Transcription initiation factor TFIID subunit

Overview
NameTranscription initiation factor TFIID subunit
Smed IDSMED30015094
Length (bp)618
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 Transcription initiation factor TFIID subunit (SMED30015094) t-SNE clustered cells

Violin plots show distribution of expression levels for Transcription initiation factor TFIID subunit (SMED30015094) in cells (dots) of each of the 12 neoblast clusters.

 

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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




SMED30015094

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
epidermisSMED30015094SMESG000022807.1 dd_Smed_v4_25497_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
BLAST of Transcription initiation factor TFIID subunit vs. TrEMBL
Match: A0A0X3PVA1 (Uncharacterized protein OS=Schistocephalus solidus OX=70667 GN=SSLN_LOCUS11355 PE=4 SV=1)

HSP 1 Score: 110.153 bits (274), Expect = 1.206e-27
Identity = 47/91 (51.65%), Postives = 62/91 (68.13%), Query Frame = 3
Query:  243 MAKRTGLNCEPYNAYIPYDLLDYYQPKNSFFTTRSGMQCRRYYCAVCGPCHLGNCNPSHRMMEWVTGTTMPDALYKAKEAEIIDDMVQSRF 515
            MA+R  +N EPYNAY+    +   +P+NSF+ T SG  C+RY+C  CGPCH  N  PS R+ EWVTGTT+PD+L+   EA +ID+  Q RF
Sbjct:    1 MARRVNVNSEPYNAYLSQKQVPQLKPENSFYNTDSGATCKRYFCGTCGPCHPVNNCPSKRVTEWVTGTTLPDSLFHVSEAYVIDEFTQGRF 91          
BLAST of Transcription initiation factor TFIID subunit vs. TrEMBL
Match: A0A564YNQ2 (Uncharacterized protein (Fragment) OS=Hymenolepis diminuta OX=6216 GN=WMSIL1_LOCUS7991 PE=4 SV=1)

HSP 1 Score: 103.219 bits (256), Expect = 4.437e-25
Identity = 47/94 (50.00%), Postives = 66/94 (70.21%), Query Frame = 3
Query:  243 MAKRTGLNCEPYNAYIPYDLLDYYQPKNSFFTTRSGMQCRRYYCAVCGPCHLGNCNPSHRMMEWVTGTTMPDALYKAKEAEIIDDMVQSRFQRK 524
            M++   +N EPYNAY+  + +   +PKN F+TT  G++C RYYCAVCG C+L   NPS R ++++T TT+PDA Y A EA II+D VQ RF+ +
Sbjct:    1 MSRHCDVNSEPYNAYLTPNQIKNLKPKNVFYTTDLGIKCGRYYCAVCGECNLAVSNPSTRFIDYLTCTTLPDAAYHATEAHIINDYVQERFREE 94          
BLAST of Transcription initiation factor TFIID subunit vs. TrEMBL
Match: A0A0R3SFM4 (Uncharacterized protein OS=Hymenolepis diminuta OX=6216 GN=HDID_LOCUS3649 PE=4 SV=1)

HSP 1 Score: 103.219 bits (256), Expect = 5.362e-25
Identity = 47/94 (50.00%), Postives = 66/94 (70.21%), Query Frame = 3
Query:  243 MAKRTGLNCEPYNAYIPYDLLDYYQPKNSFFTTRSGMQCRRYYCAVCGPCHLGNCNPSHRMMEWVTGTTMPDALYKAKEAEIIDDMVQSRFQRK 524
            M++   +N EPYNAY+  + +   +PKN F+TT  G++C RYYCAVCG C+L   NPS R ++++T TT+PDA Y A EA II+D VQ RF+ +
Sbjct:    1 MSRHCDVNSEPYNAYLTPNQIKNLKPKNVFYTTDLGIKCGRYYCAVCGECNLAVSNPSTRFIDYLTCTTLPDAAYHATEAHIINDYVQERFREE 94          
BLAST of Transcription initiation factor TFIID subunit vs. TrEMBL
Match: A0A183VME7 (Uncharacterized protein OS=Trichobilharzia regenti OX=157069 GN=TRE_LOCUS1653 PE=4 SV=1)

HSP 1 Score: 101.293 bits (251), Expect = 5.341e-24
Identity = 49/98 (50.00%), Postives = 64/98 (65.31%), Query Frame = 3
Query:  243 MAKRTGLNCEPYNAYIPYDLLDYYQPKNSFFTTRSGMQCRRYYCAVCGPCHLGNCNPSHRMMEWVTGTTMPDALYKAKEAEIIDDMVQSRFQ--RKSN 530
            M +R  +N EPY AY+    +    P N F+TT    QC+RYYCAVCG CH  N + + R+ EW+TGTT+PDAL+++ EA+IIDD  Q RF   R SN
Sbjct:    1 MTRRVDVNSEPYAAYLAPSQIPQINPTNVFYTTDG--QCKRYYCAVCGECHPVNTHRTQRLTEWLTGTTLPDALHRSSEAKIIDDFTQLRFHQARTSN 96          
BLAST of Transcription initiation factor TFIID subunit vs. TrEMBL
Match: A0A0R3WE48 (Uncharacterized protein OS=Taenia asiatica OX=60517 GN=TASK_LOCUS9076 PE=4 SV=1)

HSP 1 Score: 100.908 bits (250), Expect = 6.072e-24
Identity = 48/109 (44.04%), Postives = 66/109 (60.55%), Query Frame = 3
Query:  243 MAKRTGLNCEPYNAYIPYDLLDYYQPKNSFFTTRSGMQCRRYYCAVCGPCHLGNCNPSHRMMEWVTGTTMPDALYKAKEAEIIDDMVQSRFQRKSNIKEVLDRVKVKRP 569
            M +R   N EPYNAY+    +D  +P+N+F+TT  G +C R+YC  CG CH  N   S R++E+VTGT++PDA + A EA +IDD VQ R Q +     +    K  RP
Sbjct:    1 MTRRWNANSEPYNAYLSPRQIDQLKPENAFYTTEFGDRCERHYCGACGECHAMNACTSTRLLEYVTGTSLPDAAFHASEAYVIDDYVQRRLQVEQRKLRLEHHCKPMRP 109          
BLAST of Transcription initiation factor TFIID subunit vs. Planmine SMEST
Match: SMESG000022807.1 (SMESG000022807.1)

HSP 1 Score: 234.958 bits (598), Expect = 2.509e-80
Identity = 110/110 (100.00%), Postives = 110/110 (100.00%), Query Frame = 3
Query:  243 MAKRTGLNCEPYNAYIPYDLLDYYQPKNSFFTTRSGMQCRRYYCAVCGPCHLGNCNPSHRMMEWVTGTTMPDALYKAKEAEIIDDMVQSRFQRKSNIKEVLDRVKVKRPK 572
            MAKRTGLNCEPYNAYIPYDLLDYYQPKNSFFTTRSGMQCRRYYCAVCGPCHLGNCNPSHRMMEWVTGTTMPDALYKAKEAEIIDDMVQSRFQRKSNIKEVLDRVKVKRPK
Sbjct:    1 MAKRTGLNCEPYNAYIPYDLLDYYQPKNSFFTTRSGMQCRRYYCAVCGPCHLGNCNPSHRMMEWVTGTTMPDALYKAKEAEIIDDMVQSRFQRKSNIKEVLDRVKVKRPK 110          
BLAST of Transcription initiation factor TFIID subunit vs. Planmine SMEST
Match: SMESG000025158.1 (SMESG000025158.1)

HSP 1 Score: 110.153 bits (274), Expect = 2.766e-31
Identity = 48/88 (54.55%), Postives = 64/88 (72.73%), Query Frame = 3
Query:  243 MAKRTGLNCEPYNAYIPYDLLDYYQPKNSFFTTRSGMQCRRYYCAVCGPCHLGNCNPSHRMMEWVTGTTMPDALYKAKEAEIIDDMVQ 506
            M+ + G N EPY AY+  DL+++Y+PK  F TTR+GM+CRRY+C  CG  H  N   S R +EWVTGTTM DAL++A+EA IID+ +Q
Sbjct:    1 MSIKNGRNKEPYTAYVKDDLIEFYEPKTMFHTTRTGMECRRYFCGTCGELHSSNTCRSLRDVEWVTGTTMADALFRAREAMIIDEKLQ 88          
The following BLAST results are available for this feature:
BLAST of Transcription initiation factor TFIID subunit 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 Transcription initiation factor TFIID subunit 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 Transcription initiation factor TFIID subunit 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 Transcription initiation factor TFIID subunit 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 Transcription initiation factor TFIID subunit 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 Transcription initiation factor TFIID subunit 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 Transcription initiation factor TFIID subunit 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 Transcription initiation factor TFIID subunit vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A0X3PVA11.206e-2751.65Uncharacterized protein OS=Schistocephalus solidus... [more]
A0A564YNQ24.437e-2550.00Uncharacterized protein (Fragment) OS=Hymenolepis ... [more]
A0A0R3SFM45.362e-2550.00Uncharacterized protein OS=Hymenolepis diminuta OX... [more]
A0A183VME75.341e-2450.00Uncharacterized protein OS=Trichobilharzia regenti... [more]
A0A0R3WE486.072e-2444.04Uncharacterized protein OS=Taenia asiatica OX=6051... [more]
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BLAST of Transcription initiation factor TFIID subunit 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 Transcription initiation factor TFIID subunit 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 Transcription initiation factor TFIID subunit 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 Transcription initiation factor TFIID subunit 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 Transcription initiation factor TFIID subunit 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 Transcription initiation factor TFIID subunit vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000022807.12.509e-80100.00SMESG000022807.1[more]
SMESG000025158.12.766e-3154.55SMESG000025158.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30015094 ID=SMED30015094|Name=Transcription initiation factor TFIID subunit|organism=Schmidtea mediterranea sexual|type=transcript|length=618bp
TTATTTGAAGTAAATTTCTAGCGATACATGTATTTTGGCACAACGCAACT
AATAAACCATTTTGTGGGTTCCAGACAACATTAAATAAAATGAATATTTT
TATGTAAATTTTAAAAAATAATTTCTTTAAACTGTATTTACACTCTTAAC
GGATAATAATCGTTTTGAAAAATGCTTCATTATAATTATTTTGAATGTGA
AAAAAATGGATTTCAATATTTTAATATTGATTAAAATACAAGATGGCTAA
AAGAACTGGCCTTAATTGTGAACCATACAATGCTTACATTCCATATGATC
TTCTGGATTATTATCAACCGAAAAATTCATTTTTTACGACAAGAAGTGGA
ATGCAGTGTCGACGATATTATTGTGCAGTATGTGGTCCATGTCATTTAGG
AAACTGTAATCCCAGTCATCGAATGATGGAATGGGTAACTGGCACGACAA
TGCCAGATGCTTTATACAAGGCAAAAGAAGCAGAAATAATCGACGATATG
GTTCAGAGTAGATTTCAAAGGAAAAGTAATATAAAAGAAGTCCTTGATCG
CGTGAAAGTTAAACGCCCGAAATAAATAATATTCATTTTTGTACTCAGTT
TAAATTTGAATAACGCCA
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protein sequence of SMED30015094-orf-1

>SMED30015094-orf-1 ID=SMED30015094-orf-1|Name=SMED30015094-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=111bp
MAKRTGLNCEPYNAYIPYDLLDYYQPKNSFFTTRSGMQCRRYYCAVCGPC
HLGNCNPSHRMMEWVTGTTMPDALYKAKEAEIIDDMVQSRFQRKSNIKEV
LDRVKVKRPK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: molecular function
TermDefinition
GO:0003743translation initiation factor activity
GO:0046982protein heterodimerization activity
Vocabulary: cellular component
TermDefinition
GO:0005634nucleus
Vocabulary: biological process
TermDefinition
GO:0006367transcription initiation from RNA polymerase II promoter
GO:0006413translational initiation