SMED30032914

Overview
NameSMED30032914
Smed IDSMED30032914
Length (bp)1767
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



SMED30032914

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
reproductive organSMED30032914SMESG000075898.1 Contig48399newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30032914SMESG000075898.1 Contig48399uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
testisSMED30032914SMESG000062012.1 Contig3141GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
testisSMED30032914SMESG000075898.1 PL04017B2C05ncbi_smed_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
testisSMED30032914SMESG000075898.1 Contig3141GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Alignments
SMED30032914 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002633:3887..17157 +8610
Homology
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BLAST of SMED30032914 vs. Planmine SMEST
Match: SMESG000075898.1 (SMESG000075898.1)

HSP 1 Score: 854.744 bits (2207), Expect = 0.000e+0
Identity = 499/499 (100.00%), Postives = 499/499 (100.00%), Query Frame = 1 
Query:   76 MGGSMQDIMEMHAKIANDPWAYTRKIRDVQEQDMKDCISQHRKMENLSWYSKSNANAQMERFQWMQRKECEMLRNMQEQETELKVIKNNEHLENLMGKYLEKEKNDSLHRDRYSQYLRENDPELRILASQLREAYVGKIRLAQIDEKERLKNELATADIPYVRAMXXXXXXXXXXXXXXXXXXXXXXYNFRKQLEQQMKDKAKFDALSDTREEDRQRIESVIQENLQKMQEEKDKEFSKKMTLRKSYMDAFKDXXXXXXXXXXXXIAEENKFKEYRKETEYKNEGQMXXXXXXXXXXXXIQKRLGELLAQKQRDIDEFEAARQDVAIAQAEMQAFRHEKTERDNKEIAKRKYIDELNKFKEFSRKAELARKDEDRKLDEKIEELNKQKDEIIHQRRLKDAELKEKFKNEAQANIXXXXXXXXXXXXXXXXXXXSFINDNEKYKIDVQNERIAMLKEMAKHLYPGCIPRGMLKEKDIQYLEDPLKNFLLTKKSYPDENIN 1572
            MGGSMQDIMEMHAKIANDPWAYTRKIRDVQEQDMKDCISQHRKMENLSWYSKSNANAQMERFQWMQRKECEMLRNMQEQETELKVIKNNEHLENLMGKYLEKEKNDSLHRDRYSQYLRENDPELRILASQLREAYVGKIRLAQIDEKERLKNELATADIPYVRAMEKQFKEDQEQEKLQQFLEDEKKYNFRKQLEQQMKDKAKFDALSDTREEDRQRIESVIQENLQKMQEEKDKEFSKKMTLRKSYMDAFKDREEELQKEKERQIAEENKFKEYRKETEYKNEGQMLLKKLREENLNLIQKRLGELLAQKQRDIDEFEAARQDVAIAQAEMQAFRHEKTERDNKEIAKRKYIDELNKFKEFSRKAELARKDEDRKLDEKIEELNKQKDEIIHQRRLKDAELKEKFKNEAQANIKEKLLEKEKCHEIELETEKSFINDNEKYKIDVQNERIAMLKEMAKHLYPGCIPRGMLKEKDIQYLEDPLKNFLLTKKSYPDENIN
Sbjct:    1 MGGSMQDIMEMHAKIANDPWAYTRKIRDVQEQDMKDCISQHRKMENLSWYSKSNANAQMERFQWMQRKECEMLRNMQEQETELKVIKNNEHLENLMGKYLEKEKNDSLHRDRYSQYLRENDPELRILASQLREAYVGKIRLAQIDEKERLKNELATADIPYVRAMEKQFKEDQEQEKLQQFLEDEKKYNFRKQLEQQMKDKAKFDALSDTREEDRQRIESVIQENLQKMQEEKDKEFSKKMTLRKSYMDAFKDREEELQKEKERQIAEENKFKEYRKETEYKNEGQMLLKKLREENLNLIQKRLGELLAQKQRDIDEFEAARQDVAIAQAEMQAFRHEKTERDNKEIAKRKYIDELNKFKEFSRKAELARKDEDRKLDEKIEELNKQKDEIIHQRRLKDAELKEKFKNEAQANIKEKLLEKEKCHEIELETEKSFINDNEKYKIDVQNERIAMLKEMAKHLYPGCIPRGMLKEKDIQYLEDPLKNFLLTKKSYPDENIN 499
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BLAST of SMED30032914 vs. Planmine SMEST
Match: SMESG000075898.1 (SMESG000075898.1)

HSP 1 Score: 843.958 bits (2179), Expect = 0.000e+0
Identity = 495/495 (100.00%), Postives = 495/495 (100.00%), Query Frame = 1 
Query:   88 MQDIMEMHAKIANDPWAYTRKIRDVQEQDMKDCISQHRKMENLSWYSKSNANAQMERFQWMQRKECEMLRNMQEQETELKVIKNNEHLENLMGKYLEKEKNDSLHRDRYSQYLRENDPELRILASQLREAYVGKIRLAQIDEKERLKNELATADIPYVRAMXXXXXXXXXXXXXXXXXXXXXXYNFRKQLEQQMKDKAKFDALSDTREEDRQRIESVIQENLQKMQEEKDKEFSKKMTLRKSYMDAFKDXXXXXXXXXXXXIAEENKFKEYRKETEYKNEGQMXXXXXXXXXXXXIQKRLGELLAQKQRDIDEFEAARQDVAIAQAEMQAFRHEKTERDNKEIAKRKYIDELNKFKEFSRKAELARKDEDRKLDEKIEELNKQKDEIIHQRRLKDAELKEKFKNEAQANIXXXXXXXXXXXXXXXXXXXSFINDNEKYKIDVQNERIAMLKEMAKHLYPGCIPRGMLKEKDIQYLEDPLKNFLLTKKSYPDENIN 1572
            MQDIMEMHAKIANDPWAYTRKIRDVQEQDMKDCISQHRKMENLSWYSKSNANAQMERFQWMQRKECEMLRNMQEQETELKVIKNNEHLENLMGKYLEKEKNDSLHRDRYSQYLRENDPELRILASQLREAYVGKIRLAQIDEKERLKNELATADIPYVRAMEKQFKEDQEQEKLQQFLEDEKKYNFRKQLEQQMKDKAKFDALSDTREEDRQRIESVIQENLQKMQEEKDKEFSKKMTLRKSYMDAFKDREEELQKEKERQIAEENKFKEYRKETEYKNEGQMLLKKLREENLNLIQKRLGELLAQKQRDIDEFEAARQDVAIAQAEMQAFRHEKTERDNKEIAKRKYIDELNKFKEFSRKAELARKDEDRKLDEKIEELNKQKDEIIHQRRLKDAELKEKFKNEAQANIKEKLLEKEKCHEIELETEKSFINDNEKYKIDVQNERIAMLKEMAKHLYPGCIPRGMLKEKDIQYLEDPLKNFLLTKKSYPDENIN
Sbjct:    1 MQDIMEMHAKIANDPWAYTRKIRDVQEQDMKDCISQHRKMENLSWYSKSNANAQMERFQWMQRKECEMLRNMQEQETELKVIKNNEHLENLMGKYLEKEKNDSLHRDRYSQYLRENDPELRILASQLREAYVGKIRLAQIDEKERLKNELATADIPYVRAMEKQFKEDQEQEKLQQFLEDEKKYNFRKQLEQQMKDKAKFDALSDTREEDRQRIESVIQENLQKMQEEKDKEFSKKMTLRKSYMDAFKDREEELQKEKERQIAEENKFKEYRKETEYKNEGQMLLKKLREENLNLIQKRLGELLAQKQRDIDEFEAARQDVAIAQAEMQAFRHEKTERDNKEIAKRKYIDELNKFKEFSRKAELARKDEDRKLDEKIEELNKQKDEIIHQRRLKDAELKEKFKNEAQANIKEKLLEKEKCHEIELETEKSFINDNEKYKIDVQNERIAMLKEMAKHLYPGCIPRGMLKEKDIQYLEDPLKNFLLTKKSYPDENIN 495
[Close]
BLAST of SMED30032914 vs. Planmine SMEST
Match: SMESG000075898.1 (SMESG000075898.1)

HSP 1 Score: 836.254 bits (2159), Expect = 0.000e+0
Identity = 491/491 (100.00%), Postives = 491/491 (100.00%), Query Frame = 1 
Query:  100 MEMHAKIANDPWAYTRKIRDVQEQDMKDCISQHRKMENLSWYSKSNANAQMERFQWMQRKECEMLRNMQEQETELKVIKNNEHLENLMGKYLEKEKNDSLHRDRYSQYLRENDPELRILASQLREAYVGKIRLAQIDEKERLKNELATADIPYVRAMXXXXXXXXXXXXXXXXXXXXXXYNFRKQLEQQMKDKAKFDALSDTREEDRQRIESVIQENLQKMQEEKDKEFSKKMTLRKSYMDAFKDXXXXXXXXXXXXIAEENKFKEYRKETEYKNEGQMXXXXXXXXXXXXIQKRLGELLAQKQRDIDEFEAARQDVAIAQAEMQAFRHEKTERDNKEIAKRKYIDELNKFKEFSRKAELARKDEDRKLDEKIEELNKQKDEIIHQRRLKDAELKEKFKNEAQANIXXXXXXXXXXXXXXXXXXXSFINDNEKYKIDVQNERIAMLKEMAKHLYPGCIPRGMLKEKDIQYLEDPLKNFLLTKKSYPDENIN 1572
            MEMHAKIANDPWAYTRKIRDVQEQDMKDCISQHRKMENLSWYSKSNANAQMERFQWMQRKECEMLRNMQEQETELKVIKNNEHLENLMGKYLEKEKNDSLHRDRYSQYLRENDPELRILASQLREAYVGKIRLAQIDEKERLKNELATADIPYVRAMEKQFKEDQEQEKLQQFLEDEKKYNFRKQLEQQMKDKAKFDALSDTREEDRQRIESVIQENLQKMQEEKDKEFSKKMTLRKSYMDAFKDREEELQKEKERQIAEENKFKEYRKETEYKNEGQMLLKKLREENLNLIQKRLGELLAQKQRDIDEFEAARQDVAIAQAEMQAFRHEKTERDNKEIAKRKYIDELNKFKEFSRKAELARKDEDRKLDEKIEELNKQKDEIIHQRRLKDAELKEKFKNEAQANIKEKLLEKEKCHEIELETEKSFINDNEKYKIDVQNERIAMLKEMAKHLYPGCIPRGMLKEKDIQYLEDPLKNFLLTKKSYPDENIN
Sbjct:    1 MEMHAKIANDPWAYTRKIRDVQEQDMKDCISQHRKMENLSWYSKSNANAQMERFQWMQRKECEMLRNMQEQETELKVIKNNEHLENLMGKYLEKEKNDSLHRDRYSQYLRENDPELRILASQLREAYVGKIRLAQIDEKERLKNELATADIPYVRAMEKQFKEDQEQEKLQQFLEDEKKYNFRKQLEQQMKDKAKFDALSDTREEDRQRIESVIQENLQKMQEEKDKEFSKKMTLRKSYMDAFKDREEELQKEKERQIAEENKFKEYRKETEYKNEGQMLLKKLREENLNLIQKRLGELLAQKQRDIDEFEAARQDVAIAQAEMQAFRHEKTERDNKEIAKRKYIDELNKFKEFSRKAELARKDEDRKLDEKIEELNKQKDEIIHQRRLKDAELKEKFKNEAQANIKEKLLEKEKCHEIELETEKSFINDNEKYKIDVQNERIAMLKEMAKHLYPGCIPRGMLKEKDIQYLEDPLKNFLLTKKSYPDENIN 491
The following BLAST results are available for this feature:
BLAST of SMED30032914 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 SMED30032914 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 SMED30032914 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 SMED30032914 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 SMED30032914 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 SMED30032914 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 SMED30032914 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 SMED30032914 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30032914 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 SMED30032914 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 SMED30032914 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 SMED30032914 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 SMED30032914 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 SMED30032914 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000075898.10.000e+0100.00SMESG000075898.1[more]
SMESG000075898.10.000e+0100.00SMESG000075898.1[more]
SMESG000075898.10.000e+0100.00SMESG000075898.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30032914 ID=SMED30032914|Name=SMED30032914|organism=Schmidtea mediterranea sexual|type=transcript|length=1767bp
GTGATAAATTCTATTGAAAGTGATCAATAATAAAATAATATAAATTTTTA
TTTTAATTTAAAAATATAATTTAAAATGGGAGGCTCAATGCAAGACATAA
TGGAAATGCACGCAAAAATTGCAAACGATCCGTGGGCTTACACGAGGAAA
ATCAGAGATGTCCAGGAACAAGACATGAAAGACTGTATTAGTCAACACCG
AAAAATGGAGAATTTAAGTTGGTATTCAAAGTCAAACGCAAACGCACAAA
TGGAAAGATTTCAATGGATGCAAAGAAAAGAATGTGAAATGTTGAGAAAC
ATGCAAGAACAAGAAACTGAACTGAAAGTTATTAAAAATAATGAACATCT
AGAAAACTTAATGGGAAAATATTTGGAAAAAGAAAAAAACGATTCCCTCC
ACCGGGATCGGTATTCTCAGTATCTGAGAGAAAATGACCCAGAACTAAGA
ATTTTAGCTTCCCAACTTAGAGAGGCCTATGTCGGTAAAATTCGTTTAGC
CCAAATTGATGAAAAAGAAAGGCTGAAAAATGAATTAGCGACGGCCGATA
TTCCTTATGTTAGGGCTATGGAAAAGCAATTTAAAGAGGACCAAGAACAA
GAGAAGTTGCAACAGTTTTTGGAAGATGAAAAGAAATATAATTTTCGAAA
ACAACTAGAGCAACAAATGAAAGATAAAGCTAAATTTGATGCTTTGAGTG
ACACTCGTGAGGAAGACCGACAAAGGATTGAATCGGTAATTCAGGAAAAC
TTACAGAAGATGCAAGAGGAAAAGGATAAAGAATTTTCAAAGAAAATGAC
ATTAAGAAAATCTTATATGGATGCTTTTAAGGACAGAGAAGAAGAGTTGC
AAAAGGAAAAAGAGAGACAAATAGCTGAAGAAAATAAATTTAAAGAATAC
AGAAAAGAAACTGAATACAAAAATGAAGGACAGATGCTGTTAAAAAAACT
TAGAGAAGAAAACCTAAATCTTATTCAAAAAAGACTTGGTGAGCTATTAG
CTCAAAAACAAAGAGATATAGATGAATTCGAAGCTGCTAGACAAGATGTG
GCGATTGCTCAAGCGGAAATGCAGGCATTCAGGCATGAAAAAACCGAAAG
AGATAATAAAGAAATCGCTAAAAGAAAATATATCGATGAATTGAATAAAT
TCAAGGAATTTTCAAGAAAAGCAGAATTAGCTCGGAAAGACGAAGATAGA
AAACTCGATGAAAAAATTGAAGAATTAAATAAACAGAAGGACGAAATAAT
TCATCAAAGACGGTTGAAAGATGCAGAATTGAAGGAAAAATTCAAAAATG
AAGCTCAAGCCAATATTAAAGAGAAGCTTTTGGAAAAAGAAAAATGTCAT
GAAATTGAATTGGAAACAGAAAAGTCTTTTATTAATGACAATGAAAAATA
TAAAATTGATGTTCAAAATGAGAGAATAGCAATGTTAAAAGAAATGGCAA
AGCATTTATATCCTGGGTGTATACCAAGAGGTATGCTGAAAGAAAAGGAC
ATTCAATACTTAGAGGATCCATTAAAAAACTTTTTATTAACTAAAAAGAG
TTATCCAGATGAAAATATAAATTAAACTGATATATTAAATGATTATAATG
AATGATTATATTAAAATGTTGCTAATAAAATAAGGAGTTGTTATTAGTTT
TTAACATCGTGTTTCCAGAGTTGTGATGAAGGGAGCTGGAGTTATTCAAA
CATCATTTTCAAGCAAACGTTTATTTGATGTTTTATTATAAAATAATTAG
TAAATGATATGATAAGC
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protein sequence of SMED30032914-orf-1

>SMED30032914-orf-1 ID=SMED30032914-orf-1|Name=SMED30032914-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=500bp
MGGSMQDIMEMHAKIANDPWAYTRKIRDVQEQDMKDCISQHRKMENLSWY
SKSNANAQMERFQWMQRKECEMLRNMQEQETELKVIKNNEHLENLMGKYL
EKEKNDSLHRDRYSQYLRENDPELRILASQLREAYVGKIRLAQIDEKERL
KNELATADIPYVRAMEKQFKEDQEQEKLQQFLEDEKKYNFRKQLEQQMKD
KAKFDALSDTREEDRQRIESVIQENLQKMQEEKDKEFSKKMTLRKSYMDA
FKDREEELQKEKERQIAEENKFKEYRKETEYKNEGQMLLKKLREENLNLI
QKRLGELLAQKQRDIDEFEAARQDVAIAQAEMQAFRHEKTERDNKEIAKR
KYIDELNKFKEFSRKAELARKDEDRKLDEKIEELNKQKDEIIHQRRLKDA
ELKEKFKNEAQANIKEKLLEKEKCHEIELETEKSFINDNEKYKIDVQNER
IAMLKEMAKHLYPGCIPRGMLKEKDIQYLEDPLKNFLLTKKSYPDENIN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000208testis
PLANA:0002089reproductive organ
Vocabulary: INTERPRO
TermDefinition
IPR026504MNS1
Vocabulary: molecular function
TermDefinition
GO:0003674molecular_function
Vocabulary: cellular component
TermDefinition
GO:0005634nucleus
GO:0031514motile cilium
Vocabulary: biological process
TermDefinition
GO:0044782cilium organization
GO:0051321meiotic cell cycle
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 244..278
NoneNo IPR availableCOILSCoilCoilcoord: 215..235
NoneNo IPR availableCOILSCoilCoilcoord: 370..401
NoneNo IPR availableCOILSCoilCoilcoord: 318..338
NoneNo IPR availablePFAMPF13868TPHcoord: 117..461
e-value: 8.5E-19
score: 67.3
IPR026504Meiosis-specific nuclear structural protein 1PANTHERPTHR19265MEIOSIS-SPECIFIC NUCLEAR STRUCTURAL PROTEIN 1coord: 22..482