Colobus protein

Overview
NameColobus protein
Smed IDSMED30011970
Length (bp)1193
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast Population

▻ 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




 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of Colobus protein (SMED30011970) t-SNE clustered cells

Violin plots show distribution of expression levels for Colobus protein (SMED30011970) in cells (dots) of each of the 12 neoblast clusters.

 

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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 Colobus protein (SMED30011970) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Colobus protein (SMED30011970) 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.
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

 

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Anatomical Expression

PAGE et. al., 2020




SMED30011970

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
posterior region of the whole animalSMED30011970SMESG000005049.1 dd_Smed_v4_4427_0_1dd_Smed_v4PMID:27063937
Scimone et al., 2016
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior region of the whole animalSMED30011970SMESG000005049.1 dd_Smed_v4_4427_0_1dd_Smed_v4PMID:27063937
Scimone et al., 2016
whole organism asexual adult colorimetric in situ hybridization evidence
tail regionSMED30011970SMESG000005049.1 dd_Smed_v4_4427_0_1dd_Smed_v4PMID:27063937
Scimone et al., 2016
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
tail regionSMED30011970SMESG000005049.1 SmedASXL_019398SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
muscle cellSMED30011970SMESG000005049.1 dd_Smed_v4_4427_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior muscle cellSMED30011970SMESG000005049.1 dd_Smed_v4_4427_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior sideSMED30011970SMESG000005049.1 dd_Smed_v4_4427_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
tail regionSMED30011970SMESG000005049.1 dd_Smed_v6_4427_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
body wall musculatureSMED30011970SMESG000005049.1 dd_Smed_v4_4427_0_1dd_Smed_v4PMID:30471994
Scimone et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 4 cellSMED30011970SMESG000005049.1 dd_Smed_v4_4427_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 Colobus protein vs. TrEMBL
Match: A0A1S6KMJ6 (Colobus protein OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 285.034 bits (728), Expect = 4.329e-92
Identity = 189/204 (92.65%), Postives = 190/204 (93.14%), Query Frame = 1
Query:  577 MRIGWQELIVSPGPRINDNRESLLKMKFSENSTLSTPKSDNITNRXXXXXXXXXXXXXXXXXXXVVYKFLTQRSK--------------NFQSAKPVSLTRLETXXXXXXXXXXXXXXXXXSSVQIDYLISILPPILLDHLKEKIGDKASSQSIREIISIWLTKPDNSFLLLLQTIETLCVENRLNAELISILIQQECDQRNYV 1146
            MRIGWQELIVSPGPRINDNRESLLKMKFSENSTLSTPKSDNITNRLIPLYCILLSLIIISTTIYVVYKFLTQRSK              +FQSAKPVSLTRLETVSVNNNNCKENEKLLNSSSVQIDYLISILPPILLDHLKEKIGDKASSQSIREIISIWLTKPDNSFLLLLQTIETLCVENRLNAELISILIQQECDQRNYV
Sbjct:    1 MRIGWQELIVSPGPRINDNRESLLKMKFSENSTLSTPKSDNITNRLIPLYCILLSLIIISTTIYVVYKFLTQRSKSALSKKLNLKNFNQDFQSAKPVSLTRLETVSVNNNNCKENEKLLNSSSVQIDYLISILPPILLDHLKEKIGDKASSQSIREIISIWLTKPDNSFLLLLQTIETLCVENRLNAELISILIQQECDQRNYV 204          
BLAST of Colobus protein vs. TrEMBL
Match: A0A159X5M3 (Uncharacterized protein (Fragment) OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 274.248 bits (700), Expect = 6.817e-88
Identity = 184/201 (91.54%), Postives = 186/201 (92.54%), Query Frame = 1
Query:  577 MRIGWQELIVSPGPRINDNRESLLKMKFSENSTLSTPKSDNITNRXXXXXXXXXXXXXXXXXXXVVYKFLTQRSK--------------NFQSAKPVSLTRLETXXXXXXXXXXXXXXXXXSSVQIDYLISILPPILLDHLKEKIGDKASSQSIREIISIWLTKPDNSFLLLLQTIETLCVENRLNAELISILIQQECDQR 1137
            MR+GWQELIVSPGPRINDNRESLLKMKFSENSTLSTPKSDNITNRLIPLYCILLSLIIISTTIYVVYKFLTQRSK              +FQSAKPVSLTRLETVSVNNNNCKENEKLLNSSSVQIDYLISILPPILLDHLKEKIGDKASSQSIREIISIWLTKPDNSFLLLLQTIETLCVENR NAELISILIQQECDQR
Sbjct:    1 MRMGWQELIVSPGPRINDNRESLLKMKFSENSTLSTPKSDNITNRLIPLYCILLSLIIISTTIYVVYKFLTQRSKSALSKKLNLKNFNQDFQSAKPVSLTRLETVSVNNNNCKENEKLLNSSSVQIDYLISILPPILLDHLKEKIGDKASSQSIREIISIWLTKPDNSFLLLLQTIETLCVENRSNAELISILIQQECDQR 201          
BLAST of Colobus protein vs. Planmine SMEST
Match: SMESG000005049.1 (SMESG000005049.1)

HSP 1 Score: 277.715 bits (709), Expect = 9.368e-93
Identity = 185/204 (90.69%), Postives = 188/204 (92.16%), Query Frame = 1
Query:  577 MRIGWQELIVSPGPRINDNRESLLKMKFSENSTLSTPKSDNITNRXXXXXXXXXXXXXXXXXXXVVYKFLTQRSK--------------NFQSAKPVSLTRLETXXXXXXXXXXXXXXXXXSSVQIDYLISILPPILLDHLKEKIGDKASSQSIREIISIWLTKPDNSFLLLLQTIETLCVENRLNAELISILIQQECDQRNYV 1146
            MRIGWQELIVSPGPRINDNRESLLK+KFSENSTLSTPKSDNITNRLIPLYCILLSLIIISTTIYVVYKFLTQRSK              +FQSAKPV+LTRLETVSVNNNNCKENEKLLNSSSVQIDYLISILPPILLDHL EKIGDK SSQSIREIISIWLTKPDNSFLLLLQTIETLCVENRLNAELISILIQQECDQRNYV
Sbjct:    1 MRIGWQELIVSPGPRINDNRESLLKIKFSENSTLSTPKSDNITNRLIPLYCILLSLIIISTTIYVVYKFLTQRSKSALSKKLNLKNFNQDFQSAKPVTLTRLETVSVNNNNCKENEKLLNSSSVQIDYLISILPPILLDHLMEKIGDKTSSQSIREIISIWLTKPDNSFLLLLQTIETLCVENRLNAELISILIQQECDQRNYV 204          
The following BLAST results are available for this feature:
BLAST of Colobus protein 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 Colobus protein 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 Colobus protein 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 Colobus protein 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 Colobus protein 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 Colobus protein 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 Colobus protein 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 Colobus protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
A0A1S6KMJ64.329e-9292.65Colobus protein OS=Schmidtea mediterranea OX=79327... [more]
A0A159X5M36.817e-8891.54Uncharacterized protein (Fragment) OS=Schmidtea me... [more]
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BLAST of Colobus protein 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 Colobus protein 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 Colobus protein 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 Colobus protein 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 Colobus protein 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 Colobus protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000005049.19.368e-9390.69SMESG000005049.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30011970 ID=SMED30011970|Name=Colobus protein|organism=Schmidtea mediterranea sexual|type=transcript|length=1193bp
TCTTTTGCATTCGCTTTTTTTCAGCGCCGCCAAATACAAAGAAATAATTG
CTAAATTATATTTTTGTAAGACCTATAGAAATAAAGGTCAAAATAAAGAT
ATCGCTACTAGACCAGTTTATTCCATAAATCATAACTTATCAAAAAGGCG
GCATCATCAAAGACTGCTGTCGGTGAATTTTAAAGGCAGGTCTTGTTAAG
CAATTTGAGCCGTTTTTATTAAAAATGATTTGTAACAATTTCTTGGTCGT
ATTTAGATTTTTTTTTGGTGATACCTAGTCTCTTTAATAACATCAAATAA
TCTGAGCGGCAAACTTGAAATGCGAATGTCTATTGGATAGCACGTAGAAA
TGATTCTGTGCGATGCTGACAAATTGATGTCTAGTTTTATTCAAGCTACA
TTAATCATAAATTTGTTTTATAAGAATCGCGCGTGAACTGTGTTTTTGAT
ACATTGGATTTTCTGATAGCATTCCGTATATAAAGGGAATTCCGGGTGAA
AAATTTTCCAAATTGAAAAACTTTTTTATTTGAATTTTGGAGGGCTAAAA
ACTATTAATTAATAATAATAATAATAATGAGAATAGGTTGGCAAGAATTA
ATCGTGTCTCCTGGACCTCGGATAAATGATAATCGGGAATCTTTATTGAA
AATGAAATTCAGTGAAAATTCCACTTTATCTACGCCAAAATCAGACAACA
TAACAAATAGATTGATTCCTCTTTATTGCATTTTATTGAGTTTAATAATA
ATCTCGACCACAATTTATGTGGTTTACAAATTTTTAACTCAAAGATCAAA
AAATTTTCAATCTGCAAAACCAGTTTCGTTGACAAGATTGGAAACAGTTT
CTGTTAATAATAATAATTGTAAAGAAAACGAGAAACTTCTCAACTCTTCG
TCCGTTCAAATTGACTATCTCATATCTATTTTACCGCCAATTTTATTGGA
TCATTTAAAGGAAAAAATTGGTGATAAAGCAAGTTCACAAAGCATCAGAG
AAATAATTTCTATTTGGTTGACAAAACCTGATAATTCTTTTCTATTATTG
TTGCAAACTATTGAAACTTTATGCGTTGAAAACCGATTAAACGCAGAGCT
GATTTCGATTTTGATACAGCAAGAATGTGATCAACGTAATTATGTATAAT
TTCAACAAGAGAGACTATGTACAAATATTTTGTATTTTTTTTA
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protein sequence of SMED30011970-orf-1

>SMED30011970-orf-1 ID=SMED30011970-orf-1|Name=SMED30011970-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=191bp
MRIGWQELIVSPGPRINDNRESLLKMKFSENSTLSTPKSDNITNRLIPLY
CILLSLIIISTTIYVVYKFLTQRSKNFQSAKPVSLTRLETVSVNNNNCKE
NEKLLNSSSVQIDYLISILPPILLDHLKEKIGDKASSQSIREIISIWLTK
PDNSFLLLLQTIETLCVENRLNAELISILIQQECDQRNYV*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000018Category 4 cell
PLANA:0000101muscle cell
PLANA:0000142posterior region of the whole animal
PLANA:0000240body wall musculature
PLANA:0000421tail
PLANA:0003001lateral region of the whole animal