SMED30000230

Overview
NameSMED30000230
Smed IDSMED30000230
Length (bp)317
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




SMED30000230

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
headSMED30000230SMESG000051919.1 SmedASXL_001644SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
neuronSMED30000230SMESG000051919.1 dd_Smed_v4_17743_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
headSMED30000230SMESG000051919.1 dd_Smed_v6_17743_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30000230 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.023130:2422..2783 -1570
Homology
BLAST of SMED30000230 vs. Planmine SMEST
Match: SMESG000051919.1 (SMESG000051919.1)

HSP 1 Score: 221.09 bits (562), Expect = 1.300e-68
Identity = 105/105 (100.00%), Postives = 105/105 (100.00%), Query Frame = -2
Query:    2 KKGQDVFLECPVTYPNGAKSIDVRWKRKQWKSTIYAHSQESLDKEYVAPFYEGRLLRATGATLKLRKITAEDQDLFTCEVSFNFEKPVSLNKFPEVQQSSIYVIV 316
            KKGQDVFLECPVTYPNGAKSIDVRWKRKQWKSTIYAHSQESLDKEYVAPFYEGRLLRATGATLKLRKITAEDQDLFTCEVSFNFEKPVSLNKFPEVQQSSIYVIV
Sbjct:   28 KKGQDVFLECPVTYPNGAKSIDVRWKRKQWKSTIYAHSQESLDKEYVAPFYEGRLLRATGATLKLRKITAEDQDLFTCEVSFNFEKPVSLNKFPEVQQSSIYVIV 132          
The following BLAST results are available for this feature:
BLAST of SMED30000230 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 SMED30000230 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 SMED30000230 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 SMED30000230 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 SMED30000230 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 SMED30000230 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 SMED30000230 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 SMED30000230 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 SMED30000230 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 SMED30000230 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 SMED30000230 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 SMED30000230 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 SMED30000230 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 SMED30000230 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000051919.11.300e-68100.00SMESG000051919.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30000230 ID=SMED30000230|Name=SMED30000230|organism=Schmidtea mediterranea sexual|type=transcript|length=317bp
TGACGATTACGTAAATTGATGACTGTTGAACTTCGGGAAATTTATTCAAT
GAGACGGGTTTCTCGAAGTTGAAGGACACTTCACAAGTGAAAAGATCTTG
ATCTTCCGCTGTGATCTTTCGTAGTTTCAAAGTCGCTCCGGTTGCTCGCA
GCAGTCGGCCTTCATAAAATGGAGCGACATATTCTTTATCAAGAGATTCC
TGAGAATGAGCGTAAATTGTGCTTTTCCATTGTTTTCGTTTCCACCTCAC
ATCGATACTTTTAGCACCGTTTGGATACGTGACAGGACATTCAAGAAACA
CATCTTGACCCTTTTTC
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protein sequence of SMED30000230-orf-1

>SMED30000230-orf-1 ID=SMED30000230-orf-1|Name=SMED30000230-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=105bp
KKGQDVFLECPVTYPNGAKSIDVRWKRKQWKSTIYAHSQESLDKEYVAPF
YEGRLLRATGATLKLRKITAEDQDLFTCEVSFNFEKPVSLNKFPEVQQSS
IYVIV
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR036179Ig-like_dom_sf
IPR013783Ig-like_fold
IPR007110Ig-like_dom
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR013783Immunoglobulin-like foldGENE3DG3DSA:2.60.40.10coord: 1..104
e-value: 3.8E-13
score: 51.3
IPR007110Immunoglobulin-like domainPROSITEPS50835IG_LIKEcoord: 1..89
score: 10.263
IPR036179Immunoglobulin-like domain superfamilySUPERFAMILYSSF48726Immunoglobulincoord: 2..81