Capsule tanning factor 1

Overview
NameCapsule tanning factor 1
Smed IDSMED30033256
Length (bp)858
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast 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 Capsule tanning factor 1 (SMED30033256) t-SNE clustered cells

Violin plots show distribution of expression levels for Capsule tanning factor 1 (SMED30033256) in cells (dots) of each of the 12 neoblast clusters.

 

back to top


 

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
Homology
BLAST of Capsule tanning factor 1 vs. TrEMBL
Match: A0A1W6I195 (Capsule tanning factor 1 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 223.787 bits (569), Expect = 4.877e-71
Identity = 108/108 (100.00%), Postives = 108/108 (100.00%), Query Frame = 3
Query:  345 MFSMFKIVIGFLVLQTLFISNHSKSSKIAWDENFEAYIQRRLEFSNHSLPYSLNNCKSCLSYARKNLQLCVTCVAYGIHCMDYSKMSFKKIFNESFKYCIDFRRGRIR 668
            MFSMFKIVIGFLVLQTLFISNHSKSSKIAWDENFEAYIQRRLEFSNHSLPYSLNNCKSCLSYARKNLQLCVTCVAYGIHCMDYSKMSFKKIFNESFKYCIDFRRGRIR
Sbjct:    1 MFSMFKIVIGFLVLQTLFISNHSKSSKIAWDENFEAYIQRRLEFSNHSLPYSLNNCKSCLSYARKNLQLCVTCVAYGIHCMDYSKMSFKKIFNESFKYCIDFRRGRIR 108          
BLAST of Capsule tanning factor 1 vs. Planmine SMEST
Match: SMESG000055728.1 (SMESG000055728.1)

HSP 1 Score: 338.576 bits (867), Expect = 3.806e-117
Identity = 164/164 (100.00%), Postives = 164/164 (100.00%), Query Frame = 3
Query:  207 SKNFAKIKSEVINDVSYLNELWFILSFGLIKAILGDTESYFILGCRMFSMFKIVIGFLVLQTLFISNHSKSSKIAWDENFEAYIQRRLEFSNHSLPYSLNNCKSCLSYARKNLQLCVTCVAYGIHCMDYSKMSFKKIFNESFKYCIDFRRGRIRGKRSELNDLS 698
            SKNFAKIKSEVINDVSYLNELWFILSFGLIKAILGDTESYFILGCRMFSMFKIVIGFLVLQTLFISNHSKSSKIAWDENFEAYIQRRLEFSNHSLPYSLNNCKSCLSYARKNLQLCVTCVAYGIHCMDYSKMSFKKIFNESFKYCIDFRRGRIRGKRSELNDLS
Sbjct:  127 SKNFAKIKSEVINDVSYLNELWFILSFGLIKAILGDTESYFILGCRMFSMFKIVIGFLVLQTLFISNHSKSSKIAWDENFEAYIQRRLEFSNHSLPYSLNNCKSCLSYARKNLQLCVTCVAYGIHCMDYSKMSFKKIFNESFKYCIDFRRGRIRGKRSELNDLS 290          
The following BLAST results are available for this feature:
BLAST of Capsule tanning factor 1 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 Capsule tanning factor 1 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 Capsule tanning factor 1 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 Capsule tanning factor 1 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 Capsule tanning factor 1 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 Capsule tanning factor 1 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 Capsule tanning factor 1 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 Capsule tanning factor 1 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A1W6I1954.877e-71100.00Capsule tanning factor 1 OS=Schmidtea mediterranea... [more]
back to top
BLAST of Capsule tanning factor 1 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 Capsule tanning factor 1 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 Capsule tanning factor 1 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 Capsule tanning factor 1 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 Capsule tanning factor 1 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 Capsule tanning factor 1 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000055728.13.806e-117100.00SMESG000055728.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30033256 ID=SMED30033256|Name=Capsule tanning factor 1|organism=Schmidtea mediterranea sexual|type=transcript|length=858bp
TACCAACTGCCCATAATATTTGCCTTCGTTGTACATAATTTATAAACAAT
GGAACTGGATGGTATGTCAAGTCGTTGGATTAAATGTCGACATGTGAACA
TTGAAGAAAGTGAAGTTTTTGTGAGTTGTCCGAATTTATGAAATCCGATT
ATGTTTTTAAGATTTGGTATTACTGCTGGAATTCATAGTGTATAATAGAA
TGTATTAGTAAGAATTTTGCCAAGATAAAATCTGAAGTAATCAACGACGT
CAGTTACTTGAACGAACTATGGTTTATCTTATCTTTTGGTCTTATCAAGG
CTATTTTAGGTGATACTGAAAGTTATTTCATTCTTGGTTGTCGAATGTTC
TCAATGTTTAAAATTGTAATAGGTTTCTTGGTTCTCCAAACATTATTTAT
ATCCAATCATTCCAAATCCTCCAAAATTGCATGGGATGAGAATTTCGAGG
CCTATATTCAGCGACGACTTGAATTTTCTAACCATTCACTTCCATATTCG
TTGAACAATTGCAAATCATGTCTTTCGTACGCCCGAAAGAATTTACAGCT
TTGCGTCACTTGCGTTGCATACGGGATTCATTGCATGGACTATTCAAAGA
TGTCTTTCAAAAAGATTTTTAATGAATCTTTTAAATATTGCATTGATTTT
CGTCGAGGAAGAATCCGAGGAAAACGTTCAGAATTAAATGACTTATCTTG
ATCAATTACTTATTTAGAAATGATAAAATGTTAATGTAATATTTTTATCT
CTTTGGAATTCATCTTTGACGATTTGACGATAAATAATAATAATAAACCC
GCCTTGGTCATTTTAACGGCCTATCAGATTAATCACACTTTTACAAAAAA
GATCGGAA
back to top

protein sequence of SMED30033256-orf-1

>SMED30033256-orf-1 ID=SMED30033256-orf-1|Name=SMED30033256-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=119bp
MFSMFKIVIGFLVLQTLFISNHSKSSKIAWDENFEAYIQRRLEFSNHSLP
YSLNNCKSCLSYARKNLQLCVTCVAYGIHCMDYSKMSFKKIFNESFKYCI
DFRRGRIRGKRSELNDLS*
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 availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..23
score: 0.586