DDE_Tnp_IS1595 domain-containing protein

Overview
NameDDE_Tnp_IS1595 domain-containing protein
Smed IDSMED30030595
Length (bp)480
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 DDE_Tnp_IS1595 domain-containing protein (SMED30030595) t-SNE clustered cells

Violin plots show distribution of expression levels for DDE_Tnp_IS1595 domain-containing protein (SMED30030595) in cells (dots) of each of the 12 neoblast clusters.

 

back to top

 

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 DDE_Tnp_IS1595 domain-containing protein (SMED30030595) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for DDE_Tnp_IS1595 domain-containing protein (SMED30030595) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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
Anatomical Expression

PAGE et. al., 2020



SMED30030595

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30030595SMESG000058217.1 Contig13565newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30030595SMESG000058217.1 Contig13565uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
pharynxSMED30030595 dd_Smed_v4_42270_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 DDE_Tnp_IS1595 domain-containing protein vs. TrEMBL
Match: A0A059EXA4 (DDE_Tnp_IS1595 domain-containing protein OS=Anncaliia algerae PRA339 OX=1288291 GN=H312_02959 PE=4 SV=1)

HSP 1 Score: 72.7886 bits (177), Expect = 1.006e-13
Identity = 38/62 (61.29%), Postives = 44/62 (70.97%), Query Frame = 2 
Query:  239 FVQYTRNSDRFAVESFNNELKLAIKARKGVITEKREAFLKEFCFKFNNSGNLLTAILLLIKV 424
            F+  T   +  AVE+F+NELKLAIK RKGV TE R  FLKEFCF FNN  N L A+L LIK+
Sbjct:   33 FINKTNGVNTQAVEAFHNELKLAIKKRKGVKTELRSGFLKEFCFYFNNKNNFLDAVLGLIKI 94
[Close]
BLAST of DDE_Tnp_IS1595 domain-containing protein vs. TrEMBL
Match: A0A059EU91 (DDE_Tnp_IS1595 domain-containing protein (Fragment) OS=Anncaliia algerae PRA109 OX=1240240 GN=H311_00491 PE=4 SV=1)

HSP 1 Score: 69.3218 bits (168), Expect = 1.893e-12
Identity = 36/62 (58.06%), Postives = 43/62 (69.35%), Query Frame = 2 
Query:  239 FVQYTRNSDRFAVESFNNELKLAIKARKGVITEKREAFLKEFCFKFNNSGNLLTAILLLIKV 424
            F+   R ++  AVESF+ ELKL IK +KGV TEKR  FLKEFCF FNN  N   A++ LIKV
Sbjct:   29 FINRERGANTQAVESFHKELKLRIKQQKGVKTEKRSEFLKEFCFYFNNRSNFFGAVINLIKV 90
[Close]
BLAST of DDE_Tnp_IS1595 domain-containing protein vs. TrEMBL
Match: A0A059EVA9 (DDE_Tnp_IS1595 domain-containing protein OS=Anncaliia algerae PRA109 OX=1240240 GN=H311_00273 PE=4 SV=1)

HSP 1 Score: 72.4034 bits (176), Expect = 4.716e-12
Identity = 48/107 (44.86%), Postives = 59/107 (55.14%), Query Frame = 2 
Query:  104 PLMLTPFQLESNIETLNQKDFILYLMDLNLLKKEFLCPICNNCARFVQYTRNSDRFAVESFNNELKLAIKARKGVITEKREAFLKEFCFKFNNSGNLLTAILLLIKV 424
            P++++     S I T   K +        L K  FL     +   FV  T   +  AVE+F+NELKLAIK RKGV TE R  FLKEFCF FNN  N L A+L LIK+
Sbjct:  197 PIVISQVMPGSVIWTDEHKSY------QTLNKNGFLHQSVCHKYEFVNRTNGVNTQAVEAFHNELKLAIKKRKGVKTELRSDFLKEFCFYFNNKNNFLDAVLSLIKI 297
[Close]
BLAST of DDE_Tnp_IS1595 domain-containing protein vs. TrEMBL
Match: A0A059F0Z3 (DDE_Tnp_IS1595 domain-containing protein (Fragment) OS=Anncaliia algerae PRA339 OX=1288291 GN=H312_01613 PE=4 SV=1)

HSP 1 Score: 67.781 bits (164), Expect = 1.112e-11
Identity = 38/62 (61.29%), Postives = 43/62 (69.35%), Query Frame = 2 
Query:  239 FVQYTRNSDRFAVESFNNELKLAIKARKGVITEKREAFLKEFCFKFNNSGNLLTAILLLIKV 424
            FV      +  AVESFNN LKL IK RKG++T  RE FLKEF F FNN GNLL A+L LIK+
Sbjct:   42 FVDNLNGVNTQAVESFNNCLKLEIKRRKGILTNNREIFLKEFLFLFNNKGNLLEAVLNLIKI 103
[Close]
BLAST of DDE_Tnp_IS1595 domain-containing protein vs. TrEMBL
Match: A0A059ESF4 (DDE_Tnp_IS1595 domain-containing protein OS=Anncaliia algerae PRA109 OX=1240240 GN=H311_01143 PE=4 SV=1)

HSP 1 Score: 69.707 bits (169), Expect = 1.390e-11
Identity = 36/62 (58.06%), Postives = 43/62 (69.35%), Query Frame = 2 
Query:  239 FVQYTRNSDRFAVESFNNELKLAIKARKGVITEKREAFLKEFCFKFNNSGNLLTAILLLIKV 424
            F+   R  +  AVESF+NELKL IK +KGV TEKR  FLKEFCF FNN  N   A++ L+KV
Sbjct:  147 FINKERGDNTQAVESFHNELKLRIKQQKGVKTEKRSEFLKEFCFYFNNRSNFFGAVINLLKV 208
The following BLAST results are available for this feature:
BLAST of DDE_Tnp_IS1595 domain-containing protein 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 DDE_Tnp_IS1595 domain-containing protein 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 DDE_Tnp_IS1595 domain-containing protein 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 DDE_Tnp_IS1595 domain-containing protein 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 DDE_Tnp_IS1595 domain-containing protein 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 DDE_Tnp_IS1595 domain-containing protein 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 DDE_Tnp_IS1595 domain-containing protein 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 DDE_Tnp_IS1595 domain-containing protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A059EXA41.006e-1361.29DDE_Tnp_IS1595 domain-containing protein OS=Anncal... [more]
A0A059EU911.893e-1258.06DDE_Tnp_IS1595 domain-containing protein (Fragment... [more]
A0A059EVA94.716e-1244.86DDE_Tnp_IS1595 domain-containing protein OS=Anncal... [more]
A0A059F0Z31.112e-1161.29DDE_Tnp_IS1595 domain-containing protein (Fragment... [more]
A0A059ESF41.390e-1158.06DDE_Tnp_IS1595 domain-containing protein OS=Anncal... [more]
back to top
BLAST of DDE_Tnp_IS1595 domain-containing protein 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 DDE_Tnp_IS1595 domain-containing 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
back to top
BLAST of DDE_Tnp_IS1595 domain-containing protein 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 DDE_Tnp_IS1595 domain-containing protein 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 DDE_Tnp_IS1595 domain-containing protein 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 DDE_Tnp_IS1595 domain-containing protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30030595 ID=SMED30030595|Name=DDE_Tnp_IS1595 domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=480bp
TCGAGATCAAGTATATTAATTTCCCCCCACTATAAAAATTAATAATTAAT
AAAAACATATTAATTTAATAGATTAAATATATTTAATTTATAAAAATCAA
GACCCATTAATGCTTACACCATTTCAATTAGAAAGCAACATAGAAACTTT
GAATCAAAAGGATTTTATTTTATATCTCATGGATTTAAATTTACTTAAAA
AGGAATTTCTATGTCCTATTTGCAATAACTGTGCTCGATTCGTACAGTAC
ACAAGAAATAGTGATCGTTTTGCCGTAGAGTCTTTTAACAATGAACTAAA
ATTAGCAATAAAAGCAAGAAAAGGTGTTATTACTGAAAAAAGAGAGGCAT
TTTTAAAGGAATTTTGTTTTAAATTTAATAACAGTGGAAATTTACTTACT
GCGATTTTATTGTTAATAAAAGTTTAATTTGATTTATTTTTATTTTATAT
TTATTCGATTTATTTATTTTTTATTAAAAA
back to top

protein sequence of SMED30030595-orf-1

>SMED30030595-orf-1 ID=SMED30030595-orf-1|Name=SMED30030595-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=106bp
MLTPFQLESNIETLNQKDFILYLMDLNLLKKEFLCPICNNCARFVQYTRN
SDRFAVESFNNELKLAIKARKGVITEKREAFLKEFCFKFNNSGNLLTAIL
LLIKV*
back to top
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 98..105