SMED30021413

Overview
NameSMED30021413
Smed IDSMED30021413
Length (bp)1296
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



SMED30021413

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



PAGE Curations: 8

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30021413 SmedASXL_018504SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
head regionSMED30021413 SmedASXL_018503SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30021413 dd_Smed_v4_19281_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30021413 dd_Smed_v4_19281_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30021413 dd_Smed_v4_19281_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30021413 dd_Smed_v6_19281_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
photoreceptor neuronSMED30021413 SMED30018530smed_20140614PMID:22884275
Lapan et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
head regionSMED30021413 OX_Smed_1.0.08543ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
The following BLAST results are available for this feature:
BLAST of SMED30021413 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 SMED30021413 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 SMED30021413 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 SMED30021413 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 SMED30021413 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 SMED30021413 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 SMED30021413 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 SMED30021413 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 SMED30021413 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 SMED30021413 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 SMED30021413 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 SMED30021413 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 SMED30021413 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 SMED30021413 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30021413 ID=SMED30021413|Name=SMED30021413|organism=Schmidtea mediterranea sexual|type=transcript|length=1296bp
CTGGTTTGAAGCACTATCCGACGGCGCTAACGAAGACATACTCGCTATTG
AATCATACGAATTTGATCTATTGAATATATGCGGCAATATCTTTCCTGTG
TTAATGTATTGCGCCGCTTCTGCCACAGTTGGAGTCATTGTCATTGATTG
GGCATTTGGATTTATGTTGTATCCCAAACTCAACGGTGCTCTAATCACTC
TTTTTTGATCTGGTTGACCTGACAATGTGGAGAGTGCCGCTTCGTTGTTG
TTCCTGCGAGCCGCCATCTTGTCTAGCACCGGATCCATGCTCGCTGGGAG
GCTTTGCACTTGTACTGGGACGTTGGTCGGCAATATGTCCTGCATTATTG
CCAACTTTTGCGATTGGAACTGGTTTTGTGTTAAAATGTTNNNNNNNNNN
NNNNNNNNNNNNNGTAGAAGTGATCGCATGCTGCCTGTTCCTGAAACGCT
GCTTGGGGTCAGACTCCTTGTAAACTCGCTTCCACCAATTGATAAAGGAT
GCGAACGTTGATCTGGCCCACTCAGGGAAGGAAGCTGGCCCGTGTGTGTC
AATCCAAACCTTGTCCTGTCGTCTTGTGAATTGGGTTGCTCGATCATAAG
CGGATTCGAATGTTGCCTCGACTGCAATTGTGAATAAGCATGCCCCTCGC
TCGGATATTCGCTGCCGGAAAGTATCGACTGCGTTGGAGGTTGCGAATAT
CCCTGCGATATTGCCAACTGCTGGGTTTGAAGATTGGCAGGTTGCGATGT
AGTACCGCTCAGGCTTTCCTCCGCTCTTAATAGTGGTAGAGATTGGCGCT
GAATGTTCTCTTGTTCTCGCAGTTGGCCCTGAATCGATTGAAAATTGTGG
GCTGGTTGGTCTGTAGCTGACTGAGGGGCTAGATGGGACAGTTGAGTTAT
GCCCATCAAAGGTTGAGATGATGGGATCTGATGTTGTTGTGTCGTTTGCT
CTCGCCGATTCAATTCTGATATTAACGAATCCCCAATCTGCAGTGGCTGG
GTCATACCTTGGGATATCCCATCTAGTGCGCTTGGGTCGCTTGTCTCTAA
TGGCAGCTGGTCCTTGTACGGCGTCGCCTTCGAATTCAACGTAGCCATAC
TTCGCTGCATCTGGTCTATTTGTGGCCACATATCTGTCAAAGACACTCCA
GTCTGCGACAGCCTTCCACTCAGAATGTTCTCTAAGTGGCGTCGGTGTTG
TTTGTCGTTTGCGGCTTGGTGTAGTTGAGTTGTTAGCCAATGAGTTTGTT
GTTGCCATTCGGGTGCGTCTCCTACTATTTTACGAACGATTGGATC
back to top

protein sequence of SMED30021413-orf-1

>SMED30021413-orf-1 ID=SMED30021413-orf-1|Name=SMED30021413-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=356bp
MATTNSLANNSTTPSRKRQTTPTPLREHSEWKAVADWSVFDRYVATNRPD
AAKYGYVEFEGDAVQGPAAIRDKRPKRTRWDIPRYDPATADWGFVNIRIE
SARANDTTTSDPIISTFDGHNSTVPSSPSVSYRPTSPQFSIDSGPTARTR
EHSAPISTTIKSGGKPERYYIATCQSSNPAVGNIAGIFATSNAVDTFRQR
ISERGACLFTIAVEATFESAYDRATQFTRRQDKVWIDTHGPASFPEWARS
TFASFINWWKRVYKESDPKQRFRNRQHAITSXXXXXXXXXHFNTKPVPIA
KVGNNAGHIADQRPSTSAKPPSEHGSGARQDGGSQEQQRSGTLHIVRSTR
SKKSD*
back to top

protein sequence of SMED30021413-orf-2

>SMED30021413-orf-2 ID=SMED30021413-orf-2|Name=SMED30021413-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=432bp
DPIVRKIVGDAPEWQQQTHWLTTQLHQAANDKQHRRHLENILSGRLSQTG
VSLTDMWPQIDQMQRSMATLNSKATPYKDQLPLETSDPSALDGISQGMTQ
PLQIGDSLISELNRREQTTQQHQIPSSQPLMGITQLSHLAPQSATDQPAH
NFQSIQGQLREQENIQRQSLPLLRAEESLSGTTSQPANLQTQQLAISQGY
SQPPTQSILSGSEYPSEGHAYSQLQSRQHSNPLMIEQPNSQDDRTRFGLT
HTGQLPSLSGPDQRSHPLSIGGSEFTRSLTPSSVSGTGSMRSLLXXXXXX
XXNILTQNQFQSQKLAIMQDILPTNVPVQVQSLPASMDPVLDKMAARRNN
NEAALSTLSGQPDQKRVIRAPLSLGYNINPNAQSMTMTPTVAEAAQYINT
GKILPHIFNRSNSYDSIASMSSLAPSDSASNQ
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000017photoreceptor neuron
PLANA:0000418head