SMED30026856

Overview
NameSMED30026856
Smed IDSMED30026856
Length (bp)1385
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 



 

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




Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of SMED30026856 (SMED30026856) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30026856 (SMED30026856) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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Embryonic Expression

Davies et. al., 2017




Hover the mouse over a column in the graph to view average RPKM values per sample.
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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

 

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Anatomical Expression

PAGE et. al., 2020




SMED30026856

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
tail regionSMED30026856h1SMcG0020087 dd_Smed_v6_13559_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
Category 4 cellSMED30026856h1SMcG0020087 dd_Smed_v4_13559_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30026856 vs. Planmine SMEST
Match: SMESG000034975.1 (SMESG000034975.1)

HSP 1 Score: 293.893 bits (751), Expect = 5.222e-108
Identity = 142/142 (100.00%), Postives = 142/142 (100.00%), Query Frame = -1
Query:  873 MNSNSLGELTKVFTFDPICELCRQRLTTELGAILKCGHWYHYICLLYHNLNSGNKCKTCRESYNKMMLTVVKDIETRVVIKSCERVYELGHSLYTDKVVKGYFFLLGIYSSKFPLLIKVKINGTNHSGRILYNSYSDPIEVT 1298
            MNSNSLGELTKVFTFDPICELCRQRLTTELGAILKCGHWYHYICLLYHNLNSGNKCKTCRESYNKMMLTVVKDIETRVVIKSCERVYELGHSLYTDKVVKGYFFLLGIYSSKFPLLIKVKINGTNHSGRILYNSYSDPIEVT
Sbjct:    1 MNSNSLGELTKVFTFDPICELCRQRLTTELGAILKCGHWYHYICLLYHNLNSGNKCKTCRESYNKMMLTVVKDIETRVVIKSCERVYELGHSLYTDKVVKGYFFLLGIYSSKFPLLIKVKINGTNHSGRILYNSYSDPIEVT 142          

HSP 2 Score: 117.472 bits (293), Expect = 5.222e-108
Identity = 56/56 (100.00%), Postives = 56/56 (100.00%), Query Frame = -3
Query:  685 KEIVNMKIQGIPKTGVIICYGTIQVHNGIDMEVFPGEIAIRLFINCLPLRDKSLAR 852
            KEIVNMKIQGIPKTGVIICYGTIQVHNGIDMEVFPGEIAIRLFINCLPLRDKSLAR
Sbjct:  168 KEIVNMKIQGIPKTGVIICYGTIQVHNGIDMEVFPGEIAIRLFINCLPLRDKSLAR 223          
BLAST of SMED30026856 vs. Planmine SMEST
Match: SMESG000034973.1 (SMESG000034973.1)

HSP 1 Score: 293.893 bits (751), Expect = 5.222e-108
Identity = 142/142 (100.00%), Postives = 142/142 (100.00%), Query Frame = -1
Query:  873 MNSNSLGELTKVFTFDPICELCRQRLTTELGAILKCGHWYHYICLLYHNLNSGNKCKTCRESYNKMMLTVVKDIETRVVIKSCERVYELGHSLYTDKVVKGYFFLLGIYSSKFPLLIKVKINGTNHSGRILYNSYSDPIEVT 1298
            MNSNSLGELTKVFTFDPICELCRQRLTTELGAILKCGHWYHYICLLYHNLNSGNKCKTCRESYNKMMLTVVKDIETRVVIKSCERVYELGHSLYTDKVVKGYFFLLGIYSSKFPLLIKVKINGTNHSGRILYNSYSDPIEVT
Sbjct:    1 MNSNSLGELTKVFTFDPICELCRQRLTTELGAILKCGHWYHYICLLYHNLNSGNKCKTCRESYNKMMLTVVKDIETRVVIKSCERVYELGHSLYTDKVVKGYFFLLGIYSSKFPLLIKVKINGTNHSGRILYNSYSDPIEVT 142          

HSP 2 Score: 117.472 bits (293), Expect = 5.222e-108
Identity = 56/56 (100.00%), Postives = 56/56 (100.00%), Query Frame = -3
Query:  685 KEIVNMKIQGIPKTGVIICYGTIQVHNGIDMEVFPGEIAIRLFINCLPLRDKSLAR 852
            KEIVNMKIQGIPKTGVIICYGTIQVHNGIDMEVFPGEIAIRLFINCLPLRDKSLAR
Sbjct:  168 KEIVNMKIQGIPKTGVIICYGTIQVHNGIDMEVFPGEIAIRLFINCLPLRDKSLAR 223          
BLAST of SMED30026856 vs. Planmine SMEST
Match: SMESG000034972.1 (SMESG000034972.1)

HSP 1 Score: 317.005 bits (811), Expect = 8.255e-108
Identity = 170/170 (100.00%), Postives = 170/170 (100.00%), Query Frame = 2
Query:  176 MCSVEKPIFFNGCKSCLEICDTRSNVFSRVLCLEARKSYKCNNTQINEDNYSKQDRILGSKYHEVYWXXXXXXXXXXXXXXDCVVWRKTKKIIFFHIRTLYRKYFRKSYLQNRFNILNKKEDEELESQKKVHSNGEPTNKGLWHSYAENSTVIDSNSLSVANCQNVTNLC 685
            MCSVEKPIFFNGCKSCLEICDTRSNVFSRVLCLEARKSYKCNNTQINEDNYSKQDRILGSKYHEVYWLAVILLILILWTIIDCVVWRKTKKIIFFHIRTLYRKYFRKSYLQNRFNILNKKEDEELESQKKVHSNGEPTNKGLWHSYAENSTVIDSNSLSVANCQNVTNLC
Sbjct:    1 MCSVEKPIFFNGCKSCLEICDTRSNVFSRVLCLEARKSYKCNNTQINEDNYSKQDRILGSKYHEVYWLAVILLILILWTIIDCVVWRKTKKIIFFHIRTLYRKYFRKSYLQNRFNILNKKEDEELESQKKVHSNGEPTNKGLWHSYAENSTVIDSNSLSVANCQNVTNLC 170          
BLAST of SMED30026856 vs. Planmine SMEST
Match: SMESG000034972.1 (SMESG000034972.1)

HSP 1 Score: 232.646 bits (592), Expect = 3.217e-75
Identity = 129/129 (100.00%), Postives = 129/129 (100.00%), Query Frame = 2
Query:  176 MCSVEKPIFFNGCKSCLEICDTRSNVFSRVLCLEARKSYKCNNTQINEDNYSKQDRILGSKYHEVYWXXXXXXXXXXXXXXDCVVWRKTKKIIFFHIRTLYRKYFRKSYLQNRFNILNKKEDEELESQK 562
            MCSVEKPIFFNGCKSCLEICDTRSNVFSRVLCLEARKSYKCNNTQINEDNYSKQDRILGSKYHEVYWLAVILLILILWTIIDCVVWRKTKKIIFFHIRTLYRKYFRKSYLQNRFNILNKKEDEELESQK
Sbjct:    1 MCSVEKPIFFNGCKSCLEICDTRSNVFSRVLCLEARKSYKCNNTQINEDNYSKQDRILGSKYHEVYWLAVILLILILWTIIDCVVWRKTKKIIFFHIRTLYRKYFRKSYLQNRFNILNKKEDEELESQK 129          
BLAST of SMED30026856 vs. Planmine SMEST
Match: SMESG000006125.1 (SMESG000006125.1)

HSP 1 Score: 74.7146 bits (182), Expect = 6.239e-15
Identity = 37/123 (30.08%), Postives = 66/123 (53.66%), Query Frame = -1
Query:  918 ELTKVFTFDPI--CELCRQRLT-TELGAILKCGHWYHYICLLYHNLNSGNKCKTCRESYNKMMLTVVKDIETRVVIKSCERVYELGHSLYTDKVVKGYFFLLGIYSSKFPLLIKVKINGTNHS 1277
            +L + ++  PI  C +C++ +   E   +  C H YH+ CL  HN +  + C  C + Y+K    + + I +RVV+K+    Y +G + Y +   KGY F++G+Y   +P +  + +N T HS
Sbjct:    7 KLPEEYSHVPITTCHVCQKNINPNERLRLPNCNHEYHFSCLFIHNFDKKSTCPICHKPYDKAEFILNEKIHSRVVVKNYIYDYRIGLTHYVNDERKGYSFMIGLYRPVYPFVFTISVNSTKHS 129          
The following BLAST results are available for this feature:
BLAST of SMED30026856 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30026856 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30026856 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30026856 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30026856 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30026856 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30026856 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30026856 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30026856 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30026856 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30026856 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30026856 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30026856 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30026856 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000034975.15.222e-108100.00SMESG000034975.1[more]
SMESG000034973.15.222e-108100.00SMESG000034973.1[more]
SMESG000034972.18.255e-108100.00SMESG000034972.1[more]
SMESG000034972.13.217e-75100.00SMESG000034972.1[more]
SMESG000006125.16.239e-1530.08SMESG000006125.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30026856 ID=SMED30026856|Name=SMED30026856|organism=Schmidtea mediterranea sexual|type=transcript|length=1385bp
AATCTTATATGATTTAAATATTTAACTTTTTGATAGTTTTCATCATAAAT
ATTTATTTACTATCAATATGAATATGATTATCATTGTGACGGTCAGTAGA
GCGTTTTGTTAAAAATAATTATATCAACATTGATATTTATTTTAATTGAC
TTTATTGTAAAATTGTTCCGTAAAAATGTGTTCAGTTGAAAAACCGATAT
TTTTCAATGGGTGTAAAAGTTGTTTGGAAATTTGTGATACAAGATCCAAT
GTATTCAGCAGGGTCTTGTGCCTGGAGGCTAGGAAATCGTATAAATGCAA
CAATACTCAGATAAATGAAGATAATTATTCGAAACAGGACAGAATATTAG
GATCAAAATATCATGAGGTTTACTGGCTTGCGGTAATTCTGTTAATATTA
ATTCTCTGGACTATTATAGATTGTGTGGTTTGGAGAAAAACTAAAAAAAT
CATATTCTTCCACATTCGAACCTTGTATAGGAAATATTTCAGGAAGTCAT
ACTTGCAAAATCGTTTTAATATTCTAAATAAAAAGGAAGATGAAGAATTG
GAATCACAAAAGAAAGTTCATTCAAATGGAGAACCCACAAATAAAGGACT
CTGGCACTCCTATGCTGAGAATAGTACAGTTATAGATAGCAACAGTTTGT
CAGTGGCCAACTGTCAAAATGTTACAAATTTGTGTCTTGCCAAGGATTTA
TCTCGGAGGGGCAGACAATTGATGAAAAGTCTTATTGCGATTTCTCCAGG
AAAGACTTCCATGTCGATTCCGTTATGAACTTGTATTGTTCCATAACAAA
TAATCACTCCAGTCTTCGGTATTCCTTGAATTTTCATATTTACAATCTCT
TTCGTCGTTTTTTAACTTCCTTTGTTACCTCAATTGGATCAGAATAGCTG
TTGTAAAGAATTCGCCCCGAATGATTCGTTCCGTTGATCTTAACCTTGAT
TAGCAGTGGAAATTTGGAACTGTAGATTCCAAGCAAAAAGAAATATCCTT
TGACAACCTTGTCTGTATATAAGCTGTGGCCTAACTCATACACTCTTTCA
CAACTTTTAATTACGACTCGAGTTTCTATGTCTTTGACGACCGTCAACAT
CATTTTGTTATAGGATTCTCTGCAAGTTTTACACTTGTTACCGGAATTTA
GATTGTGATATAATAGGCAAATATAATGATACCAATGTCCACATTTTAGG
ATTGCCCCGAGTTCGGTGGTCAACCTTTGTCGACACAGCTCACAAATCGG
ATCAAATGTGAAAACCTTTGTTAATTCTCCCAAAGAATTCGAATTCATTT
AATTTAATTTAATAATAACAGCTTTTAGATAATTATTAATATTTTATATT
GGCTGCTTATGTAATTAGTGATTATGTAATCTGTA
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protein sequence of SMED30026856-orf-1

>SMED30026856-orf-1 ID=SMED30026856-orf-1|Name=SMED30026856-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=153bp
MNSNSLGELTKVFTFDPICELCRQRLTTELGAILKCGHWYHYICLLYHNL
NSGNKCKTCRESYNKMMLTVVKDIETRVVIKSCERVYELGHSLYTDKVVK
GYFFLLGIYSSKFPLLIKVKINGTNHSGRILYNSYSDPIEVTKEVKKRRK
RL*
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protein sequence of SMED30026856-orf-2

>SMED30026856-orf-2 ID=SMED30026856-orf-2|Name=SMED30026856-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=201bp
MCSVEKPIFFNGCKSCLEICDTRSNVFSRVLCLEARKSYKCNNTQINEDN
YSKQDRILGSKYHEVYWLAVILLILILWTIIDCVVWRKTKKIIFFHIRTL
YRKYFRKSYLQNRFNILNKKEDEELESQKKVHSNGEPTNKGLWHSYAENS
TVIDSNSLSVANCQNVTNLCLAKDLSRRGRQLMKSLIAISPGKTSMSIPL
*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000018Category 4 cell
PLANA:0000421tail
Vocabulary: INTERPRO
TermDefinition
IPR001841Znf_RING
IPR013083Znf_RING/FYVE/PHD
Vocabulary: molecular function
TermDefinition
GO:0008270zinc ion binding
GO:0005515protein binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 65..87