAST of SMED30027970 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 SMED30027970 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 SMED30027970 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 SMED30027970 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 SMED30027970 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 SMED30027970 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30027970 ID=SMED30027970|Name=SMED30027970|organism=Schmidtea mediterranea sexual|type=transcript|length=1114bp
CAGGTATTTATTATTAAATTTTGAATTAGAGTAGTCAAAATGGAATAGAA
ATATATTTTTTAATTTCAATTAATTTCTTATATCTCTTTGGTACTTCTAC
AGTGACTATGTGCGCCAAATCTGTAACGTACTTCGTCATTGTGTAATCTA
TGCGCAATTTCGCACCAGCCTCAACAAAGATGTGGGCATAATTGCACAAT
ATTTTCAAGATCAATAGTCCCGTAGTGAAAAGCCCCTCGAAAACGCGTTT
TAGTTCTTGTAGTGATACATCACATGCTATTGTTGAAAACTATCACGATA
TTCGTGACTTCCTCATGGTCATTTTGAAAGATCAGAATGAACCTTCAATT
GATGTGCAGGAAGCCGTGTCATTTGATAATATCATGTACTGTTAAAAAGA
AGCATCTATAGTAATCCTATGGAATGGCATCTTGATGTGAATTTAAAAGA
CTTTTGTAGCTAAGCAGATGTCGGATATCACCTTGAACACTGTGGTTCTC
GTTTACGATTTGCGAAATCGCTTGAATATTTATGAAAATCTTGACAAGAA
ACTCACAGGGAATGATGAATATCCAGGTTGGAAAGTGTTCCACGATGTGA
ACCATAAAGAAATGAGACGATTTGAAGTTCGCGTGATAAATTCTGATCAC
AGACGTTCTTCGTACTTATTAACAGATTTACAACCTGCTTTGAGTGAATG
CTCTAGATCATACAGCAATGCCCCGAAGAATTTTAACTTTCTTACATCGT
TCTGGATTGTGGAAGTCACTGAAATACGATCAACTGAACAACTTGTGAAC
TTATATTCAAAGAATTTGGATTCGGGATTACCTGATGAATTCTTATTACT
TGTTCATTTCGTGGCTTCGGAAGAAAATGTATTCCCTGAAATCTTATATA
AAACGCTGAAAACCCAACATCTGGAATCCACTTTTCAAATGTTAACATCA
CCCTACAAAAGTACTTGTCCCTTTCTGTATAAATTTCGAAGCTGTAAGAT
CATTCTTGAAACTCAGTCGCACTAAAAACAAATTCGATCAGTCTATAAAT
ACTTTCCATTGAAACTGAATTAATTTAAATACTTGTAAATGAATTTCTAT
CTGTAAATTAATAA
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protein sequence of SMED30027970-orf-1

>SMED30027970-orf-1 ID=SMED30027970-orf-1|Name=SMED30027970-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=186bp
MSDITLNTVVLVYDLRNRLNIYENLDKKLTGNDEYPGWKVFHDVNHKEMR
RFEVRVINSDHRRSSYLLTDLQPALSECSRSYSNAPKNFNFLTSFWIVEV
TEIRSTEQLVNLYSKNLDSGLPDEFLLLVHFVASEENVFPEILYKTLKTQ
HLESTFQMLTSPYKSTCPFLYKFRSCKIILETQSH*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: molecular function
TermDefinition
GO:0003676nucleic acid binding
GO:0046983protein dimerization activity