SMED30020960

Overview
NameSMED30020960
Smed IDSMED30020960
Length (bp)619
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



SMED30020960

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30020960 SmedASXL_062894SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30020960 SmedASXL_062894SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of SMED30020960 vs. Ensembl Human
Match: SETMAR (SET domain and mariner transposase fusion gene [Source:HGNC Symbol;Acc:HGNC:10762])

HSP 1 Score: 68.5514 bits (166), Expect = 5.686e-13
Identity = 52/154 (33.77%), Postives = 73/154 (47.40%), Query Frame = -3 
Query:  234 LILCNNNDIFY*-IVTCNEK*IIYDNLRYSTS*--------HFLKPVLHQKIMILVV-----------------NG*NENYC*RILSTNI*DASEITTFEYAITNRKTTNFLGDNIHLLISA*TLQKLDEAGFEILPRAAYLPYPSQNDYHLFK 617
            LIL N+N+ F   IVTC+EK I+YDN R S           HF KP+LH K +++ +                    +E Y   I   N     ++   + A+ NRK    L DN    ++  TLQKL+E G+E+LP   Y P     +YH+FK
Sbjct:  479 LILRNHNEPFLDRIVTCDEKWILYDNRRRSAQWLDQEEAPKHFPKPILHPKKVMVTIWWSAAGLIHYSFLNPGETITSEKYAQEIDEMN----QKLQRLQLALVNRKGPILLHDNARPHVAQPTLQKLNELGYEVLPHPPYSPDLLPTNYHVFK 628
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BLAST of SMED30020960 vs. Ensembl Human
Match: SETMAR (SET domain and mariner transposase fusion gene [Source:HGNC Symbol;Acc:HGNC:10762])

HSP 1 Score: 67.0106 bits (162), Expect = 1.733e-12
Identity = 53/154 (34.42%), Postives = 74/154 (48.05%), Query Frame = -3 
Query:  234 LILCNNNDIFY*-IVTCNEK*IIYDNLRYSTS*--------HFLKPVLH-QKIMILVVNG*----------------NENYC*RILSTNI*DASEITTFEYAITNRKTTNFLGDNIHLLISA*TLQKLDEAGFEILPRAAYLPYPSQNDYHLFK 617
            LIL N+N+ F   IVTC+EK I+YDN R S           HF KP+LH +K+M+ +                    +E Y   I   N     ++   + A+ NRK    L DN    ++  TLQKL+E G+E+LP   Y P     +YH+FK
Sbjct:  340 LILRNHNEPFLDRIVTCDEKWILYDNRRRSAQWLDQEEAPKHFPKPILHPKKVMVTIWWSAAGLIHYSFLNPGETITSEKYAQEIDEMN----QKLQRLQLALVNRKGPILLHDNARPHVAQPTLQKLNELGYEVLPHPPYSPDLLPTNYHVFK 489
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BLAST of SMED30020960 vs. UniProt/SwissProt
Match: sp|Q53H47|SETMR_HUMAN (Histone-lysine N-methyltransferase SETMAR OS=Homo sapiens OX=9606 GN=SETMAR PE=1 SV=2)

HSP 1 Score: 68.5514 bits (166), Expect = 2.731e-12
Identity = 52/154 (33.77%), Postives = 73/154 (47.40%), Query Frame = -3 
Query:  234 LILCNNNDIFY*-IVTCNEK*IIYDNLRYSTS*--------HFLKPVLHQKIMILVV-----------------NG*NENYC*RILSTNI*DASEITTFEYAITNRKTTNFLGDNIHLLISA*TLQKLDEAGFEILPRAAYLPYPSQNDYHLFK 617
            LIL N+N+ F   IVTC+EK I+YDN R S           HF KP+LH K +++ +                    +E Y   I   N     ++   + A+ NRK    L DN    ++  TLQKL+E G+E+LP   Y P     +YH+FK
Sbjct:  479 LILRNHNEPFLDRIVTCDEKWILYDNRRRSAQWLDQEEAPKHFPKPILHPKKVMVTIWWSAAGLIHYSFLNPGETITSEKYAQEIDEMN----QKLQRLQLALVNRKGPILLHDNARPHVAQPTLQKLNELGYEVLPHPPYSPDLLPTNYHVFK 628
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BLAST of SMED30020960 vs. TrEMBL
Match: A0A5S6QLP9 (Uncharacterized protein OS=Trichuris muris OX=70415 PE=4 SV=1)

HSP 1 Score: 70.4774 bits (171), Expect = 2.674e-11
Identity = 57/154 (37.01%), Postives = 71/154 (46.10%), Query Frame = -3 
Query:  234 LILCNNNDIF-Y*IVTCNEK*IIYDNLRYSTS*--------HFLKPVLHQKIMILVVNG*NENYC*RILSTNI*DASEITTFEY-----------------AITNRKTTNFLGDNIHLLISA*TLQKLDEAGFEILPRAAYLPYPSQNDYHLFK 617
            L+L N ND F   IVTC+EK I+YDN R S+           F KP +HQK ++L V          I+  NI  A E  T +                  A+TNRK    L DN    +S  T+QKL   G+E LP   Y P  S  DYH+FK
Sbjct:    2 LLLRNKNDPFLARIVTCDEKWILYDNRRRSSQWLDKGAAPKRFPKPDVHQKKVMLTVWWSATG----IIHYNILKAGETVTAQTYCSELEKMHEKLQRARPALTNRKGPILLHDNARPHVSQMTVQKLHHLGYETLPHPPYSPDLSPTDYHIFK 151
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BLAST of SMED30020960 vs. TrEMBL
Match: A0A5S6QCX4 (Uncharacterized protein OS=Trichuris muris OX=70415 PE=4 SV=1)

HSP 1 Score: 71.2478 bits (173), Expect = 4.901e-11
Identity = 54/154 (35.06%), Postives = 71/154 (46.10%), Query Frame = -3 
Query:  234 LILCNNNDIF-Y*IVTCNEK*IIYDNLRYSTS*--------HFLKPVLHQKIMILVVNG*N-----------------ENYC*RILSTNI*DASEITTFEYAITNRKTTNFLGDNIHLLISA*TLQKLDEAGFEILPRAAYLPYPSQNDYHLFK 617
            L+L N ND F   ++TC+EK I+YDN R S+          HF KP +HQK ++L V                     E YC  +  T+     ++     A+ NRK    L DN    IS  T+QKL   G+E LP   Y P  S  DYH+FK
Sbjct:  134 LLLRNKNDPFLARMITCDEKWILYDNRRRSSQWLDKGQPPKHFPKPEVHQKKVLLTVWWSATGIIHYSLLKPGQTVTAETYCTELEKTH----EKLQRSRPALANRKGPILLHDNARPHISQMTIQKLHHLGYETLPHPPYSPDLSPTDYHIFK 283
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BLAST of SMED30020960 vs. TrEMBL
Match: A0A5S6QNF3 (Uncharacterized protein OS=Trichuris muris OX=70415 PE=4 SV=1)

HSP 1 Score: 70.4774 bits (171), Expect = 9.345e-11
Identity = 57/154 (37.01%), Postives = 71/154 (46.10%), Query Frame = -3 
Query:  234 LILCNNNDIF-Y*IVTCNEK*IIYDNLRYSTS*--------HFLKPVLHQKIMILVVNG*NENYC*RILSTNI*DASEITTFEY-----------------AITNRKTTNFLGDNIHLLISA*TLQKLDEAGFEILPRAAYLPYPSQNDYHLFK 617
            L+L N ND F   IVTC+EK I+YDN R S+           F KP +HQK ++L V          I+  NI  A E  T +                  A+TNRK    L DN    +S  T+QKL   G+E LP   Y P  S  DYH+FK
Sbjct:  134 LLLRNKNDPFLARIVTCDEKWILYDNRRRSSQWLDKGAAPKRFPKPDVHQKKVMLTVWWSATG----IIHYNILKAGETVTAQTYCSELEKMHEKLQRTRPALTNRKGPILLHDNARPHVSQMTVQKLHHLGYETLPHPPYSPDLSPTDYHIFK 283
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BLAST of SMED30020960 vs. TrEMBL
Match: A0A0L7RA29 (Histone-lysine N-methyltransferase SETMAR (Fragment) OS=Habropoda laboriosa OX=597456 GN=WH47_00853 PE=4 SV=1)

HSP 1 Score: 70.0922 bits (170), Expect = 1.385e-10
Identity = 55/154 (35.71%), Postives = 73/154 (47.40%), Query Frame = -3 
Query:  234 LILCNNNDIF-Y*IVTCNEK*IIYDNLRYSTS*--------HFLKPVLHQKIMILVV----------NG*N-------ENYC*RILSTNI*DASEITTFEYAITNRKTTNFLGDNIHLLISA*TLQKLDEAGFEILPRAAYLPYPSQNDYHLFK 617
             +L N ND F + +VTC+EK I+YDN R S           HF KP  HQ+ +++ V          N  N       E YC  I + +     ++     A+ NRK    L DN    ++  TLQKL+E G+E LP  AY P  S  DYH FK
Sbjct:  119 FLLRNKNDPFLHRLVTCDEKWIMYDNRRRSAQWLDHDEKPKHFPKPKQHQRKVMVTVWWSAVGIIHYNFLNPGETITAEKYCREIDNMH----EKLEQLNPALINRKGPILLHDNARPHVAQLTLQKLNELGYETLPHPAYSPDLSPTDYHFFK 268
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BLAST of SMED30020960 vs. TrEMBL
Match: A0A0L7QJL5 (Histone-lysine N-methyltransferase SETMAR (Fragment) OS=Habropoda laboriosa OX=597456 GN=WH47_10341 PE=4 SV=1)

HSP 1 Score: 69.707 bits (169), Expect = 1.513e-10
Identity = 55/154 (35.71%), Postives = 73/154 (47.40%), Query Frame = -3 
Query:  234 LILCNNNDIF-Y*IVTCNEK*IIYDNLRYSTS*--------HFLKPVLHQKIMILVV----------NG*N-------ENYC*RILSTNI*DASEITTFEYAITNRKTTNFLGDNIHLLISA*TLQKLDEAGFEILPRAAYLPYPSQNDYHLFK 617
             +L N ND F + +VTC+EK I+YDN R S           HF KP  HQ+ +++ V          N  N       E YC  I + +     ++     A+ NRK    L DN    ++  TLQKL+E G+E LP  AY P  S  DYH FK
Sbjct:  119 FLLRNKNDPFLHRLVTCDEKWIMYDNRRRSAQWLDHDEKPKHFPKPKQHQRKVMVTVWWSAVGIIHYNFLNPGETIIAEKYCREIDNMH----EKLEQLNPALINRKGPILLHDNARPHVAQLTLQKLNELGYETLPHPAYSPDLSPTDYHFFK 268
The following BLAST results are available for this feature:
BLAST of SMED30020960 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 2
Match NameE-valueIdentityDescription
SETMAR5.686e-1333.77SET domain and mariner transposase fusion gene [So... [more]
SETMAR1.733e-1234.42SET domain and mariner transposase fusion gene [So... [more]
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BLAST of SMED30020960 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 SMED30020960 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 SMED30020960 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 SMED30020960 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 SMED30020960 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 SMED30020960 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 1
Match NameE-valueIdentityDescription
sp|Q53H47|SETMR_HUMAN2.731e-1233.77Histone-lysine N-methyltransferase SETMAR OS=Homo ... [more]
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BLAST of SMED30020960 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A5S6QLP92.674e-1137.01Uncharacterized protein OS=Trichuris muris OX=7041... [more]
A0A5S6QCX44.901e-1135.06Uncharacterized protein OS=Trichuris muris OX=7041... [more]
A0A5S6QNF39.345e-1137.01Uncharacterized protein OS=Trichuris muris OX=7041... [more]
A0A0L7RA291.385e-1035.71Histone-lysine N-methyltransferase SETMAR (Fragmen... [more]
A0A0L7QJL51.513e-1035.71Histone-lysine N-methyltransferase SETMAR (Fragmen... [more]
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BLAST of SMED30020960 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 SMED30020960 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 SMED30020960 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 SMED30020960 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 SMED30020960 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 SMED30020960 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

>SMED30020960 ID=SMED30020960|Name=SMED30020960|organism=Schmidtea mediterranea sexual|type=transcript|length=619bp
TGATATTGAAGGGAAATTATAAGGGATTTTACAAGCCAATTTACAAGGGT
TATTTTTAAAAAAAATAGCTCGATTGGCATTTAAATTTATTGTTCGAAGT
TGAATCCGTTAAAATCAATAGTTTTGTCACGCGTGATACTAGTTTTTATA
TTCCGATTCTGCAAAACTCCTGGGTTCTGTACACGACGAATTCTCATAGT
ATTTTGTTAGTTGAAGCATTTTGTTGCAGAAAGTTTGAACAAATGGTAGT
CGTTTTGCGAGGGATAAGGTAAATATGCGGCCCGTGGAAGAATCTCAAAA
CCAGCTTCGTCCAGTTTCTGAAGGGTTTATGCTGAGATAAGCAGATGGAT
ATTATCGCCGAGAAAATTTGTGGTCTTTCTATTGGTTATTGCGTATTCAA
ACGTTGTAATTTCTGATGCATCTCATATATTTGTCGACAGTATTCTCTAG
CAGTAATTTTCATTTCAGCCGTTGACAACTAAAATCATTATCTTTTGATG
TAAAACAGGCTTTAAAAAATGTTATGAAGTCGAATATCGCAGATTGTCAT
ATATGATCTATTTCTCGTTGCAAGTCACAATTCAATAGAAGATATCATTA
TTGTTGCACAGGATGAGTG
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell
PLANA:0002111X2 cell