SMED30015625

Overview
NameSMED30015625
Smed IDSMED30015625
Length (bp)993
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



SMED30015625

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
Smed sexual biotypeSMED30015625SMESG000017189.1 Contig4951GPL15192PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
testisSMED30015625SMESG000017189.1 HO005874.1ncbi_smed_estsPMID:22074376
Chong et al., 2011		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
testisSMED30015625SMESG000017189.1 DN312402.1ncbi_smed_estsPMID:22074376
Chong et al., 2011		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Alignments
SMED30015625 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.003725:5524..10191 -4854
Homology
[Close]
BLAST of SMED30015625 vs. Planmine SMEST
Match: SMESG000017189.1 (SMESG000017189.1)

HSP 1 Score: 461.455 bits (1186), Expect = 5.683e-166
Identity = 226/226 (100.00%), Postives = 226/226 (100.00%), Query Frame = 3 
Query:  204 MKGSRVKLLVFYSLNFLLATNTFYMTIQAVMGLSFSYRFRLLIGEQPMELETFAAASGIIILFISVVMLLIVIKKMKRIKEWYIPSSQWICCMELVYLLFFLSLEMNTYRYLRDNMEFSFSIYYSDNDYKGLIDSLQLENECCGGTNITNYYQDLGKDGFEIAQSCCKTNGEVCRPNSTSFNQETCLDVIYEKVYTVYNHILVPVALLILLQYASAFLLNLSTTDE 881
            MKGSRVKLLVFYSLNFLLATNTFYMTIQAVMGLSFSYRFRLLIGEQPMELETFAAASGIIILFISVVMLLIVIKKMKRIKEWYIPSSQWICCMELVYLLFFLSLEMNTYRYLRDNMEFSFSIYYSDNDYKGLIDSLQLENECCGGTNITNYYQDLGKDGFEIAQSCCKTNGEVCRPNSTSFNQETCLDVIYEKVYTVYNHILVPVALLILLQYASAFLLNLSTTDE
Sbjct:    1 MKGSRVKLLVFYSLNFLLATNTFYMTIQAVMGLSFSYRFRLLIGEQPMELETFAAASGIIILFISVVMLLIVIKKMKRIKEWYIPSSQWICCMELVYLLFFLSLEMNTYRYLRDNMEFSFSIYYSDNDYKGLIDSLQLENECCGGTNITNYYQDLGKDGFEIAQSCCKTNGEVCRPNSTSFNQETCLDVIYEKVYTVYNHILVPVALLILLQYASAFLLNLSTTDE 226
[Close]
BLAST of SMED30015625 vs. Planmine SMEST
Match: SMESG000017189.1 (SMESG000017189.1)

HSP 1 Score: 415.231 bits (1066), Expect = 4.279e-148
Identity = 202/202 (100.00%), Postives = 202/202 (100.00%), Query Frame = 3 
Query:  276 MTIQAVMGLSFSYRFRLLIGEQPMELETFAAASGIIILFISVVMLLIVIKKMKRIKEWYIPSSQWICCMELVYLLFFLSLEMNTYRYLRDNMEFSFSIYYSDNDYKGLIDSLQLENECCGGTNITNYYQDLGKDGFEIAQSCCKTNGEVCRPNSTSFNQETCLDVIYEKVYTVYNHILVPVALLILLQYASAFLLNLSTTDE 881
            MTIQAVMGLSFSYRFRLLIGEQPMELETFAAASGIIILFISVVMLLIVIKKMKRIKEWYIPSSQWICCMELVYLLFFLSLEMNTYRYLRDNMEFSFSIYYSDNDYKGLIDSLQLENECCGGTNITNYYQDLGKDGFEIAQSCCKTNGEVCRPNSTSFNQETCLDVIYEKVYTVYNHILVPVALLILLQYASAFLLNLSTTDE
Sbjct:    1 MTIQAVMGLSFSYRFRLLIGEQPMELETFAAASGIIILFISVVMLLIVIKKMKRIKEWYIPSSQWICCMELVYLLFFLSLEMNTYRYLRDNMEFSFSIYYSDNDYKGLIDSLQLENECCGGTNITNYYQDLGKDGFEIAQSCCKTNGEVCRPNSTSFNQETCLDVIYEKVYTVYNHILVPVALLILLQYASAFLLNLSTTDE 202
The following BLAST results are available for this feature:
BLAST of SMED30015625 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 SMED30015625 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 SMED30015625 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 SMED30015625 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 SMED30015625 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 SMED30015625 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 SMED30015625 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 SMED30015625 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 SMED30015625 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 SMED30015625 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 SMED30015625 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 SMED30015625 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 SMED30015625 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 SMED30015625 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000017189.15.683e-166100.00SMESG000017189.1[more]
SMESG000017189.14.279e-148100.00SMESG000017189.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30015625 ID=SMED30015625|Name=SMED30015625|organism=Schmidtea mediterranea sexual|type=transcript|length=993bp
ACAAAACACCGATTAGTTCAAATACGACTTGAAAAGGTTTCCGTTTACCG
TAAACGCTAAATTCCAGAAGTAGAAACAGCCAAAGCTTTAACGGGACAGT
TTTTCTATTTCCCCAAAAGGTTAAAGGTAAATATTTATATAATATTGATT
GCGATAGATTTCTTATAACAAATATTTACGGATTAAAATGGACACCTGAC
AGGATGAAAGGGAGCCGCGTTAAGTTATTGGTGTTTTACTCTTTGAACTT
TCTGCTAGCGACCAACACATTCTATATGACGATTCAAGCCGTCATGGGGT
TATCCTTCAGCTACAGATTTCGTCTGCTGATAGGAGAACAGCCGATGGAA
TTGGAAACCTTTGCGGCGGCTAGCGGGATTATTATTCTTTTTATTTCGGT
TGTAATGTTACTAATTGTAATCAAAAAGATGAAGCGGATAAAGGAATGGT
ACATCCCATCAAGTCAATGGATATGTTGCATGGAACTGGTATATTTGCTA
TTCTTTCTCTCTCTGGAAATGAACACATACAGATACTTGAGAGATAATAT
GGAGTTCAGTTTTTCTATATATTACTCCGACAACGACTACAAGGGTTTGA
TAGATTCACTTCAATTAGAAAATGAATGTTGCGGTGGGACAAATATTACA
AACTATTATCAAGATTTGGGCAAAGATGGATTCGAAATTGCACAGAGTTG
CTGCAAAACGAATGGAGAGGTTTGCCGTCCAAACTCGACGTCGTTTAATC
AAGAAACCTGCCTTGATGTTATTTATGAGAAAGTTTACACGGTCTATAAC
CATATCTTAGTGCCAGTGGCACTTTTAATTTTACTCCAATATGCCTCGGC
TTTTCTTTTAAATTTATCTACAACCGATGAATAGTTATGAATAATGTTCA
TAGATAAATTATGGGCCCTAATAAAATTGATTTTCATTCTAAAAATAGTT
CAATTTGATTGTAGTAGGTCGGAGGCGTTGAACACCTAAAAGA
back to top

protein sequence of SMED30015625-orf-1

>SMED30015625-orf-1 ID=SMED30015625-orf-1|Name=SMED30015625-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=227bp
MKGSRVKLLVFYSLNFLLATNTFYMTIQAVMGLSFSYRFRLLIGEQPMEL
ETFAAASGIIILFISVVMLLIVIKKMKRIKEWYIPSSQWICCMELVYLLF
FLSLEMNTYRYLRDNMEFSFSIYYSDNDYKGLIDSLQLENECCGGTNITN
YYQDLGKDGFEIAQSCCKTNGEVCRPNSTSFNQETCLDVIYEKVYTVYNH
ILVPVALLILLQYASAFLLNLSTTDE*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000208testis
Vocabulary: INTERPRO
TermDefinition
IPR018499Tetraspanin/Peripherin
IPR008952Tetraspanin_EC2_sf
Vocabulary: cellular component
TermDefinition
GO:0016021integral component of membrane
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR008952Tetraspanin, EC2 domain superfamilyGENE3DG3DSA:1.10.1450.10coord: 106..192
e-value: 3.4E-7
score: 32.0
IPR008952Tetraspanin, EC2 domain superfamilySUPERFAMILYSSF48652Tetraspanincoord: 111..192
IPR018499Tetraspanin/PeripherinPFAMPF00335Tetraspanincoord: 40..216
e-value: 2.1E-12
score: 47.3
NoneNo IPR availableTMHMMTMhelixcoord: 51..73
NoneNo IPR availableTMHMMTMhelixcoord: 9..31
NoneNo IPR availableTMHMMTMhelixcoord: 197..219