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.t2 TSS g6552.t2 17617999 17617999
chr_2 g6552 g6552.t2 isoform g6552.t2 17618103 17619099
chr_2 g6552 g6552.t2 exon g6552.t2.exon1 17618103 17618904
chr_2 g6552 g6552.t2 cds g6552.t2.CDS1 17618381 17618904
chr_2 g6552 g6552.t2 exon g6552.t2.exon2 17618964 17619099
chr_2 g6552 g6552.t2 cds g6552.t2.CDS2 17618964 17619099
chr_2 g6552 g6552.t2 TTS g6552.t2 17619310 17619310

Sequences

>g6552.t2 Gene=g6552 Length=938
ATGGATAATTTAATGAGCCCGTATTCCAATTTAAGCATGGGTACAACGACACCCTTGCAT
CATCCAGATGAGGATTTAGCAAATTTCCAACATCAACAGCAAAATAATGTTTATTTACCT
AAACAAATGAATTTCGCTCCTCCTCATGCACCACCACCGCCTTTAATGATGGCACAACCG
CAAACACCGGTAAGTTATCAATTCTTAATTTTAAGTATCTTAAGTAACATCTCTCTCTCT
CTCTCTCATTTTTTTTAAAGCAAAGCCATTTTATTCCTATGACACCTCAACAACAACCAG
CCTCAGTTTCTGAAATTCCATCATCGATTCCAAAAGTTAATACACCGGCAATTGATGCAA
GTCCTATGTTTATGAACCCAATGACTCCACTAGATTCATCTATCCTTCCTCAATTACAAA
ATATTGTATCAACAGTTAATCTAAATTGCAAGCTTGATCTTAAAAAAATTGCACTTCACG
CGAGAAATGCAGAGTATAATCCAAAACGTTTTGCAGCCGTCATTATGAGAATTAGAGAAC
CAAGAACAACAGCCTTAATTTTTTCATCTGGTAAAATGGTGTGTACTGGAGCTAAAAGTG
AAGATGATTCTCGATTAGCTGCAAGAAAATATGCTCGTATCATTCAAAAGTTAGGCTTTA
ATGCCAAGTTTTTAGATTTTAAAATTCAGAATATGGTGGGTAGTTGTGACGTTAAATTTC
CTATTCGATTAGAAGGACTTGTGCTTACACATAGCAAGTTTAGCAGTTACGAACCTGAAT
TGTTTCCTGGTTTAATTTACCGTATGGTGAAACCCAGAATAGTTTTGCTGATATTTGTTA
GTGGGAAAGTAGTATTGACTGGAGCAAAAGTTCGACAAGAAATATATGATGCATTTGATA
ATATTTTTCCTATTCTAAAATCATTCAAAAAATCTTAA

>g6552.t2 Gene=g6552 Length=219
MTPQQQPASVSEIPSSIPKVNTPAIDASPMFMNPMTPLDSSILPQLQNIVSTVNLNCKLD
LKKIALHARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEDDSRLAARKYAR
IIQKLGFNAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHSKFSSYEPELFPGLIYRMVKPR
IVLLIFVSGKVVLTGAKVRQEIYDAFDNIFPILKSFKKS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g6552.t2 CDD cd04516 TBP_eukaryotes 44 216 1.44905E-129
15 g6552.t2 Gene3D G3DSA:3.30.310.10 - 51 132 2.5E-43
14 g6552.t2 Gene3D G3DSA:3.30.310.10 - 133 219 1.4E-40
5 g6552.t2 Hamap MF_00408 TATA-box-binding protein [tbp]. 40 219 27.353252
3 g6552.t2 PANTHER PTHR10126:SF37 TATA BOX-BINDING PROTEIN-LIKE PROTEIN 2 24 219 2.0E-138
4 g6552.t2 PANTHER PTHR10126 TATA-BOX BINDING PROTEIN 24 219 2.0E-138
9 g6552.t2 PRINTS PR00686 Transcription initiation factor TFIID signature 46 61 3.6E-68
10 g6552.t2 PRINTS PR00686 Transcription initiation factor TFIID signature 70 89 3.6E-68
11 g6552.t2 PRINTS PR00686 Transcription initiation factor TFIID signature 89 107 3.6E-68
8 g6552.t2 PRINTS PR00686 Transcription initiation factor TFIID signature 136 152 3.6E-68
6 g6552.t2 PRINTS PR00686 Transcription initiation factor TFIID signature 160 175 3.6E-68
7 g6552.t2 PRINTS PR00686 Transcription initiation factor TFIID signature 179 195 3.6E-68
1 g6552.t2 Pfam PF00352 Transcription factor TFIID (or TATA-binding protein, TBP) 45 124 1.3E-33
2 g6552.t2 Pfam PF00352 Transcription factor TFIID (or TATA-binding protein, TBP) 133 215 7.8E-31
17 g6552.t2 ProSitePatterns PS00351 Transcription factor TFIID repeat signature. 164 213 -
13 g6552.t2 SUPERFAMILY SSF55945 TATA-box binding protein-like 42 135 2.51E-35
12 g6552.t2 SUPERFAMILY SSF55945 TATA-box binding protein-like 127 217 2.51E-30

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

Pathway

  • This transcript belongs to the following pathways

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. There were no conditions that were differentially expressed