SMED30028180

Overview
NameSMED30028180
Smed IDSMED30028180
Length (bp)803
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



SMED30028180

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



PAGE Curations: 10

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
oocyteSMED30028180h1SMcG0001489 Contig925GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30028180h1SMcG0001489 Contig925GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30028180h1SMcG0020533 Contig26272uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30028180h1SMcG0020533 Contig26272newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
oocyteSMED30028180h1SMcG0020534 Contig925GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30028180h1SMcG0020534 Contig925GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
oocyteSMED30028180h1SMcG0020532 Contig925GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30028180h1SMcG0020532 Contig925GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
oocyteSMED30028180h1SMcG0020533 Contig925GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30028180h1SMcG0020533 Contig925GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30028180 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001392:39615..40396 +3910
Homology
[Close]
BLAST of SMED30028180 vs. Planmine SMEST
Match: SMESG000010389.1 (SMESG000010389.1)

HSP 1 Score: 394.43 bits (1012), Expect = 2.865e-140
Identity = 246/246 (100.00%), Postives = 246/246 (100.00%), Query Frame = 3 
Query:   24 MNYLKYFVLILAVYESSGLDSYGTVGEGPIAYDAPNHGVHTTEVEYGKGNGGFDLSNDRYGKPLGGGELHEGYSEHHSDESSDNINVDKGYGSKDLGDSYSGVNGGEYQGNVVGTNYGNNDRDGGHKGSTLGLNYGDNNPADEYRNGNEGTDGYKERDDDEARYRKGSKYIKNIYGEXXXXXXXXXXXXXXXXXXXXXXXXNCYGYGKKYQLRXXXXXXXXXXXXXXXTITKYATTKPAVHSKRYY 761
            MNYLKYFVLILAVYESSGLDSYGTVGEGPIAYDAPNHGVHTTEVEYGKGNGGFDLSNDRYGKPLGGGELHEGYSEHHSDESSDNINVDKGYGSKDLGDSYSGVNGGEYQGNVVGTNYGNNDRDGGHKGSTLGLNYGDNNPADEYRNGNEGTDGYKERDDDEARYRKGSKYIKNIYGEKKLAKLRNILNLKKLIKKRKYAKKNCYGYGKKYQLRKYIHKKPYGHHGHGKTITKYATTKPAVHSKRYY
Sbjct:    1 MNYLKYFVLILAVYESSGLDSYGTVGEGPIAYDAPNHGVHTTEVEYGKGNGGFDLSNDRYGKPLGGGELHEGYSEHHSDESSDNINVDKGYGSKDLGDSYSGVNGGEYQGNVVGTNYGNNDRDGGHKGSTLGLNYGDNNPADEYRNGNEGTDGYKERDDDEARYRKGSKYIKNIYGEKKLAKLRNILNLKKLIKKRKYAKKNCYGYGKKYQLRKYIHKKPYGHHGHGKTITKYATTKPAVHSKRYY 246
[Close]
BLAST of SMED30028180 vs. Planmine SMEST
Match: SMESG000010378.1 (SMESG000010378.1)

HSP 1 Score: 253.062 bits (645), Expect = 2.545e-85
Identity = 175/247 (70.85%), Postives = 178/247 (72.06%), Query Frame = 3 
Query:   24 MNYLKYFVLILAVYESSGLDSYGTVGEGPIAYDAPNHGVHTTEVEYGKGNGGFDLSNDRYGKPLGGGELHEGYSEHHSDESSDNINVDKGYGSKDLGDSYSGVNGGEYQGNVVGTNYGNNDRDGGHKGSTLGLNYGDNNPADEYRNGNEGTDGYKERDDDEARYRKGSKYIKNIYGEXXXXXXXXXXXXXXXXXXXXXXXXNCYGYG-KKYQLRXXXXXXXXXXXXXXXTITKYATTKPAVHSKRYY 761
            MNYLKYFVLILAVYESSGLDSYGTVGE PIAYDAPNHGVHTTEVEYGKGNGGFDLSN+ Y                          VDKGYGSKDLGDSYSGVNGGEYQGNVVGTNYG                  DNNPADEYRNGNEGTDGYKERDDDEARYRKGSKYIKNIYGEKKL KLR+                   GYG  KYQLRKYIH+KPYGHHGHGKTITKYA TKPAVHSKRYY
Sbjct:    1 MNYLKYFVLILAVYESSGLDSYGTVGEEPIAYDAPNHGVHTTEVEYGKGNGGFDLSNNPY--------------------------VDKGYGSKDLGDSYSGVNGGEYQGNVVGTNYG------------------DNNPADEYRNGNEGTDGYKERDDDEARYRKGSKYIKNIYGEKKLTKLRHGKRRT--------------GYGINKYQLRKYIHQKPYGHHGHGKTITKYAPTKPAVHSKRYY 189
The following BLAST results are available for this feature:
BLAST of SMED30028180 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 SMED30028180 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 SMED30028180 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 SMED30028180 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 SMED30028180 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 SMED30028180 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 SMED30028180 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 SMED30028180 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 SMED30028180 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 SMED30028180 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 SMED30028180 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 SMED30028180 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 SMED30028180 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 SMED30028180 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000010389.12.865e-140100.00SMESG000010389.1[more]
SMESG000010378.12.545e-8570.85SMESG000010378.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30028180 ID=SMED30028180|Name=SMED30028180|organism=Schmidtea mediterranea sexual|type=transcript|length=803bp
GATCTTGGAATATTCATTCAGAAATGAATTATTTGAAATATTTTGTTTTA
ATCTTAGCTGTTTATGAAAGTTCCGGATTGGATTCCTATGGCACCGTTGG
TGAGGGGCCGATTGCGTATGACGCCCCTAATCATGGAGTCCATACAACTG
AGGTTGAGTATGGTAAAGGCAATGGAGGATTTGATCTTTCTAATGACCGT
TATGGAAAGCCACTGGGAGGTGGGGAGTTACACGAGGGATATAGTGAACA
TCATTCTGATGAAAGTTCTGATAATATTAATGTTGACAAGGGGTATGGAA
GTAAAGATTTAGGAGATAGTTATAGTGGAGTAAATGGAGGTGAATATCAA
GGAAATGTTGTCGGAACTAATTACGGCAATAATGATCGAGATGGAGGACA
TAAAGGCAGCACTTTAGGACTAAATTACGGTGATAATAATCCTGCAGACG
AATATCGCAATGGTAATGAAGGAACAGATGGATATAAAGAGAGAGATGAT
GATGAGGCAAGATATAGAAAAGGTTCCAAATATATTAAAAATATTTATGG
TGAGAAAAAGTTGGCAAAGCTTCGAAATATTTTAAATCTTAAAAAGCTCA
TCAAAAAACGAAAATATGCGAAGAAGAATTGTTACGGATATGGCAAAAAG
TATCAATTGAGGAAATATATTCACAAGAAACCTTACGGCCACCATGGCCA
TGGGAAGACCATAACCAAGTACGCCACTACCAAGCCGGCGGTCCACAGCA
AGCGCTATTATTAGCTTAATAAATTTGTCATTTGAAAAAAAAAGATCGGA
AGA
back to top

protein sequence of SMED30028180-orf-1

>SMED30028180-orf-1 ID=SMED30028180-orf-1|Name=SMED30028180-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=254bp
SWNIHSEMNYLKYFVLILAVYESSGLDSYGTVGEGPIAYDAPNHGVHTTE
VEYGKGNGGFDLSNDRYGKPLGGGELHEGYSEHHSDESSDNINVDKGYGS
KDLGDSYSGVNGGEYQGNVVGTNYGNNDRDGGHKGSTLGLNYGDNNPADE
YRNGNEGTDGYKERDDDEARYRKGSKYIKNIYGEKKLAKLRNILNLKKLI
KKRKYAKKNCYGYGKKYQLRKYIHKKPYGHHGHGKTITKYATTKPAVHSK
RYY*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000074oocyte
PLANA:0000231vitelline gland
PLANA:0002089reproductive organ
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 141..165
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..24
score: 0.483