Vimentin type intermediate filament associated

Overview
NameVimentin type intermediate filament associated
Smed IDSMED30005787
Length (bp)1557
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 Vimentin type intermediate filament associated (SMED30005787) t-SNE clustered cells

Violin plots show distribution of expression levels for Vimentin type intermediate filament associated (SMED30005787) 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 Vimentin type intermediate filament associated (SMED30005787) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Vimentin type intermediate filament associated (SMED30005787) 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



SMED30005787

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
pharynxSMED30005787h1SMcG0013502 dd_Smed_v4_4718_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30005787h1SMcG0013502 dd_Smed_v4_4718_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of Vimentin type intermediate filament associated vs. TrEMBL
Match: A0A267E872 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig030366g2 PE=4 SV=1)

HSP 1 Score: 74.7146 bits (182), Expect = 1.214e-11
Identity = 46/136 (33.82%), Postives = 79/136 (58.09%), Query Frame = 3 
Query:   75 LFMWYSTNTMNKTYIDEANKHLQALTDQNVXXXXXXXXXXXXXXXXXXXVKEIIQDMARRSQEHTKELSEKLTKAEARCRKLEMQLETKEMEISISDNKSKLMEEIIKYKPLLAKLTICLEQAEQYSQTGYNQRQY 482
            L MW S    NKT I+EANKHL A+ ++   LE +  +   +   K+ E  +++ +M+ R Q     + +KL+KA  +  +L   LE K+ E+     + ++++E+++YK  LAK+TI LEQ EQ+++   N+  Y
Sbjct:   24 LSMWSSAGPHNKTSIEEANKHLSAMMERVAQLEARCADMEAQAQQKDAEAHQMVSEMSARYQREMDAMGQKLSKATTQVNRLTDLLERKDHEMRTLRQRCQMVDELVQYKTALAKITITLEQVEQFTKYNVNREAY 159
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BLAST of Vimentin type intermediate filament associated vs. TrEMBL
Match: A0A267E8X0 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig032660g1 PE=4 SV=1)

HSP 1 Score: 74.7146 bits (182), Expect = 1.429e-11
Identity = 46/136 (33.82%), Postives = 79/136 (58.09%), Query Frame = 3 
Query:   75 LFMWYSTNTMNKTYIDEANKHLQALTDQNVXXXXXXXXXXXXXXXXXXXVKEIIQDMARRSQEHTKELSEKLTKAEARCRKLEMQLETKEMEISISDNKSKLMEEIIKYKPLLAKLTICLEQAEQYSQTGYNQRQY 482
            L MW S    NKT I+EANKHL A+ ++   LE +  +   +   K+ E  +++ +M+ R Q     + +KL+KA  +  +L   LE K+ E+     + ++++E+++YK  LAK+TI LEQ EQ+++   N+  Y
Sbjct:   26 LSMWSSAGPHNKTSIEEANKHLSAMMERVAQLEARCADMEAQAQQKDAEAHQMVSEMSARYQREMDAMGQKLSKATTQVNRLTDLLERKDHEMRTLRQRCQMVDELVQYKTALAKITITLEQVEQFTKYNVNREAY 161
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BLAST of Vimentin type intermediate filament associated vs. TrEMBL
Match: A0A267GML6 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig034246g1 PE=4 SV=1)

HSP 1 Score: 74.7146 bits (182), Expect = 1.528e-11
Identity = 46/136 (33.82%), Postives = 79/136 (58.09%), Query Frame = 3 
Query:   75 LFMWYSTNTMNKTYIDEANKHLQALTDQNVXXXXXXXXXXXXXXXXXXXVKEIIQDMARRSQEHTKELSEKLTKAEARCRKLEMQLETKEMEISISDNKSKLMEEIIKYKPLLAKLTICLEQAEQYSQTGYNQRQY 482
            L MW S    NKT I+EANKHL A+ ++   LE +  +   +   K+ E  +++ +M+ R Q     + +KL+KA  +  +L   LE K+ E+     + ++++E+++YK  LAK+TI LEQ EQ+++   N+  Y
Sbjct:   30 LSMWSSAGPHNKTSIEEANKHLSAMMERVAQLEARCADMEAQAQQKDAEAHQMVSEMSARYQREMDAMGQKLSKATTQVNRLTDLLERKDHEMRTLRQRCQMVDELVQYKTALAKITITLEQVEQFTKYNVNREAY 165
[Close]
BLAST of Vimentin type intermediate filament associated vs. TrEMBL
Match: Q5DEF9 (SJCHGC05947 protein OS=Schistosoma japonicum OX=6182 GN=EWB00_003818 PE=2 SV=1)

HSP 1 Score: 68.1662 bits (165), Expect = 1.933e-9
Identity = 46/125 (36.80%), Postives = 81/125 (64.80%), Query Frame = 3 
Query:   81 MWYSTNTMNKTYIDEANKHLQALTDQNVXXXXXXXXXXXXXXXXXXXVKEIIQDMARRSQEHTKELSEKLTKAEARCRKLEMQLETKEMEISISDNKSKLMEEIIKYKPLLAKLTICLEQAEQYS 455
            MW+S  T  KT+I+EAN+HL ALT++   LET+LK   ++L  KE +   ++Q++  + +     L++ + K   + ++LE  L  ++ E+S+   + ++ +E+++YK  LAKLTI +EQAEQY+
Sbjct:    1 MWFS-GTQPKTHIEEANRHLSALTNKIRELETQLKSKEKELNQKEEDFGIVMQEIHVKREAEINNLNDLIFKQNVKLQRLERDLLNRDSELSVLRKRCRMFDEVLRYKATLAKLTITMEQAEQYA 124
[Close]
BLAST of Vimentin type intermediate filament associated vs. TrEMBL
Match: A0A183LHL2 (Uncharacterized protein OS=Schistosoma margrebowiei OX=48269 GN=SMRZ_LOCUS3287 PE=4 SV=1)

HSP 1 Score: 67.3958 bits (163), Expect = 3.983e-9
Identity = 46/125 (36.80%), Postives = 79/125 (63.20%), Query Frame = 3 
Query:   81 MWYSTNTMNKTYIDEANKHLQALTDQNVXXXXXXXXXXXXXXXXXXXVKEIIQDMARRSQEHTKELSEKLTKAEARCRKLEMQLETKEMEISISDNKSKLMEEIIKYKPLLAKLTICLEQAEQYS 455
            MW++  T  KT+I+EAN+HL ALT +   LE +LK   E+L  KE +   ++Q++  + +     L+E + K   + ++LE  L  ++ E+S+   + ++ +E+++YK  LAKLTI +EQAEQY+
Sbjct:    1 MWFN-GTQPKTHIEEANRHLNALTTRIKELEIQLKTKEEELNKKEEDFNIVMQEVHVKRETEVNNLNELIFKQNVKLQRLERDLLNRDSELSVLRKRCRMFDEVLRYKATLAKLTITMEQAEQYA 124
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BLAST of Vimentin type intermediate filament associated vs. Planmine SMEST
Match: SMESG000058278.1 (SMESG000058278.1)

HSP 1 Score: 296.975 bits (759), Expect = 2.932e-99
Identity = 166/167 (99.40%), Postives = 167/167 (100.00%), Query Frame = 3 
Query:  102 MNKTYIDEANKHLQALTDQNVXXXXXXXXXXXXXXXXXXXVKEIIQDMARRSQEHTKELSEKLTKAEARCRKLEMQLETKEMEISISDNKSKLMEEIIKYKPLLAKLTICLEQAEQYSQTGYNQRQYYTNNPVKGQYMNNSDMSTLVEKAAMSLPIYDTQQNGNNFH 602
            MNKTYIDEANKHLQALTDQNVLLETKLKEANEKLLAKETEVKEIIQDMARRSQEHTKELSEKLTKAEARCRKLEMQLETKEMEISISDNKSKLMEEIIKYKPLLAKLTICLEQAEQYSQTGYNQRQYYTNNPVKGQYMNN+DMSTLVEKAAMSLPIYDTQQNGNNFH
Sbjct:    1 MNKTYIDEANKHLQALTDQNVLLETKLKEANEKLLAKETEVKEIIQDMARRSQEHTKELSEKLTKAEARCRKLEMQLETKEMEISISDNKSKLMEEIIKYKPLLAKLTICLEQAEQYSQTGYNQRQYYTNNPVKGQYMNNNDMSTLVEKAAMSLPIYDTQQNGNNFH 167
[Close]
BLAST of Vimentin type intermediate filament associated vs. Planmine SMEST
Match: SMESG000058279.1 (SMESG000058279.1)

HSP 1 Score: 189.504 bits (480), Expect = 3.178e-54
Identity = 94/108 (87.04%), Postives = 94/108 (87.04%), Query Frame = -2 
Query:  777 QIGELKQENISFVVLSKGDLSDYYTNEIRQLLSYPRIISYKTSGKVHDLCQLDGSANRYFMETENRLEYHLGFPNDYSDRSLKRFIRKCEPGDFMPVTEKTQADSLND 1100
            QIGELKQENISFVVLSKGDLSDYYTNEIRQLLSYPRIISYKTSGKVHDLCQLDGSANRYFMETEN              RSLKRFIRKCEPGDFMPVTEKTQADSLND
Sbjct:  350 QIGELKQENISFVVLSKGDLSDYYTNEIRQLLSYPRIISYKTSGKVHDLCQLDGSANRYFMETEN--------------RSLKRFIRKCEPGDFMPVTEKTQADSLND 443
The following BLAST results are available for this feature:
BLAST of Vimentin type intermediate filament associated 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 Vimentin type intermediate filament associated 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 Vimentin type intermediate filament associated 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 Vimentin type intermediate filament associated 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 Vimentin type intermediate filament associated 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 Vimentin type intermediate filament associated 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 Vimentin type intermediate filament associated 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 Vimentin type intermediate filament associated vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A267E8721.214e-1133.82Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
A0A267E8X01.429e-1133.82Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
A0A267GML61.528e-1133.82Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
Q5DEF91.933e-936.80SJCHGC05947 protein OS=Schistosoma japonicum OX=61... [more]
A0A183LHL23.983e-936.80Uncharacterized protein OS=Schistosoma margrebowie... [more]
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BLAST of Vimentin type intermediate filament associated 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 Vimentin type intermediate filament associated 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 Vimentin type intermediate filament associated 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 Vimentin type intermediate filament associated 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 Vimentin type intermediate filament associated 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 Vimentin type intermediate filament associated vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000058278.12.932e-9999.40SMESG000058278.1[more]
SMESG000058279.13.178e-5487.04SMESG000058279.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30005787 ID=SMED30005787|Name=Vimentin type intermediate filament associated|organism=Schmidtea mediterranea sexual|type=transcript|length=1557bp
CTCAAAAGTTCATAATTGAAATATAATTACATGGATAATTACTAAAATTA
TAATCAAATTATTTAACTTTTATTTTGTTTATGTGGTATTCTACTAATAC
TATGAATAAAACTTATATCGACGAAGCAAACAAACATTTGCAAGCTTTAA
CTGATCAAAATGTCCTTTTAGAAACAAAGCTGAAAGAAGCCAACGAAAAA
TTATTGGCTAAAGAAACTGAAGTCAAAGAAATTATTCAAGATATGGCCAG
AAGGAGTCAAGAACATACCAAAGAACTTTCCGAAAAGCTCACTAAAGCCG
AAGCGAGGTGTCGTAAATTGGAAATGCAATTAGAAACAAAAGAAATGGAA
ATCTCAATTTCAGATAATAAATCCAAATTAATGGAAGAAATAATCAAATA
TAAGCCTTTGCTTGCAAAACTAACGATTTGTCTTGAACAGGCAGAACAAT
ATTCGCAAACGGGTTATAATCAACGACAGTATTATACAAACAATCCAGTA
AAAGGTCAATATATGAATAATAGTGATATGTCTACACTTGTTGAAAAAGC
AGCTATGTCGTTACCCATCTATGATACCCAACAAAATGGAAATAATTTTC
ATTGAAATAAAAAACAAATTAAAAAATTCGCTGTAATAGTGCATATCTAT
GATCTTCGAACGTGTGCGGAATGTGTAAGCACACACAATTACAAATTTCT
AGCATACACACAATCATTATTTGAATTCAATTGTTGGTATTAAATTTATT
CTTGTATTGATTAATTCATAACATCAGTCATTTAATGAATCAGCCTGCGT
TTTTTCTGTGACTGGCATAAAATCACCGGGTTCGCATTTTCGAATGAATC
GTTTCAAAGACCTATCCGAATAATCATTAGGGAAACCCAAATGGTATTCT
AACCTGTTTTCCGTTTCCATGAAGTATCGATTAGCACTGCCGTCCAATTG
GCAAAGGTCATGCACCTTTCCAGATGTTTTATAGGAAATTATTCTCGGAT
ATGATAATAATTGCCTGATTTCATTAGTATAATAATCTGATAAGTCGCCT
TTACTTAAAACCACAAATGAAATATTTTCTTGTTTTAATTCTCCAATTTG
CTAAATTTAATAAAAATAATTCAATATTTTTGGAAACAGTTTTGGATAAT
TGTTGACAACTCTAATATTTTTCAGTGTTGTTAGGAACAGACCGGGTATG
TTGCTATGCAATGATTGTAAATTTCACATTATATCAGATGCGGAATTCCA
ATTGTTTCATAAATGATTTCTGTTTATTATAACGAATTATTTGAATGATG
CTCGCAATGAGGAATGAATCATCCAATTAAGGATGACCCATGGAGAAAAT
CACACAAAGATGACAGTGAAATAGGTCGATCCAATTAACCAGTTATGAAT
CAGATCTGAGTTGGATGTTTTAATTAGAAATTTGGTTTAAAAAACTAAAA
TGGTCAAATAATTGAATGCATAAATCAATGCACCTAAATCAATTAATTGG
TAAAAATTCCAAGAATCTTCAACTAATTTCTAAATTAATTTTTGTTTATC
GAAAGTC
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protein sequence of SMED30005787-orf-1

>SMED30005787-orf-1 ID=SMED30005787-orf-1|Name=SMED30005787-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=175bp
MWYSTNTMNKTYIDEANKHLQALTDQNVLLETKLKEANEKLLAKETEVKE
IIQDMARRSQEHTKELSEKLTKAEARCRKLEMQLETKEMEISISDNKSKL
MEEIIKYKPLLAKLTICLEQAEQYSQTGYNQRQYYTNNPVKGQYMNNSDM
STLVEKAAMSLPIYDTQQNGNNFH*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002032epidermal cell
PLANA:0002109X1 cell
Vocabulary: INTERPRO
TermDefinition
IPR038809VMAC
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 13..54
NoneNo IPR availableCOILSCoilCoilcoord: 56..90
NoneNo IPR availablePANTHERPTHR34707FAMILY NOT NAMEDcoord: 8..161
IPR038809Vimentin-type intermediate filament-associated coiled-coil proteinPANTHERPTHR34707:SF1VIMENTIN-TYPE INTERMEDIATE FILAMENT-ASSOCIATED COILED-COIL PROTEINcoord: 8..161