SMED30006883

Overview
NameSMED30006883
Smed IDSMED30006883
Length (bp)759
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



SMED30006883

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



PAGE Curations: 15

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30006883SMESG000063750.1 SmedASXL_012359SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
head regionSMED30006883SMESG000063750.1 SmedASXL_006037SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30006883SMESG000063750.1 dd_Smed_v4_17076_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30006883SMESG000063750.1 dd_Smed_v4_17076_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30006883SMESG000063750.1 dd_Smed_v4_17076_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
non-ciliated neuronSMED30006883SMESG000063750.1 dd_Smed_v4_17076_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30006883SMESG000063795.1 SMESG000063750.1 Contig55890newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30006883SMESG000063795.1 SMESG000063750.1 Contig55890uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30006883SMESG000063750.1 Contig45084newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30006883SMESG000063750.1 Contig45084uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30006883SMESG000063750.1 dd_Smed_v6_17076_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
oocyteSMED30006883SMESG000063750.1 Contig45084newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
oocyteSMED30006883SMESG000063750.1 Contig45084uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30006883SMESG000063750.1 Contig45084newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30006883SMESG000063750.1 Contig45084uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30006883 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004129:20911..27810 -3698
Homology
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BLAST of SMED30006883 vs. TrEMBL
Match: K1RVV6 (Uncharacterized protein OS=Crassostrea gigas OX=29159 GN=CGI_10026729 PE=4 SV=1)

HSP 1 Score: 92.0485 bits (227), Expect = 1.885e-17
Identity = 39/79 (49.37%), Postives = 59/79 (74.68%), Query Frame = 2 
Query:  482 IKREESIIYQTVHPDQDKEISIDNLESALQVVNRQLLSKNEFNYIYHILKLPHHPRINMQTFSCIAALSEKVTHLDASI 718
             +R++S +Y+T+HPD D E++ + LE ALQ+VN  LL++NEF+Y+YHIL L    ++N + F  IAALSE++TH+D  I
Sbjct:  483 FRRQQSFLYKTLHPDPDVEMNREELEGALQIVNHNLLTENEFSYMYHILNLTGRRKVNFKLFCVIAALSERITHMDPVI 561
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BLAST of SMED30006883 vs. TrEMBL
Match: A0A1I8GZL3 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 87.4261 bits (215), Expect = 7.308e-17
Identity = 46/98 (46.94%), Postives = 64/98 (65.31%), Query Frame = 2 
Query:  425 ELLKSNQRKAAETNPVLMSIKREESIIYQTVHPDQDKEISIDNLESALQVVNRQLLSKNEFNYIYHILKLPHHPRINMQTFSCIAALSEKVTHLDASI 718
            E L+ ++R+AA     L    RE+S++YQ +HP  D E++ID +E ALQ +N  L++K E  Y+YHIL LP   R+N + FS IAALSEKV  L+  I
Sbjct:   49 EQLEPSRRQAAGGADFL----REQSLLYQKLHPAIDLELNIDLVEEALQDINGHLITKKEMQYVYHILNLPARTRVNFRLFSVIAALSEKVVQLEPII 142
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BLAST of SMED30006883 vs. TrEMBL
Match: V4BAS6 (Uncharacterized protein OS=Lottia gigantea OX=225164 GN=LOTGIDRAFT_235648 PE=4 SV=1)

HSP 1 Score: 88.1965 bits (217), Expect = 4.989e-16
Identity = 42/91 (46.15%), Postives = 60/91 (65.93%), Query Frame = 2 
Query:  446 RKAAETNPVLMSIKREESIIYQTVHPDQDKEISIDNLESALQVVNRQLLSKNEFNYIYHILKLPHHPRINMQTFSCIAALSEKVTHLDASI 718
            R+  ET+P     +R++S++Y T+ P  D EI +DNL  +LQ VN  LL+  E +++YH+L LP   +IN + FS +AALSEKVT LD  I
Sbjct: 1025 RQFTETHPA--DFRRQQSVLYNTLRPTPDYEIKLDNLRESLQQVNNHLLTDRECDFLYHVLDLPGREKINFRLFSVVAALSEKVTQLDPMI 1113
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BLAST of SMED30006883 vs. TrEMBL
Match: A0A2R2MTE6 (uncharacterized protein LOC106167849 isoform X4 OS=Lingula unguis OX=7574 GN=LOC106167849 PE=4 SV=1)

HSP 1 Score: 87.0409 bits (214), Expect = 1.141e-15
Identity = 50/151 (33.11%), Postives = 90/151 (59.60%), Query Frame = 2 
Query:  260 ISNKEIVKKIDSLIRKKISKMNEFLPKWAELNQIRKTLNQITVKILNLKIKRQKLELLKSNQR-KAAETNPVLMSIKREESIIYQTVHPDQDKEISIDNLESALQVVNRQLLSKNEFNYIYHILKLPHHPRINMQTFSCIAALSEKVTHLD 709
            ++  EI+ ++DS +   IS M E     A+L+ I K + ++  ++     +++++E+   +   K    N      +R++S +YQ ++P  D EI+++ +E+ALQ +N  LL+  EF ++YH+L LP   R+N++ FS +AALSEKV  LD
Sbjct:  970 LTADEIIGRLDSKMWSMISNMPEVTRTDAQLSIIEKKMAELEARMNITDEEKREMEIYTRDLFLKEQIENERTREFRRKQSPLYQQINPVPDVEINVEEVEAALQRINNNLLTDREFQFVYHVLDLPGRHRLNLKLFSAVAALSEKVKQLD 1120
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BLAST of SMED30006883 vs. TrEMBL
Match: A0A2R2MSZ1 (uncharacterized protein LOC106167849 isoform X1 OS=Lingula unguis OX=7574 GN=LOC106167849 PE=4 SV=1)

HSP 1 Score: 87.0409 bits (214), Expect = 1.252e-15
Identity = 50/151 (33.11%), Postives = 90/151 (59.60%), Query Frame = 2 
Query:  260 ISNKEIVKKIDSLIRKKISKMNEFLPKWAELNQIRKTLNQITVKILNLKIKRQKLELLKSNQR-KAAETNPVLMSIKREESIIYQTVHPDQDKEISIDNLESALQVVNRQLLSKNEFNYIYHILKLPHHPRINMQTFSCIAALSEKVTHLD 709
            ++  EI+ ++DS +   IS M E     A+L+ I K + ++  ++     +++++E+   +   K    N      +R++S +YQ ++P  D EI+++ +E+ALQ +N  LL+  EF ++YH+L LP   R+N++ FS +AALSEKV  LD
Sbjct: 1334 LTADEIIGRLDSKMWSMISNMPEVTRTDAQLSIIEKKMAELEARMNITDEEKREMEIYTRDLFLKEQIENERTREFRRKQSPLYQQINPVPDVEINVEEVEAALQRINNNLLTDREFQFVYHVLDLPGRHRLNLKLFSAVAALSEKVKQLD 1484
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BLAST of SMED30006883 vs. Planmine SMEST
Match: SMESG000063750.1 (SMESG000063750.1)

HSP 1 Score: 357.066 bits (915), Expect = 2.790e-116
Identity = 180/181 (99.45%), Postives = 181/181 (100.00%), Query Frame = 2 
Query:  167 DSLENEIAMKIKEKYPKVVEKLKYSKSEESAISNKEIVKKIDSLIRKKISKMNEFLPKWAELNQIRKTLNQITVKILNLKIKRQKLELLKSNQRKAAETNPVLMSIKREESIIYQTVHPDQDKEISIDNLESALQVVNRQLLSKNEFNYIYHILKLPHHPRINMQTFSCIAALSEKVTHLD 709
            DSLENEIAMKIKEKYPKVVEKLKYSKSEESAISNKEIVKKIDSLIRKKISKMNEFLPKWAELNQIRKTLNQITVKILNLKIKRQKLELLKSNQRKAAETNPVLMSIKREESIIYQTVHPDQDKEISIDNLESALQVVNRQLLSKNEFNYIYHILKLPHHPRINMQTFSCIAALSEKVTHL+
Sbjct:  763 DSLENEIAMKIKEKYPKVVEKLKYSKSEESAISNKEIVKKIDSLIRKKISKMNEFLPKWAELNQIRKTLNQITVKILNLKIKRQKLELLKSNQRKAAETNPVLMSIKREESIIYQTVHPDQDKEISIDNLESALQVVNRQLLSKNEFNYIYHILKLPHHPRINMQTFSCIAALSEKVTHLE 943
The following BLAST results are available for this feature:
BLAST of SMED30006883 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 SMED30006883 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 SMED30006883 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 SMED30006883 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 SMED30006883 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 SMED30006883 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 SMED30006883 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 SMED30006883 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
K1RVV61.885e-1749.37Uncharacterized protein OS=Crassostrea gigas OX=29... [more]
A0A1I8GZL37.308e-1746.94Uncharacterized protein OS=Macrostomum lignano OX=... [more]
V4BAS64.989e-1646.15Uncharacterized protein OS=Lottia gigantea OX=2251... [more]
A0A2R2MTE61.141e-1533.11uncharacterized protein LOC106167849 isoform X4 OS... [more]
A0A2R2MSZ11.252e-1533.11uncharacterized protein LOC106167849 isoform X1 OS... [more]
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BLAST of SMED30006883 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 SMED30006883 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 SMED30006883 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 SMED30006883 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 SMED30006883 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 SMED30006883 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000063750.12.790e-11699.45SMESG000063750.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30006883 ID=SMED30006883|Name=SMED30006883|organism=Schmidtea mediterranea sexual|type=transcript|length=759bp
TGGAAAGTTCTCAAAAATAATAAAATGTCAAATATAATATAAAATATTGA
TCGATAGTCTATAAAAAGAAGAAGTGAAAATAAAGGGAATTTCAAATAGT
GATAATGTCTTAAAATTGTGGAAATATGGAACATTTCCGCAGCTATGTCA
AACCTAAATTAATTTAGATTCGCTCGAAAATGAAATAGCGATGAAAATTA
AAGAAAAATACCCAAAGGTTGTGGAAAAATTGAAGTACTCAAAATCGGAA
GAAAGTGCGATATCTAATAAGGAAATTGTAAAAAAGATTGATTCGTTAAT
AAGAAAAAAAATATCAAAAATGAATGAATTTTTACCAAAATGGGCAGAAT
TGAATCAAATCAGAAAAACTCTCAATCAGATTACAGTAAAAATATTAAAT
TTAAAAATAAAAAGACAAAAATTAGAATTGCTAAAATCGAATCAAAGAAA
AGCAGCGGAAACCAATCCAGTTTTGATGAGCATAAAGCGAGAAGAGTCAA
TCATTTATCAAACGGTTCATCCGGATCAGGATAAAGAAATCAGTATTGAT
AATCTAGAATCGGCTCTTCAAGTTGTCAATCGCCAATTATTATCAAAAAA
TGAATTTAATTACATTTACCATATCCTGAAATTACCTCATCATCCAAGAA
TAAATATGCAGACCTTCAGTTGTATTGCAGCTTTATCAGAAAAAGTCACA
CATTTAGATGCCTCAATAGCCACATCAAGGTATTCGATTGGAACAAAGTA
GAGAGCGAC
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protein sequence of SMED30006883-orf-1

>SMED30006883-orf-1 ID=SMED30006883-orf-1|Name=SMED30006883-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=187bp
MKIKEKYPKVVEKLKYSKSEESAISNKEIVKKIDSLIRKKISKMNEFLPK
WAELNQIRKTLNQITVKILNLKIKRQKLELLKSNQRKAAETNPVLMSIKR
EESIIYQTVHPDQDKEISIDNLESALQVVNRQLLSKNEFNYIYHILKLPH
HPRINMQTFSCIAALSEKVTHLDASIATSRYSIGTK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000074oocyte
PLANA:0000099neuron
PLANA:0000231vitelline gland
PLANA:0000418head
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availablePANTHERPTHR35538FAMILY NOT NAMEDcoord: 99..174
NoneNo IPR availablePANTHERPTHR35538:SF3coord: 99..174