SMED30024240

Overview
NameSMED30024240
Smed IDSMED30024240
Length (bp)2250
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




SMED30024240

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
testis primordiumSMED30024240SMESG000026886.1 PL08007A2H10_SE3GPL10652PMID:20844018
Wang et al., 2010
whole organism juvenile cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30024240 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000162:145823..148072 +11241
Homology
BLAST of SMED30024240 vs. Planmine SMEST
Match: SMESG000026886.1 (SMESG000026886.1)

HSP 1 Score: 685.256 bits (1767), Expect = 0.000e+0
Identity = 348/348 (100.00%), Postives = 348/348 (100.00%), Query Frame = 1
Query:   40 MNIILPKAVSAEGVHLESTDEESKGSDVSQKTYQAFKAIVDEESEVKSVEWATEKDRVKPPFIVRMINDDRIDPLYKFNTHLKLQEMNKDRFIPHNEIKLVRNEKRKNSLLNHICLALSTVGCILIIAIEFVYICIGINHFRNCGLVDIYLITSGIFHIIIIVLEWIRGRIWNVKHHKESLACIHIFQITSGXXXXXXXXXXXXXXTIGFAWIMVPYTESLNRIDKDEEIQVIYMSTVIFLTQTYCTVTFYHSAIIYQTYVLCVFIFRLVVLCFGQTCRNLFSKIASSYGSDNSLTIPFVGTNDLSNRLPPISSFRLYGQHQQPIEMRTIHGGSTCMINTHPEWRDKL 1083
            MNIILPKAVSAEGVHLESTDEESKGSDVSQKTYQAFKAIVDEESEVKSVEWATEKDRVKPPFIVRMINDDRIDPLYKFNTHLKLQEMNKDRFIPHNEIKLVRNEKRKNSLLNHICLALSTVGCILIIAIEFVYICIGINHFRNCGLVDIYLITSGIFHIIIIVLEWIRGRIWNVKHHKESLACIHIFQITSGIFLLIIYFFSLIWFTIGFAWIMVPYTESLNRIDKDEEIQVIYMSTVIFLTQTYCTVTFYHSAIIYQTYVLCVFIFRLVVLCFGQTCRNLFSKIASSYGSDNSLTIPFVGTNDLSNRLPPISSFRLYGQHQQPIEMRTIHGGSTCMINTHPEWRDKL
Sbjct:    1 MNIILPKAVSAEGVHLESTDEESKGSDVSQKTYQAFKAIVDEESEVKSVEWATEKDRVKPPFIVRMINDDRIDPLYKFNTHLKLQEMNKDRFIPHNEIKLVRNEKRKNSLLNHICLALSTVGCILIIAIEFVYICIGINHFRNCGLVDIYLITSGIFHIIIIVLEWIRGRIWNVKHHKESLACIHIFQITSGIFLLIIYFFSLIWFTIGFAWIMVPYTESLNRIDKDEEIQVIYMSTVIFLTQTYCTVTFYHSAIIYQTYVLCVFIFRLVVLCFGQTCRNLFSKIASSYGSDNSLTIPFVGTNDLSNRLPPISSFRLYGQHQQPIEMRTIHGGSTCMINTHPEWRDKL 348          
BLAST of SMED30024240 vs. Planmine SMEST
Match: SMESG000080775.1 (SMESG000080775.1)

HSP 1 Score: 84.7297 bits (208), Expect = 3.792e-17
Identity = 87/294 (29.59%), Postives = 125/294 (42.52%), Query Frame = 1
Query:  238 INDDRIDPLYKFNTHLKLQEMNKDRFIPHNEIKLVRNEKRKNSLLNHICLALSTVGCILIIAIEFVYICIGINHFRNCGLVDIYLITSGIFHIIIIVLEWIRGRIW-----------NVKHHKESLACIHIFQITSGXXXXXXXXXXXXXXTIGFAWIMVPYTESL-NRIDKDEEIQVIYMSTVIFLTQTYCTVTFYHSAIIYQTYVLCVFIFRLVVLCFGQTCRNLFSKIA--SSYGSDNSLTIPFVGTNDLSNRLPPISSFRLYGQHQQPIEMRTIHG----GSTCMINTHP 1065
            I +  I+PL      + L  MN+     + +I+ +               +LST     II  E   I +G+     C LVDIYLI SG FH +II+LEW +  IW           N  H +  ++CI +           +Y  SL+WFT+GFAWI   +   L N   K +E+ +I  +         CT  FY  AI YQ  V  +F+ R+++ C    C++L +K    +S GS  S       TN L + LPP+         Q       I+     G  CMI   P
Sbjct:  121 IANQSIEPLSNAEELIILNPMNRPYDGNYQKIRFM--------------FSLSTFLSFTIILFELGAIAVGVVFTNTCELVDIYLIVSGCFHSLIIILEWTKSWIWIQSSNPVVPDSNSDHMQLFVSCILMM----------LYCVSLVWFTVGFAWIPNVFVLPLSNETPKVKEVVIIQNNKTYTQIIPVCTEGFYIYAICYQVVVAILFLIRIIMCCLSHFCKSLCTKFVTHTSPGSCESHL-----TNPLHDLLPPMRGPLYRWGFQNEGHASGINALYNSGQLCMITPIP 385          
The following BLAST results are available for this feature:
BLAST of SMED30024240 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 SMED30024240 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 SMED30024240 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 SMED30024240 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 SMED30024240 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 SMED30024240 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 SMED30024240 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 SMED30024240 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 SMED30024240 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 SMED30024240 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 SMED30024240 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 SMED30024240 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 SMED30024240 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 SMED30024240 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000026886.10.000e+0100.00SMESG000026886.1[more]
SMESG000080775.13.792e-1729.59SMESG000080775.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30024240 ID=SMED30024240|Name=SMED30024240|organism=Schmidtea mediterranea sexual|type=transcript|length=2250bp
TTTTATTGAACGGATTCAAATTCACTTACATCAAACGTAATGAATATTAT
ATTACCAAAGGCCGTTTCGGCCGAAGGTGTACACCTAGAATCAACAGATG
AAGAATCAAAAGGATCTGATGTTTCACAAAAGACTTATCAAGCCTTCAAA
GCAATAGTAGACGAAGAGTCCGAAGTGAAAAGCGTTGAATGGGCAACGGA
AAAAGATCGAGTGAAACCTCCGTTCATTGTCCGAATGATCAATGACGACC
GAATAGACCCATTGTATAAGTTCAACACCCATCTGAAATTGCAAGAAATG
AATAAGGATAGGTTTATTCCACACAATGAAATAAAGTTAGTTCGAAACGA
AAAAAGAAAGAATTCGTTGCTAAATCATATTTGTCTGGCGTTGTCAACTG
TTGGTTGTATACTAATCATAGCGATTGAATTTGTATACATTTGCATAGGG
ATAAATCATTTCCGGAATTGTGGCCTCGTTGATATCTATCTCATTACTTC
AGGTATTTTTCACATAATAATTATCGTTCTGGAATGGATCCGAGGCCGGA
TTTGGAATGTAAAACATCACAAAGAATCTTTGGCTTGCATTCACATCTTT
CAAATAACGTCAGGAATATTTCTATTGATAATATACTTTTTTTCCCTAAT
TTGGTTCACGATCGGGTTTGCCTGGATCATGGTACCGTACACCGAGAGCC
TAAATCGAATTGATAAAGATGAAGAAATCCAAGTTATATATATGAGCACT
GTAATTTTTCTTACACAAACATATTGCACCGTCACCTTCTATCACAGTGC
TATCATTTACCAAACTTACGTCCTTTGTGTTTTTATTTTTCGATTAGTTG
TGCTGTGTTTTGGACAGACGTGTCGCAATTTATTTTCCAAAATCGCCTCA
AGCTATGGCTCAGATAATTCATTAACAATTCCATTTGTGGGTACAAATGA
TTTAAGTAATAGGTTACCCCCGATTTCATCCTTCAGGCTATATGGGCAAC
ACCAACAGCCAATTGAAATGAGAACAATTCACGGCGGCAGTACATGCATG
ATAAACACCCATCCCGAGTGGAGAGATAAACTGTAGTAACGATGTTAGAT
AAAATTGTATAAAGCCTACAAAAAGAACATTTCGTTCGGTTCCAAAATAT
GAATTTCATTTAATGTTTCTAAGTCTTTAGGTGAGGTTCAATGGAATTAG
AAAATAAAGACAATCTTTATTGGATGAAGCTTCTATTGAAGGCGAGTGAC
CGTCTATTGAAATGAAAACATGTAGGAGGAAACTTAGGAAACTTTCTCTT
TTGTTTAAATCAAATCCTGTAGAAATCCTAATTCTACCAGATGTCAAAGG
CAGTTGGATGGATCTATCAAAAACTCATTCCAAGGTAATAATGTTAGATG
TAGACTTTAATTAAAGTCTAGAACGTAAAAAGCTTGGAATACACCGAAAT
CTTAAAAGAATTAATATTCAGATTTACAGCATAAAATCTATTTTTTCATA
GAAATTAAAACCTACATTTCTAAATACAAATTTAAATTTTCCATTTTTTG
CTGATTAAATTTTTAGAAGTTGCATCCAGAATGGATTAGAAAGGAGACCT
TCAGTTGTCTCATAAAACTCTTTAGAATGCCTGATTTGATTCTTTGTTAA
ATATAAATTTCTTCGATGAAATTAAAACTTCAGACTTCTTTTATATCTGA
TGATTAAAACAGAAATACTTTCTCTTATGCGCAAGCTCAAACATAATCAT
CCACAAACTTTATGGATCTTTAGCTTCGACCTGTTTTTCGTTATTCCTTA
TACTTCGATTCAGGACTTTCCGATTCACAGATCGGCGAAAATTCATTTTT
TCTTTGACTTGCAAAAGGATTTTCTTCATTATTTCCATAATTTTCTCTGT
TAGTAAATCAAACATCCAAGGCAGGTAAAGTGATTCCATTCACGGATATC
TAAGTTTTTGAATTCAGCTCAGTCACAATTCCATGTCTCTATGGGGTGAA
ACAATAAGCTCCTTGGACATTCACTTGAAATCACTAAACTATATTGAAAC
TTAAGATCAAAGAAGATTTTGAGGTTTATTTTGAAATAGCCAGTGATGAG
TTGTAGCCGGTTTCCATCGGTTCGGTAGATGTAAACCTTCTACGAGCAAG
TCCACTTCAAATATAATTCACTAATACAGTTTTAATTCGTCCAAGTCCCG
TTGTTAAATTTATATATTCTCCTATAGCAGGCCTGCCCCAACTAAACCGA
back to top

protein sequence of SMED30024240-orf-1

>SMED30024240-orf-1 ID=SMED30024240-orf-1|Name=SMED30024240-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=349bp
MNIILPKAVSAEGVHLESTDEESKGSDVSQKTYQAFKAIVDEESEVKSVE
WATEKDRVKPPFIVRMINDDRIDPLYKFNTHLKLQEMNKDRFIPHNEIKL
VRNEKRKNSLLNHICLALSTVGCILIIAIEFVYICIGINHFRNCGLVDIY
LITSGIFHIIIIVLEWIRGRIWNVKHHKESLACIHIFQITSGIFLLIIYF
FSLIWFTIGFAWIMVPYTESLNRIDKDEEIQVIYMSTVIFLTQTYCTVTF
YHSAIIYQTYVLCVFIFRLVVLCFGQTCRNLFSKIASSYGSDNSLTIPFV
GTNDLSNRLPPISSFRLYGQHQQPIEMRTIHGGSTCMINTHPEWRDKL*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0003304testis primordium
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 250..272
NoneNo IPR availableTMHMMTMhelixcoord: 193..215
NoneNo IPR availableTMHMMTMhelixcoord: 146..168
NoneNo IPR availableTMHMMTMhelixcoord: 114..136