SMED30033058

Overview
NameSMED30033058
Smed IDSMED30033058
Length (bp)866
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.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

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

 

back to top
Anatomical Expression

PAGE et. al., 2020



SMED30033058

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
head regionSMED30033058h1SMcG0011879 SmedASXL_007394SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parenchymaSMED30033058h1SMcG0011879 dd_Smed_v4_17579_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30033058 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000639:104176..107606 +4314
Homology
[Close]
BLAST of SMED30033058 vs. Planmine SMEST
Match: SMESG000007748.1 (SMESG000007748.1)

HSP 1 Score: 417.542 bits (1072), Expect = 1.668e-149
Identity = 206/209 (98.56%), Postives = 208/209 (99.52%), Query Frame = 2 
Query:   41 MQFFFELILTWVTLSTLNCRIVLDKRNDISCINGNCIRVAYSLYFNNSTLFMAIESKTSCVNVLCNDCEFKGDWTLTSTKRKYYLTRSVGLCQSPMRRNLSEFFLMSSENNYYGSVCYTAIDISCISFRCSKIRYNLNCFAKGYTMNSYFSEYCSDSFCNNCYSSKRWVLNKNSKVVYVEREVDSCHPTRIMELTDFFILENSNFREFW 667
            MQFFFELILTWVTLSTLNCRIVLDKRNDISCINGNCIRVAYSLYFNNSTLFMAIESKTSCVNVLCNDCEFKGDWTLTSTKRKYYLTRSVGLCQSPMRRNLSEFFLMSSENNYYGSVCYTAIDISCISFRCSKIRYNLNCFAKGYTMNSYFSEYCSDSFCNNCYSSKRWVLNKNSKVVYVEREVDSCHPTRIMELTDFFILENSNFR+ +
Sbjct:    1 MQFFFELILTWVTLSTLNCRIVLDKRNDISCINGNCIRVAYSLYFNNSTLFMAIESKTSCVNVLCNDCEFKGDWTLTSTKRKYYLTRSVGLCQSPMRRNLSEFFLMSSENNYYGSVCYTAIDISCISFRCSKIRYNLNCFAKGYTMNSYFSEYCSDSFCNNCYSSKRWVLNKNSKVVYVEREVDSCHPTRIMELTDFFILENSNFRKLF 209
[Close]
BLAST of SMED30033058 vs. Planmine SMEST
Match: SMESG000017163.1 (SMESG000017163.1)

HSP 1 Score: 242.276 bits (617), Expect = 1.123e-79
Identity = 118/240 (49.17%), Postives = 153/240 (63.75%), Query Frame = 2 
Query:   41 MQFFFELILTWVTLSTLNCRIVLDKRNDISCINGNCIRVAYSLYFNNSTLFMAIESKTSCVNVLCNDCEFKGDWTLTSTKRKYYLTRSVGLCQSPMRRNLSEFFLMSSENNYYGSVCYTAIDISCISFRCSKIRYNLNCFAKGYTMNSYFSEYCSDSFCNNCYSSKRWVLNKNSKVVYVEREVDSCHPTRIMELTDFFILENSNF----------------REFWNSSRIMTIIITWILF 712
            M F  EL + W+T+   +C   +D++NDI CINGNC R+ Y+LY NNS   M + SK  C NV C +C+ KG+W L   +  Y+L R +  CQS +++NL + F MS +  YYG+ CYTA+DI+C S++CSK+RYNLNC++KGYTM SY SE+CS+ +C  C     W L K  K VY+ERE D C  T  M+LTDFF LENSNF                R FWN+SRI  I ITWILF
Sbjct:    1 MYFLLELTVLWLTVPYGSCLTTVDEKNDIICINGNCTRLTYTLYINNSIFHMNVSSKIPCKNVHCINCKVKGEWRLVFRQGAYHLVRPIESCQSIIQKNLEDLFPMSDDRTYYGAFCYTAVDIACFSYKCSKVRYNLNCYSKGYTMESYHSEFCSNLYCQRCLKRNPWKLVKYFKQVYLERETDDCQTTNAMQLTDFFSLENSNFQLPLSSSDFQSYDAYSRTFWNTSRIKIISITWILF 240
[Close]
BLAST of SMED30033058 vs. Planmine SMEST
Match: SMESG000017154.1 (SMESG000017154.1)

HSP 1 Score: 107.457 bits (267), Expect = 1.128e-27
Identity = 65/209 (31.10%), Postives = 101/209 (48.33%), Query Frame = 2 
Query:  104 VLDKRNDISCINGNCIRVAYSLYFNNSTLFMAIESKTSCVNVLCNDCEFKGDWTLTSTKRKYYLTRSVGLCQSPMRRNLSEFFLMSSENNYYGSVCYTAIDISCISFRCSKIRYNLNCFAKGYTMNSYFSEYCSDSFCNNCYSSKRWVLNKNSKVVYVEREVDSCHPTRIMELTDFF-------ILENSNF-------REFWNSSRIMT 688
            ++ +R DI C NG C  V Y LY ++S   M + +K+ C  + CN+C +KGDWTL ++   YYLTR+  LC +   RN +E F   S +N         +DI+C S++C+   Y      K   + +Y    CSD  C  C     W LNK     +++R+  SC     + + DFF       + +  +F       +  WN+ RI+ 
Sbjct:   19 IISERTDIRCANGACYNVVYELYQDSSGYRMNVVTKSDCPPINCNNCVYKGDWTLIASSGAYYLTRNTFLCLADSFRNFTEIFPDPSSSN--------MVDIACNSYQCTIYHY----IIKEPFLYTYNLGKCSDFSCEGCNMCNYWQLNKTQSYTFLQRQTSSCQALTRIRMEDFFPPSGIPQVYQQHDFISSEILYKSSWNTPRILA 215
[Close]
BLAST of SMED30033058 vs. Planmine SMEST
Match: SMESG000017181.1 (SMESG000017181.1)

HSP 1 Score: 98.2117 bits (243), Expect = 2.721e-24
Identity = 66/227 (29.07%), Postives = 109/227 (48.02%), Query Frame = 2 
Query:   53 FELILTWVTLSTLNCRIVLDKRNDISCINGNCIRVAYSLYFNNSTL--FMAIESKTSCVNVLCNDCEFKGDWTLTSTKRKYYLTRSVGLCQSPMRRNLSEFFLMSSENNYYGSVCYTAIDISCISFRCSKIRYNLNCFAKGYTMNSYFSEYCSDSFCNNCYSSKRWVLNKNSKVVYVEREVDSCHPTRIMELTDFF--ILENSNFREFWNSSRIMTIIITWILFFSM 721
            F +I   +  + L C  + ++RNDI+C N  C  V Y LY+++ +   ++ +  ++ C +V CN+C +KG+W L      Y+L RS   C +   RN +E F  SS  N          DI+C ++ CSK  Y    F        Y    CS   C  C +   W     +    ++R V SC     + + DFF  + + S  +EFW+  RI+++II+ + F ++
Sbjct:    3 FLVIFLLLLRNALGCSFI-NERNDITCANRTCNNVRYRLYYDDQSYHYYVNVAGESVCPSVNCNNCSYKGNWMLGKASGTYFLYRSTNSCSTDSIRNFTEIFPSSSPLN--------VTDIACSNYGCSKYNY---LFESSKLYTKYLGN-CSYPSCEGCKTLTPWQYVNGNSYNLLQRNVSSCPSITRINMEDFFRRLDQISFVKEFWDGGRILSVIISCVSFVAL 216
[Close]
BLAST of SMED30033058 vs. Planmine SMEST
Match: SMESG000017150.1 (SMESG000017150.1)

HSP 1 Score: 90.1225 bits (222), Expect = 3.703e-21
Identity = 61/210 (29.05%), Postives = 101/210 (48.10%), Query Frame = 2 
Query:  104 VLDKRNDISCINGNCIRVAYSLYFNNSTLFMAIESKTSCVNVLCNDCEFKGDWTLTSTKRKYYLTRSVGLCQSPMRRNLSEFFLMSSENNYYGSVCYTAIDISCISFRCSKIRYNLNCFAKGYTMNSYFSEYCSDSFCNNCYSSKRWVLNKNSKVVYVEREVDSCHPTRIMELTDFFILENSNFREFWNSSRIMTIII----TWILFFSM 721
            +L++RNDI+C  GNC +V Y+L+   +   M I SK+SC +V C +C  K DW++     +Y L+R+   C++  R+   + F+  SEN+          D +C   +C +  Y    F KG    S F  +C   +C  C  +++W    N     +ERE  +C   R+     +F LE    +    +S    +I+    TWI+ F +
Sbjct:   18 LLNQRNDITCEAGNCTKVQYNLFNGTNGYIMIIASKSSCDSVYCLNCSLKTDWSMILENGEYILSRNAKSCEAERRKRFIDTFV--SENS-------PVTDFTCEENQCKQFVY----FNKG-AFYSSFMGFCELGYCRQCSMARKWHQADNFGTRVLERETYNCS-ARVKIPMKYFFLEQDKPQNLSPTSERPYVIVQRKHTWIIVFGI 212
The following BLAST results are available for this feature:
BLAST of SMED30033058 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033058 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033058 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033058 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033058 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033058 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033058 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033058 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033058 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033058 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033058 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033058 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033058 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30033058 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000007748.11.668e-14998.56SMESG000007748.1[more]
SMESG000017163.11.123e-7949.17SMESG000017163.1[more]
SMESG000017154.11.128e-2731.10SMESG000017154.1[more]
SMESG000017181.12.721e-2429.07SMESG000017181.1[more]
SMESG000017150.13.703e-2129.05SMESG000017150.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30033058 ID=SMED30033058|Name=SMED30033058|organism=Schmidtea mediterranea sexual|type=transcript|length=866bp
TGATTGATTTTCTTGTTTTCATTTTCACATAATTTCTTTCATGCAGTTTT
TCTTTGAATTAATTTTAACTTGGGTCACCCTTTCAACTCTCAACTGTCGG
ATTGTGCTTGACAAAAGGAACGATATAAGTTGCATAAATGGGAATTGCAT
TCGCGTTGCGTACAGCCTCTACTTTAATAATTCGACTCTTTTCATGGCCA
TTGAATCGAAAACTAGTTGCGTAAATGTGCTTTGCAATGACTGCGAATTC
AAAGGCGACTGGACGTTGACTAGCACTAAAAGAAAGTATTACTTGACGAG
ATCCGTTGGATTGTGTCAATCACCAATGCGAAGAAATCTTAGCGAATTCT
TTCTAATGTCAAGCGAAAATAATTATTACGGATCCGTTTGCTATACAGCA
ATTGATATATCCTGTATTTCATTCAGGTGCTCAAAAATCAGATATAACCT
CAATTGTTTTGCCAAAGGCTACACAATGAATTCGTATTTTTCGGAATATT
GCAGTGACTCATTCTGCAATAACTGCTATTCAAGTAAGAGATGGGTACTC
AACAAAAATTCCAAAGTCGTCTACGTTGAACGAGAAGTTGATAGTTGCCA
TCCCACCAGAATCATGGAATTAACCGATTTCTTTATTCTAGAAAATTCAA
ATTTTCGTGAATTTTGGAATTCCTCAAGAATAATGACAATTATCATAACT
TGGATTTTGTTTTTTTCTATGATTCTTGGTCTTTTGATTTGTCATCTACT
CAACTTGAATTCTTCTTGATTGTTTACAAATGTTTCTTATAACTGTAACC
GTTTTCTTTTAATATACTGGATAGTCATATAAAAGAATCTTATCAAATAA
TTAAGAATAGGTCACC
back to top

protein sequence of SMED30033058-orf-1

>SMED30033058-orf-1 ID=SMED30033058-orf-1|Name=SMED30033058-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=243bp
MQFFFELILTWVTLSTLNCRIVLDKRNDISCINGNCIRVAYSLYFNNSTL
FMAIESKTSCVNVLCNDCEFKGDWTLTSTKRKYYLTRSVGLCQSPMRRNL
SEFFLMSSENNYYGSVCYTAIDISCISFRCSKIRYNLNCFAKGYTMNSYF
SEYCSDSFCNNCYSSKRWVLNKNSKVVYVEREVDSCHPTRIMELTDFFIL
ENSNFREFWNSSRIMTIIITWILFFSMILGLLICHLLNLNSS*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..15
score: 0.65
NoneNo IPR availableTMHMMTMhelixcoord: 217..239