SMED30027198

Overview
NameSMED30027198
Smed IDSMED30027198
Length (bp)1458
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



SMED30027198

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
testisSMED30027198SMESG000029885.1 GCR125smed_ncbi_20200123PMID:27163480
Saberi et al., 2016		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Alignments
SMED30027198 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001073:35112..36616 +6017
Homology
[Close]
BLAST of SMED30027198 vs. TrEMBL
Match: A0A193KUD2 (GCR125 OS=Schmidtea mediterranea OX=79327 GN=gcr125 PE=2 SV=1)

HSP 1 Score: 677.552 bits (1747), Expect = 0.000e+0
Identity = 365/367 (99.46%), Postives = 367/367 (100.00%), Query Frame = -2 
Query:  330 MNDTMEYSSWINMKLYXXXXXXXXXXXXXXXGNSFVLYILLYKHIRFPPFCFWLRCTCIGNMVIVIQQGLFLILYLCFYPKQVIGIDLRIFDSIICKFFMFVHEFSYSWTTGSLATLYLVKIIIIVTQSNEIDNSKNNFKICLILSFLMLTYSMLWPIIYDVRLKNGLNICTPKSDFLFLLEGQARFVYQSFVIVGIITGANCYLVYFLCHTSKVVQKIQRSDSFSIGSKESRLTAKLAKINKIIYFIIFVNFLWIVCNVPFMSYSFIVNMYDEKNXXXXXXXXXYMPLYYGFMVSSYFYNCLSWIIYIYTCSSLRRHMRITTYGFFVRFGLYEAYFIEKIKSEIFNNSSEIEKQTNSSDVTVEVGK 1430
            MNDTMEYSSWINMKLYFFIWFIP+ITTIGFFGNSFVLYILLYKHIRFPPFCFWLRCTCIGNMVIVIQQG+FLILYLCFYPKQVIGIDLRIFDSIICKFFMFVHEFSYSWTTGSLATLYLVKIIIIVTQSNEIDNSKNNFKICLILSFLMLTYSMLWPIIYDVRLKNGLNICTPKSDFLFLLEGQARFVYQSFVIVGIITGANCYLVYFLCHTSKVVQKIQRSDSFSIGSKESRLTAKLAKINKIIYFIIFVNFLWIVCNVPFMSYSFIVNMYDEKNSFYYFFSSFYMPLYYGFMVSSYFYNCLSWIIYIYTCSSLRRHMRITTYGFFVRFGLYEAYFIEKIKSEIFNNSSEIEKQTNSSDVTVEVGK
Sbjct:    1 MNDTMEYSSWINMKLYFFIWFIPLITTIGFFGNSFVLYILLYKHIRFPPFCFWLRCTCIGNMVIVIQQGVFLILYLCFYPKQVIGIDLRIFDSIICKFFMFVHEFSYSWTTGSLATLYLVKIIIIVTQSNEIDNSKNNFKICLILSFLMLTYSMLWPIIYDVRLKNGLNICTPKSDFLFLLEGQARFVYQSFVIVGIITGANCYLVYFLCHTSKVVQKIQRSDSFSIGSKESRLTAKLAKINKIIYFIIFVNFLWIVCNVPFMSYSFIVNMYDEKNSFYYFFSSFYMPLYYGFMVSSYFYNCLSWIIYIYTCSSLRRHMRITTYGFFVRFGLYEAYFIEKIKSEIFNNSSEIEKQTNSSDVTVEVGK 367
[Close]
BLAST of SMED30027198 vs. Planmine SMEST
Match: SMESG000029885.1 (SMESG000029885.1)

HSP 1 Score: 590.112 bits (1520), Expect = 0.000e+0
Identity = 306/306 (100.00%), Postives = 306/306 (100.00%), Query Frame = -2 
Query:  330 MVIVIQQGLFLILYLCFYPKQVIGIDLRIFDSIICKFFMFVHEFSYSWTTGSLATLYLVKIIIIVTQSNEIDNSKNNFKICLILSFLMLTYSMLWPIIYDVRLKNGLNICTPKSDFLFLLEGQARFVYQSFVIVGIITGANCYLVYFLCHTSKVVQKIQRSDSFSIGSKESRLTAKLAKINKIIYFIIFVNFLWIVCNVPFMSYSFIVNMYDEKNXXXXXXXXXYMPLYYGFMVSSYFYNCLSWIIYIYTCSSLRRHMRITTYGFFVRFGLYEAYFIEKIKSEIFNNSSEIEKQTNSSDVTVEVGK 1247
            MVIVIQQGLFLILYLCFYPKQVIGIDLRIFDSIICKFFMFVHEFSYSWTTGSLATLYLVKIIIIVTQSNEIDNSKNNFKICLILSFLMLTYSMLWPIIYDVRLKNGLNICTPKSDFLFLLEGQARFVYQSFVIVGIITGANCYLVYFLCHTSKVVQKIQRSDSFSIGSKESRLTAKLAKINKIIYFIIFVNFLWIVCNVPFMSYSFIVNMYDEKNSFYYFFSSFYMPLYYGFMVSSYFYNCLSWIIYIYTCSSLRRHMRITTYGFFVRFGLYEAYFIEKIKSEIFNNSSEIEKQTNSSDVTVEVGK
Sbjct:    1 MVIVIQQGLFLILYLCFYPKQVIGIDLRIFDSIICKFFMFVHEFSYSWTTGSLATLYLVKIIIIVTQSNEIDNSKNNFKICLILSFLMLTYSMLWPIIYDVRLKNGLNICTPKSDFLFLLEGQARFVYQSFVIVGIITGANCYLVYFLCHTSKVVQKIQRSDSFSIGSKESRLTAKLAKINKIIYFIIFVNFLWIVCNVPFMSYSFIVNMYDEKNSFYYFFSSFYMPLYYGFMVSSYFYNCLSWIIYIYTCSSLRRHMRITTYGFFVRFGLYEAYFIEKIKSEIFNNSSEIEKQTNSSDVTVEVGK 306
The following BLAST results are available for this feature:
BLAST of SMED30027198 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 SMED30027198 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 SMED30027198 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 SMED30027198 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 SMED30027198 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 SMED30027198 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 SMED30027198 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 SMED30027198 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A193KUD20.000e+099.46GCR125 OS=Schmidtea mediterranea OX=79327 GN=gcr12... [more]
back to top
BLAST of SMED30027198 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 SMED30027198 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 SMED30027198 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 SMED30027198 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 SMED30027198 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 SMED30027198 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000029885.10.000e+0100.00SMESG000029885.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30027198 ID=SMED30027198|Name=SMED30027198|organism=Schmidtea mediterranea sexual|type=transcript|length=1458bp
GAAACTAAGTTTTGCATCAAGGTCATTACATTTTATTTTAGATTAACATT
TGATATTTTAATTAACTTAATTAAAATTTGATTAATTAACTCAACTTTAA
TTGATTAATAATAAATTAAATAACAACAAACTGTGGAAATTCGACAATAA
TACTGATTTAGTTAATTTTTATTTTTCCCTTTGGAAGCGTAGGTTGACTA
AAGTCCCTCAGAATCAATATTATGTTTTGTTGAACGCGTCTAAAGTATTA
AAAAAATATATTAATTTAATTAATTAAAATTAAATAAAATTAAATCTCAA
TATCATTCGTACAACTTTCTGTAAGGCTACTTTCCAACTTCAACTGTAAC
GTCGGAACTGTTGGTTTGCTTTTCAATTTCTGATGAATTATTGAAAATTT
CCGACTTTATTTTCTCAATAAAATAAGCTTCATACAAACCGAATCTGACA
AAAAACCCATAAGTAGTGATCCTCATATGACGCCGGAGACTAGAACATGT
GTAAATGTAAATGATCCACGACAGGCAATTATAAAAGTAGCTAGATACCA
TAAATCCGTAGTAAAGAGGCATATAGAAACTGCTAAAAAAATAGTAAAAT
GAATTTTTCTCATCATACATATTGACTATGAAGCTGTAGCTCATGAAGGG
CACATTGCAAACTATCCAGAGGAAGTTGACGAATATTATAAAATATATAA
TTTTATTAATTTTTGCCAATTTAGCCGTTAAACGAGATTCTTTAGATCCA
ATTGAGAAGCTATCGCTTCTTTGAATCTTTTGAACGACCTTTGACGTGTG
GCATAGGAAATATACCAAATAACAATTGGCCCCAGTTATTATTCCGACGA
TGACAAACGACTGATAGACAAATCTCGCCTGGCCTTCCAATAAGAATAGA
AAATCGCTTTTCGGTGTACAAATGTTAAGGCCATTCTTCAATCTGACATC
GTAAATTATTGGCCACAACATTGAGTAGGTCAGCATTAAAAATGACAGAA
TTAGACAAATTTTAAAATTGTTTTTAGAATTATCAATTTCGTTTGACTGG
GTGACAATAATGATAATCTTAACCAGGTACAAAGTCGCCAATGATCCGGT
GGTCCACGAGTACGAAAATTCGTGGACAAACATAAAGAACTTGCAAATGA
TGGAGTCAAATATCCGTAAGTCGATGCCAATGACCTGTTTGGGATAAAAG
CATAGGTATAAGATGAGAAATAGCCCTTGTTGAATGACAATTACCATATT
CCCAATGCAAGTGCATCTTAACCAGAAACAAAATGGAGGGAATCTGATAT
GTTTATAAAGTAAAATATATAATACAAATGAATTTCCGAAAAATCCTATT
GTTGTGATTATAGGAATAAACCAAATGAAAAAATATAATTTCATGTTTAT
CCATGAGGAATATTCCATAGTATCATTCATATTTTATTTATATCATTATT
AAATTGAT
back to top

protein sequence of SMED30027198-orf-1

>SMED30027198-orf-1 ID=SMED30027198-orf-1|Name=SMED30027198-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=368bp
MNDTMEYSSWINMKLYFFIWFIPIITTIGFFGNSFVLYILLYKHIRFPPF
CFWLRCTCIGNMVIVIQQGLFLILYLCFYPKQVIGIDLRIFDSIICKFFM
FVHEFSYSWTTGSLATLYLVKIIIIVTQSNEIDNSKNNFKICLILSFLML
TYSMLWPIIYDVRLKNGLNICTPKSDFLFLLEGQARFVYQSFVIVGIITG
ANCYLVYFLCHTSKVVQKIQRSDSFSIGSKESRLTAKLAKINKIIYFIIF
VNFLWIVCNVPFMSYSFIVNMYDEKNSFYYFFSSFYMPLYYGFMVSSYFY
NCLSWIIYIYTCSSLRRHMRITTYGFFVRFGLYEAYFIEKIKSEIFNNSS
EIEKQTNSSDVTVEVGK*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000208testis
Vocabulary: INTERPRO
TermDefinition
IPR017452GPCR_Rhodpsn_7TM
Vocabulary: cellular component
TermDefinition
GO:0016021integral component of membrane