SMED30033968

Overview
NameSMED30033968
Smed IDSMED30033968
Length (bp)734
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



SMED30033968

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parenchymaSMED30033968 dd_Smed_v4_24986_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
Homology
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BLAST of SMED30033968 vs. Planmine SMEST
Match: SMESG000040671.1 (SMESG000040671.1)

HSP 1 Score: 103.219 bits (256), Expect = 6.052e-28
Identity = 46/59 (77.97%), Postives = 54/59 (91.53%), Query Frame = 2 
Query:  386 YKKNISNADEKVIDGKWYIRNEDQLHSKKDLIEAWRQILEAPPFNDCMPIEDKQNMENA 562
            YKKNIS+A EKVIDGKW++RNEDQ+HS KDLIEAWR ILEAPPF+DC PIED++NM+ A
Sbjct:   51 YKKNISSAAEKVIDGKWFLRNEDQVHSNKDLIEAWRPILEAPPFSDCRPIEDQRNMDYA 109
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BLAST of SMED30033968 vs. Planmine SMEST
Match: SMESG000040682.1 (SMESG000040682.1)

HSP 1 Score: 102.834 bits (255), Expect = 1.116e-26
Identity = 47/66 (71.21%), Postives = 57/66 (86.36%), Query Frame = 2 
Query:  386 YKKNISNADEKVIDGKWYIRNEDQLHSKKDLIEAWRQILEAPPFNDCMPIEDKQNMENALMKISTA 583
            YKKNIS+A EKVIDGKW +RNE+Q+HS ++LIEAWR IL+APPFNDC PIED++N    LM+ISTA
Sbjct:   68 YKKNISSAAEKVIDGKWSLRNEEQMHSNEELIEAWRPILDAPPFNDCRPIEDQRNTGYDLMEISTA 133
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BLAST of SMED30033968 vs. Planmine SMEST
Match: SMESG000030694.1 (SMESG000030694.1)

HSP 1 Score: 68.1662 bits (165), Expect = 6.384e-13
Identity = 33/57 (57.89%), Postives = 44/57 (77.19%), Query Frame = 2 
Query:  383 WYKKNISNADEKVIDGKWYIRNEDQLHSKKDLIEAWRQILEAPPFNDCMPIEDKQNM 553
             YKKNIS+A EK I+GKW I+ E++ H+ KDLI+AW+ ILEAPPF+D    E+ Q+M
Sbjct:  274 LYKKNISSAAEKAINGKWSIKPEEEYHNNKDLIKAWKPILEAPPFSDSQ--ENIQSM 328
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BLAST of SMED30033968 vs. Planmine SMEST
Match: SMESG000011541.1 (SMESG000011541.1)

HSP 1 Score: 52.373 bits (124), Expect = 1.182e-7
Identity = 27/40 (67.50%), Postives = 34/40 (85.00%), Query Frame = 2 
Query:  614 KMAKIDIRKHSAEI*FSNAQVLLKFLNNDKGNELDIWSSW 733
            KMA IDIR H AEI +S+AQVL++F+ N+KG +LDIWSSW
Sbjct:   16 KMA-IDIRMHWAEIRYSDAQVLIEFIMNEKGIKLDIWSSW 54
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BLAST of SMED30033968 vs. Planmine SMEST
Match: SMESG000001175.1 (SMESG000001175.1)

HSP 1 Score: 49.2914 bits (116), Expect = 1.120e-6
Identity = 24/41 (58.54%), Postives = 31/41 (75.61%), Query Frame = 2 
Query:  611 IKMAKIDIRKHSAEI*FSNAQVLLKFLNNDKGNELDIWSSW 733
            + M  +DIR H AEI FS++QVL+ F+ N KG +LDIWSSW
Sbjct:    5 MAMKNMDIRMHWAEIRFSDSQVLIDFIINKKGIKLDIWSSW 45
The following BLAST results are available for this feature:
BLAST of SMED30033968 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 SMED30033968 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 SMED30033968 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 SMED30033968 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 SMED30033968 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 SMED30033968 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 SMED30033968 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 SMED30033968 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 SMED30033968 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 SMED30033968 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 SMED30033968 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 SMED30033968 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 SMED30033968 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 SMED30033968 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000040671.16.052e-2877.97SMESG000040671.1[more]
SMESG000040682.11.116e-2671.21SMESG000040682.1[more]
SMESG000030694.16.384e-1357.89SMESG000030694.1[more]
SMESG000011541.11.182e-767.50SMESG000011541.1[more]
SMESG000001175.11.120e-658.54SMESG000001175.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30033968 ID=SMED30033968|Name=SMED30033968|organism=Schmidtea mediterranea sexual|type=transcript|length=734bp
TTCATCAGTAATTTAAATTTCCCCTCCTTTCTTGTAAGGTAAAGGGTATG
GAAATCCAGAGAATATCCTGTGGGCGATATCCACGGAAAAAGCACCTCGG
CTCTGAAGGACTAACTATCCTAAAGCGCTTAAATCTATGAACTGGTTACA
ACCAAAAAAACTACTAAAGAGTCAGGTGCCACTGCGCCTGCACCAGTTTC
TCTAGAAGCTACAGATGAGGTACTCCAGTTACGAAGTGTTCCTGAAGTCA
ATCTACCTACGAATTCTATGGACGGAGGACAGACATCATCACCAACACAC
CGATGCAAAAACTGCGATAGAAAATCCAGAACTAAAGCTGGACTGCAGCA
ACATCGACGAAAGGCTCATACCAACGAATTTATGGTACAAAAAGAACATC
TCAAATGCAGATGAGAAAGTAATCGATGGGAAATGGTATATAAGAAACGA
AGATCAATTGCATTCAAAAAAAGATCTCATTGAAGCATGGAGACAGATAC
TGGAAGCCCCTCCATTTAACGACTGTATGCCTATTGAGGATAAACAAAAT
ATGGAGAACGCTTTAATGAAGATAAGCACAGCCACTTAAAAATGCTCCAA
AAAATTTTGAATAAAGATGGCGAAAATCGACATTCGAAAGCACTCGGCGG
AAATCTGATTTTCTAATGCCCAAGTGCTTCTCAAATTTTTGAATAATGAT
AAAGGGAATGAACTAGACATATGGAGCAGCTGGA
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protein sequence of SMED30033968-orf-1

>SMED30033968-orf-1 ID=SMED30033968-orf-1|Name=SMED30033968-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=125bp
MRYSSYEVFLKSIYLRILWTEDRHHHQHTDAKTAIENPELKLDCSNIDER
LIPTNLWYKKNISNADEKVIDGKWYIRNEDQLHSKKDLIEAWRQILEAPP
FNDCMPIEDKQNMENALMKISTAT*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: INTERPRO
TermDefinition
IPR007087Znf_C2H2
Vocabulary: molecular function
TermDefinition
GO:0046872metal ion binding
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..18
score: 0.522