TATA-box-binding protein

Overview
NameTATA-box-binding protein
Smed IDSMED30027382
Length (bp)832
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 TATA-box-binding protein (SMED30027382) t-SNE clustered cells

Violin plots show distribution of expression levels for TATA-box-binding protein (SMED30027382) 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 TATA-box-binding protein (SMED30027382) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for TATA-box-binding protein (SMED30027382) 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.
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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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Homology
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BLAST of TATA-box-binding protein vs. Planmine SMEST
Match: SMESG000080313.1 (SMESG000080313.1)

HSP 1 Score: 274.633 bits (701), Expect = 5.392e-94
Identity = 135/141 (95.74%), Postives = 136/141 (96.45%), Query Frame = 3 
Query:  348 MLSNINYKGRYSIPDMKFPFGKPQQVVDRSGKYPIIFFRSGKCRVMGCKQPLKTGDLKYNIHDLQIQSITVTIDIGKFINLYELQRKVNCIFEPEIFPALRLQKYNPSCVNIFSSGKVVILGIKSLDYNDYVENIKSEITM 770
            MLSNINYKGRYSIPDMKFPFGKPQQVVDRSGKYPIIFFR  KCRVMGCKQPLKTGDLKYNIHDLQIQSITVTIDIGKFINLYE QRKVNCIFEPEIFPALRLQKYNPSC NIFSSGKVVILGIKSLDYNDYVE IKSEIT+
Sbjct:    1 MLSNINYKGRYSIPDMKFPFGKPQQVVDRSGKYPIIFFRLRKCRVMGCKQPLKTGDLKYNIHDLQIQSITVTIDIGKFINLYEFQRKVNCIFEPEIFPALRLQKYNPSCANIFSSGKVVILGIKSLDYNDYVEYIKSEITI 141
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BLAST of TATA-box-binding protein vs. Planmine SMEST
Match: SMESG000061492.1 (SMESG000061492.1)

HSP 1 Score: 183.726 bits (465), Expect = 2.788e-58
Identity = 83/129 (64.34%), Postives = 106/129 (82.17%), Query Frame = 3 
Query:  348 MLSNINYKGRYSIPDMKFPFGKPQQVVDRSGKYPIIFFRSGKCRVMGCKQPLKTGDLKYNIHDLQIQSITVTIDIGKFINLYELQRKVNCIFEPEIFPALRLQKYNPSCVNIFSSGKVVILGIKSLDYN 734
            M+SNINY+GR  +  MKFP GKPQ VVDRSGKYPI+ F+SGKCR+MGCK+PL+ GDLKY I DLQIQS+++ ID+G  INLY L       ++PE+FPALRL KY+P CVN+F+SGKVV++GIK+L+Y+
Sbjct:    1 MISNINYRGRCEVTGMKFPAGKPQHVVDRSGKYPILLFKSGKCRIMGCKRPLQEGDLKYQIQDLQIQSLSLNIDMGCRINLYGLSTTTENFYKPELFPALRLVKYHPLCVNVFASGKVVVMGIKTLEYS 129
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BLAST of TATA-box-binding protein vs. Planmine SMEST
Match: SMESG000064561.1 (SMESG000064561.1)

HSP 1 Score: 181.03 bits (458), Expect = 1.971e-51
Identity = 83/90 (92.22%), Postives = 86/90 (95.56%), Query Frame = -1 
Query:    2 MELRNDAVYQVVGPSGCGKTLFACNLLQSNLFKSKFNKIYWHRGADEEHGLTQNQFCKLKMTIIKGFDKNWSSRLHQGDVIIIDDLYQEA 271
            MEL+NDAVY VVGPSGCGKTLF CN LQSNLFKSKFNKIYW+RGADEEHGLTQNQFCKLKMTIIKGFDKNW +RLHQGDVIIIDDLYQEA
Sbjct:    1 MELKNDAVYPVVGPSGCGKTLFVCNELQSNLFKSKFNKIYWYRGADEEHGLTQNQFCKLKMTIIKGFDKNWPARLHQGDVIIIDDLYQEA 90
[Close]
BLAST of TATA-box-binding protein vs. Planmine SMEST
Match: SMESG000065288.1 (SMESG000065288.1)

HSP 1 Score: 165.622 bits (418), Expect = 5.945e-46
Identity = 76/91 (83.52%), Postives = 84/91 (92.31%), Query Frame = -1 
Query:    2 MELRNDAVYQVVGPSGCGKTLFACNLLQSNLFKSKFNKIYWHRGADEEHGLTQNQFCKLK-MTIIKGFDKNWSSRLHQGDVIIIDDLYQEA 271
            MELRNDAVYQ+VGPSG GKT+F C LL+SNLF++KFNKIYWHRGADEEHGLTQ+ FCKLK M I+KGFDKNWSSRL +GDVIIIDDLYQEA
Sbjct:    1 MELRNDAVYQIVGPSGSGKTMFVCKLLKSNLFQTKFNKIYWHRGADEEHGLTQDNFCKLKNMKIVKGFDKNWSSRLRKGDVIIIDDLYQEA 91
[Close]
BLAST of TATA-box-binding protein vs. Planmine SMEST
Match: SMESG000061056.1 (SMESG000061056.1)

HSP 1 Score: 165.236 bits (417), Expect = 7.611e-46
Identity = 76/91 (83.52%), Postives = 84/91 (92.31%), Query Frame = -1 
Query:    2 MELRNDAVYQVVGPSGCGKTLFACNLLQSNLFKSKFNKIYWHRGADEEHGLTQNQFCKLK-MTIIKGFDKNWSSRLHQGDVIIIDDLYQEA 271
            MELRNDAVYQ+VGPSG GKT+F C LL+SNLF++KFNKIYWHRGADEEHGLTQ+ FCKLK M I+KGFDKNWSSRL +GDVIIIDDLYQEA
Sbjct:    1 MELRNDAVYQIVGPSGSGKTMFVCKLLKSNLFQTKFNKIYWHRGADEEHGLTQDNFCKLKNMKIVKGFDKNWSSRLRKGDVIIIDDLYQEA 91
The following BLAST results are available for this feature:
BLAST of TATA-box-binding 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 TATA-box-binding 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 TATA-box-binding 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 TATA-box-binding 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 TATA-box-binding 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 TATA-box-binding 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 TATA-box-binding 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 TATA-box-binding protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of TATA-box-binding 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 TATA-box-binding 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 TATA-box-binding 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 TATA-box-binding 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 TATA-box-binding 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 TATA-box-binding protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000080313.15.392e-9495.74SMESG000080313.1[more]
SMESG000061492.12.788e-5864.34SMESG000061492.1[more]
SMESG000064561.11.971e-5192.22SMESG000064561.1[more]
SMESG000065288.15.945e-4683.52SMESG000065288.1[more]
SMESG000061056.17.611e-4683.52SMESG000061056.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30027382 ID=SMED30027382|Name=TATA-box-binding protein|organism=Schmidtea mediterranea sexual|type=transcript|length=832bp
TAGCTTCCTGGTATAGATCATCGATAATAATAACATCGCCTTGATGTAAT
CTAGATGACCAATTTTTATCAAATCCTTTAATTATTGTCATTTTCAATTT
ACAGAATTGATTTTGAGTAAGTCCATGTTCTTCGTCAGCTCCTCTATGCC
AATATATTTTGTTGAATTTTGATTTGAACAAGTTCGATTGTAATAAATTA
CATGCAAATAAAGTCTTTCCACAACCACTTGGTCCAACTACTTGATATAC
AGCATCATTTCTTAATTCCATTTTATTAATAATTATTTATTTAATTGTTT
ATATTTGTTTTAATTTTTAGAATTACTTGAATTGAAATTATTTGAAAATG
TTGAGTAATATAAATTATAAAGGAAGATATTCTATACCTGATATGAAATT
CCCATTTGGAAAACCACAACAAGTTGTAGATCGATCAGGTAAGTATCCGA
TAATATTTTTCAGATCGGGGAAATGTCGGGTAATGGGATGTAAGCAACCT
CTAAAAACTGGGGATTTGAAATATAATATACATGATTTACAAATTCAATC
AATCACTGTAACAATCGATATTGGAAAATTTATAAATCTATATGAATTAC
AAAGAAAGGTGAATTGTATATTTGAACCAGAAATATTTCCAGCATTACGT
CTTCAAAAATATAATCCATCATGTGTCAATATATTTTCAAGTGGGAAAGT
AGTAATACTCGGAATAAAATCCTTGGATTATAATGATTATGTGGAAAATA
TTAAATCAGAAATAACTATGTTAATAAATTAATAAATATTTTGTTTGAAT
TTGTTTAATTTATTAAGTATTAAAAAATGTCA
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protein sequence of SMED30027382-orf-1

>SMED30027382-orf-1 ID=SMED30027382-orf-1|Name=SMED30027382-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=145bp
MLSNINYKGRYSIPDMKFPFGKPQQVVDRSGKYPIIFFRSGKCRVMGCKQ
PLKTGDLKYNIHDLQIQSITVTIDIGKFINLYELQRKVNCIFEPEIFPAL
RLQKYNPSCVNIFSSGKVVILGIKSLDYNDYVENIKSEITMLIN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002089reproductive organ
Vocabulary: INTERPRO
TermDefinition
IPR000814TBP
IPR012295TBP_dom_sf
IPR027417P-loop_NTPase
IPR000605Helicase_SF3_ssDNA/RNA_vir
Vocabulary: biological process
TermDefinition
GO:0006352DNA-templated transcription, initiation
GO:0006351transcription, DNA-templated
GO:0006355regulation of transcription, DNA-templated
GO:0006413translational initiation
Vocabulary: molecular function
TermDefinition
GO:0003677DNA binding
GO:0003724RNA helicase activity
GO:0003723RNA binding
GO:0003700transcription factor activity, sequence-specific DNA binding
GO:0003743translation initiation factor activity