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.t1 TSS g6552.t1 17617999 17617999
chr_2 g6552 g6552.t1 isoform g6552.t1 17618103 17619099
chr_2 g6552 g6552.t1 exon g6552.t1.exon1 17618103 17618291
chr_2 g6552 g6552.t1 cds g6552.t1.CDS1 17618103 17618291
chr_2 g6552 g6552.t1 exon g6552.t1.exon2 17618363 17618904
chr_2 g6552 g6552.t1 cds g6552.t1.CDS2 17618363 17618904
chr_2 g6552 g6552.t1 exon g6552.t1.exon3 17618964 17619099
chr_2 g6552 g6552.t1 cds g6552.t1.CDS3 17618964 17619099
chr_2 g6552 g6552.t1 TTS g6552.t1 17619310 17619310

Sequences

>g6552.t1 Gene=g6552 Length=867
ATGGATAATTTAATGAGCCCGTATTCCAATTTAAGCATGGGTACAACGACACCCTTGCAT
CATCCAGATGAGGATTTAGCAAATTTCCAACATCAACAGCAAAATAATGTTTATTTACCT
AAACAAATGAATTTCGCTCCTCCTCATGCACCACCACCGCCTTTAATGATGGCACAACCG
CAAACACCGCAAAGCCATTTTATTCCTATGACACCTCAACAACAACCAGCCTCAGTTTCT
GAAATTCCATCATCGATTCCAAAAGTTAATACACCGGCAATTGATGCAAGTCCTATGTTT
ATGAACCCAATGACTCCACTAGATTCATCTATCCTTCCTCAATTACAAAATATTGTATCA
ACAGTTAATCTAAATTGCAAGCTTGATCTTAAAAAAATTGCACTTCACGCGAGAAATGCA
GAGTATAATCCAAAACGTTTTGCAGCCGTCATTATGAGAATTAGAGAACCAAGAACAACA
GCCTTAATTTTTTCATCTGGTAAAATGGTGTGTACTGGAGCTAAAAGTGAAGATGATTCT
CGATTAGCTGCAAGAAAATATGCTCGTATCATTCAAAAGTTAGGCTTTAATGCCAAGTTT
TTAGATTTTAAAATTCAGAATATGGTGGGTAGTTGTGACGTTAAATTTCCTATTCGATTA
GAAGGACTTGTGCTTACACATAGCAAGTTTAGCAGTTACGAACCTGAATTGTTTCCTGGT
TTAATTTACCGTATGGTGAAACCCAGAATAGTTTTGCTGATATTTGTTAGTGGGAAAGTA
GTATTGACTGGAGCAAAAGTTCGACAAGAAATATATGATGCATTTGATAATATTTTTCCT
ATTCTAAAATCATTCAAAAAATCTTAA

>g6552.t1 Gene=g6552 Length=288
MDNLMSPYSNLSMGTTTPLHHPDEDLANFQHQQQNNVYLPKQMNFAPPHAPPPPLMMAQP
QTPQSHFIPMTPQQQPASVSEIPSSIPKVNTPAIDASPMFMNPMTPLDSSILPQLQNIVS
TVNLNCKLDLKKIALHARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEDDS
RLAARKYARIIQKLGFNAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHSKFSSYEPELFPG
LIYRMVKPRIVLLIFVSGKVVLTGAKVRQEIYDAFDNIFPILKSFKKS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g6552.t1 CDD cd04516 TBP_eukaryotes 113 285 2.53848E-131
14 g6552.t1 Gene3D G3DSA:3.30.310.10 - 120 201 4.5E-43
15 g6552.t1 Gene3D G3DSA:3.30.310.10 - 202 288 2.6E-40
5 g6552.t1 Hamap MF_00408 TATA-box-binding protein [tbp]. 109 288 27.353252
3 g6552.t1 PANTHER PTHR10126:SF37 TATA BOX-BINDING PROTEIN-LIKE PROTEIN 2 67 288 2.9E-139
4 g6552.t1 PANTHER PTHR10126 TATA-BOX BINDING PROTEIN 67 288 2.9E-139
8 g6552.t1 PRINTS PR00686 Transcription initiation factor TFIID signature 115 130 1.3E-67
6 g6552.t1 PRINTS PR00686 Transcription initiation factor TFIID signature 139 158 1.3E-67
7 g6552.t1 PRINTS PR00686 Transcription initiation factor TFIID signature 158 176 1.3E-67
11 g6552.t1 PRINTS PR00686 Transcription initiation factor TFIID signature 205 221 1.3E-67
10 g6552.t1 PRINTS PR00686 Transcription initiation factor TFIID signature 229 244 1.3E-67
9 g6552.t1 PRINTS PR00686 Transcription initiation factor TFIID signature 248 264 1.3E-67
2 g6552.t1 Pfam PF00352 Transcription factor TFIID (or TATA-binding protein, TBP) 114 193 2.2E-33
1 g6552.t1 Pfam PF00352 Transcription factor TFIID (or TATA-binding protein, TBP) 202 284 1.4E-30
17 g6552.t1 ProSitePatterns PS00351 Transcription factor TFIID repeat signature. 233 282 -
13 g6552.t1 SUPERFAMILY SSF55945 TATA-box binding protein-like 111 204 4.71E-35
12 g6552.t1 SUPERFAMILY SSF55945 TATA-box binding protein-like 196 286 4.55E-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.

Raw TPM values