Gene loci information

Transcript annotation

  • This transcript has been annotated as TBP-related factor.

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 g5386 g5386.t2 TSS g5386.t2 9313412 9313412
chr_2 g5386 g5386.t2 isoform g5386.t2 9313592 9314575
chr_2 g5386 g5386.t2 exon g5386.t2.exon1 9313592 9313639
chr_2 g5386 g5386.t2 cds g5386.t2.CDS1 9313592 9313639
chr_2 g5386 g5386.t2 exon g5386.t2.exon2 9313988 9314575
chr_2 g5386 g5386.t2 cds g5386.t2.CDS2 9313988 9314575
chr_2 g5386 g5386.t2 TTS g5386.t2 9314608 9314608

Sequences

>g5386.t2 Gene=g5386 Length=636
ATGGAACTCGATTCACCACTTAAACAAATTTTAGGAAGTCCTTTAAAAATCCCGACTAGT
TCAATTCAACAAGCACCTTCAGGTCCACAAGAGGCAATAAATTCAATAAAAATTCAAAAT
TGTGTTGCAAGTGTATCTCTTGGATGTGAGCTAAATCTTCAAATGATAAATTATCGTACA
CGAAATTCAGAATACAATCCACAAAGATTTCATGGAGTAGTGATGAGAATTAGAGAACCA
AGATGTACAGCTTTAATATTTCGATCTGGAAAATTAGTATGCACAGGTGCTAGAAATGAA
GGTGATGCACATTTAGCTGCAAGAAAATTTGCTAGAATAATTCAAAAATTAGGTCATGAT
GTAAAATTTATCGACTTTAAAGTGCAAAATTTAGTCGCTACCGTTGATCTTCGATTTCCA
ATTCGTTTAGAAAATCTAAATCAAGTACATGGACAATTTTCATCCTATGAGCCTGAACTG
TTTCCAGGACTTATATATCGAATGGTTCGACCTCGAGTTGTTCTTTTAATTTTTGTAAAT
GGTAAAATTGTGTTCACCGGCGCAAAATCAAATCAAGATATTGCCGAGAGCTTAGAGAAT
ATTTATCCAATTCTGCAAAGTTTTAAGAAAAATTAA

>g5386.t2 Gene=g5386 Length=211
MELDSPLKQILGSPLKIPTSSIQQAPSGPQEAINSIKIQNCVASVSLGCELNLQMINYRT
RNSEYNPQRFHGVVMRIREPRCTALIFRSGKLVCTGARNEGDAHLAARKFARIIQKLGHD
VKFIDFKVQNLVATVDLRFPIRLENLNQVHGQFSSYEPELFPGLIYRMVRPRVVLLIFVN
GKIVFTGAKSNQDIAESLENIYPILQSFKKN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g5386.t2 CDD cd04516 TBP_eukaryotes 37 208 3.823E-109
15 g5386.t2 Gene3D G3DSA:3.30.310.10 - 43 123 2.7E-37
14 g5386.t2 Gene3D G3DSA:3.30.310.10 - 124 211 7.8E-37
5 g5386.t2 Hamap MF_00408 TATA-box-binding protein [tbp]. 32 211 28.869585
3 g5386.t2 PANTHER PTHR10126:SF41 TBP-RELATED FACTOR 26 211 7.7E-107
4 g5386.t2 PANTHER PTHR10126 TATA-BOX BINDING PROTEIN 26 211 7.7E-107
7 g5386.t2 PRINTS PR00686 Transcription initiation factor TFIID signature 38 53 2.0E-55
11 g5386.t2 PRINTS PR00686 Transcription initiation factor TFIID signature 62 81 2.0E-55
10 g5386.t2 PRINTS PR00686 Transcription initiation factor TFIID signature 81 99 2.0E-55
9 g5386.t2 PRINTS PR00686 Transcription initiation factor TFIID signature 128 144 2.0E-55
6 g5386.t2 PRINTS PR00686 Transcription initiation factor TFIID signature 152 167 2.0E-55
8 g5386.t2 PRINTS PR00686 Transcription initiation factor TFIID signature 171 187 2.0E-55
2 g5386.t2 Pfam PF00352 Transcription factor TFIID (or TATA-binding protein, TBP) 36 116 1.0E-31
1 g5386.t2 Pfam PF00352 Transcription factor TFIID (or TATA-binding protein, TBP) 125 207 5.9E-30
17 g5386.t2 ProSitePatterns PS00351 Transcription factor TFIID repeat signature. 156 205 -
12 g5386.t2 SUPERFAMILY SSF55945 TATA-box binding protein-like 33 128 2.83E-34
13 g5386.t2 SUPERFAMILY SSF55945 TATA-box binding protein-like 120 209 2.67E-30

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5386/g5386.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5386.t2.fa.iupred3.txt does not exist

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