Gene loci information

Transcript annotation

  • This transcript has been annotated as TATA-box-binding protein.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_2 g6552 g6552.t3 TSS g6552.t3 17617999 17617999
chr_2 g6552 g6552.t3 isoform g6552.t3 17618103 17620180
chr_2 g6552 g6552.t3 exon g6552.t3.exon1 17618103 17619241
chr_2 g6552 g6552.t3 cds g6552.t3.CDS1 17618381 17618908
chr_2 g6552 g6552.t3 exon g6552.t3.exon2 17619304 17619617
chr_2 g6552 g6552.t3 TTS g6552.t3 17619310 17619310
chr_2 g6552 g6552.t3 exon g6552.t3.exon3 17619671 17620024
chr_2 g6552 g6552.t3 exon g6552.t3.exon4 17620101 17620180

Sequences

>g6552.t3 Gene=g6552 Length=1887
ATGGATAATTTAATGAGCCCGTATTCCAATTTAAGCATGGGTACAACGACACCCTTGCAT
CATCCAGATGAGGATTTAGCAAATTTCCAACATCAACAGCAAAATAATGTTTATTTACCT
AAACAAATGAATTTCGCTCCTCCTCATGCACCACCACCGCCTTTAATGATGGCACAACCG
CAAACACCGGTAAGTTATCAATTCTTAATTTTAAGTATCTTAAGTAACATCTCTCTCTCT
CTCTCTCATTTTTTTTAAAGCAAAGCCATTTTATTCCTATGACACCTCAACAACAACCAG
CCTCAGTTTCTGAAATTCCATCATCGATTCCAAAAGTTAATACACCGGCAATTGATGCAA
GTCCTATGTTTATGAACCCAATGACTCCACTAGATTCATCTATCCTTCCTCAATTACAAA
ATATTGTATCAACAGTTAATCTAAATTGCAAGCTTGATCTTAAAAAAATTGCACTTCACG
CGAGAAATGCAGAGTATAATCCAAAACGTTTTGCAGCCGTCATTATGAGAATTAGAGAAC
CAAGAACAACAGCCTTAATTTTTTCATCTGGTAAAATGGTGTGTACTGGAGCTAAAAGTG
AAGATGATTCTCGATTAGCTGCAAGAAAATATGCTCGTATCATTCAAAAGTTAGGCTTTA
ATGCCAAGTTTTTAGATTTTAAAATTCAGAATATGGTGGGTAGTTGTGACGTTAAATTTC
CTATTCGATTAGAAGGACTTGTGCTTACACATAGCAAGTTTAGCAGTTACGAACCTGAAT
TGTTTCCTGGTTTAATTTACCGGTAAGTACTAAACTTTTAAAATAAAGCGTTATATCTTT
AATTCTGATTTTCTTTTATAGTATGGTGAAACCCAGAATAGTTTTGCTGATATTTGTTAG
TGGGAAAGTAGTATTGACTGGAGCAAAAGTTCGACAAGAAATATATGATGCATTTGATAA
TATTTTTCCTATTCTAAAATCATTCAAAAAATCTTAAAAGTAAGAACATTCAGTGTGCAA
AGAGCACCTTTTGCTCATAACAAAACAAAATCTACTTAGAAAATAAGATGATGTTCGTGT
GTGGAAATATTCTTCTGGTATCGCACGTGTCATCAAATCACACAATTTTTATTCTATCCA
ATTACCAAAAAAAGTAGATACTTTTATTACGAGACAATTCTTAGTATGTGTAAAGGATTT
AAAATTAATTAATGCAATTTGCCATCAATCCACCAAGACTTTCAAAATCAATCTTTTCTG
AGATGTGTTTTGTTTTGATCGTTTCTTCCTGCTTAATAATTGTAACTAAATCTCCAGAAA
GTGTCCAGTTATTTTTCTTAACCCATTGCGTTAATTGTTTGTCATCAATATTTCCTAGTA
ATCGTGATAGGTAGACTTTATCGATAGTTTGGAAAGTTGTTCCTACCACATGACACACAA
ATTTACGAATTGAACTTACATAAAATCCAGTAATTTTCTCAAAGAGCTCATTCTTATCCT
TATTTTGAACATGCTGCCAGAAAAGCACAAAGTCGCATTGCTCTAGGATGTCAGCAATAT
AGATGATTTCTTTTACCGTATCATCGCGCATTTGAACAGGTAGAAGAAGATATTTGCATA
GAACAAAATCACTGAATGGAAGGTTTGTTATGGCTTTCAACAAAATCAACTGAGTAATTG
GTAAATTCATCATATGCGGATTGAACTGATAGAATTTTAGAACTGCCAAATTTGCATCTA
AGTCATAAGTATTTTCCTTTGCTTGCTCCTGAACATATTTTTCAAGAAATGGAAAATGTT
TTGGATTACTCACCTTTCTATGCTCTTCAACATTTCAGGGATGGTCATTGTTGTACCATC
ATCGGTTGTAATCATTTTTGTAGCCAT

>g6552.t3 Gene=g6552 Length=175
MTPQQQPASVSEIPSSIPKVNTPAIDASPMFMNPMTPLDSSILPQLQNIVSTVNLNCKLD
LKKIALHARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEDDSRLAARKYAR
IIQKLGFNAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHSKFSSYEPELFPGLIYR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g6552.t3 CDD cd04516 TBP_eukaryotes 44 175 1.24109E-101
14 g6552.t3 Gene3D G3DSA:3.30.310.10 - 51 132 1.5E-43
13 g6552.t3 Gene3D G3DSA:3.30.310.10 - 133 175 5.2E-16
3 g6552.t3 PANTHER PTHR10126:SF37 TATA BOX-BINDING PROTEIN-LIKE PROTEIN 2 24 175 4.6E-105
4 g6552.t3 PANTHER PTHR10126 TATA-BOX BINDING PROTEIN 24 175 4.6E-105
7 g6552.t3 PRINTS PR00686 Transcription initiation factor TFIID signature 46 61 9.1E-56
8 g6552.t3 PRINTS PR00686 Transcription initiation factor TFIID signature 70 89 9.1E-56
9 g6552.t3 PRINTS PR00686 Transcription initiation factor TFIID signature 89 107 9.1E-56
6 g6552.t3 PRINTS PR00686 Transcription initiation factor TFIID signature 136 152 9.1E-56
5 g6552.t3 PRINTS PR00686 Transcription initiation factor TFIID signature 160 175 9.1E-56
1 g6552.t3 Pfam PF00352 Transcription factor TFIID (or TATA-binding protein, TBP) 45 124 7.5E-34
2 g6552.t3 Pfam PF00352 Transcription factor TFIID (or TATA-binding protein, TBP) 133 175 2.8E-12
12 g6552.t3 ProSitePatterns PS00351 Transcription factor TFIID repeat signature. 73 122 -
11 g6552.t3 SUPERFAMILY SSF55945 TATA-box binding protein-like 42 135 1.46E-35
10 g6552.t3 SUPERFAMILY SSF55945 TATA-box binding protein-like 127 175 1.02E-12

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0003677 DNA binding MF
GO:0006352 DNA-templated transcription, initiation BP

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.

Raw TPM values