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.t1 TSS g5386.t1 9313412 9313412
chr_2 g5386 g5386.t1 isoform g5386.t1 9313592 9314575
chr_2 g5386 g5386.t1 exon g5386.t1.exon1 9313592 9313639
chr_2 g5386 g5386.t1 cds g5386.t1.CDS1 9313592 9313639
chr_2 g5386 g5386.t1 exon g5386.t1.exon2 9313976 9314575
chr_2 g5386 g5386.t1 cds g5386.t1.CDS2 9313976 9314575
chr_2 g5386 g5386.t1 TTS g5386.t1 9314608 9314608

Sequences

>g5386.t1 Gene=g5386 Length=648
ATGGAACTCGATTCACCACTTAAACAAATTTTAGGAAGTCCTTTAAAAATCCCACAACAG
ATCCCGACTAGTTCAATTCAACAAGCACCTTCAGGTCCACAAGAGGCAATAAATTCAATA
AAAATTCAAAATTGTGTTGCAAGTGTATCTCTTGGATGTGAGCTAAATCTTCAAATGATA
AATTATCGTACACGAAATTCAGAATACAATCCACAAAGATTTCATGGAGTAGTGATGAGA
ATTAGAGAACCAAGATGTACAGCTTTAATATTTCGATCTGGAAAATTAGTATGCACAGGT
GCTAGAAATGAAGGTGATGCACATTTAGCTGCAAGAAAATTTGCTAGAATAATTCAAAAA
TTAGGTCATGATGTAAAATTTATCGACTTTAAAGTGCAAAATTTAGTCGCTACCGTTGAT
CTTCGATTTCCAATTCGTTTAGAAAATCTAAATCAAGTACATGGACAATTTTCATCCTAT
GAGCCTGAACTGTTTCCAGGACTTATATATCGAATGGTTCGACCTCGAGTTGTTCTTTTA
ATTTTTGTAAATGGTAAAATTGTGTTCACCGGCGCAAAATCAAATCAAGATATTGCCGAG
AGCTTAGAGAATATTTATCCAATTCTGCAAAGTTTTAAGAAAAATTAA

>g5386.t1 Gene=g5386 Length=215
MELDSPLKQILGSPLKIPQQIPTSSIQQAPSGPQEAINSIKIQNCVASVSLGCELNLQMI
NYRTRNSEYNPQRFHGVVMRIREPRCTALIFRSGKLVCTGARNEGDAHLAARKFARIIQK
LGHDVKFIDFKVQNLVATVDLRFPIRLENLNQVHGQFSSYEPELFPGLIYRMVRPRVVLL
IFVNGKIVFTGAKSNQDIAESLENIYPILQSFKKN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g5386.t1 CDD cd04516 TBP_eukaryotes 41 212 4.62328E-109
14 g5386.t1 Gene3D G3DSA:3.30.310.10 - 47 127 2.9E-37
15 g5386.t1 Gene3D G3DSA:3.30.310.10 - 128 215 8.1E-37
5 g5386.t1 Hamap MF_00408 TATA-box-binding protein [tbp]. 36 215 28.869585
3 g5386.t1 PANTHER PTHR10126:SF41 TBP-RELATED FACTOR 20 215 4.5E-107
4 g5386.t1 PANTHER PTHR10126 TATA-BOX BINDING PROTEIN 20 215 4.5E-107
9 g5386.t1 PRINTS PR00686 Transcription initiation factor TFIID signature 42 57 2.2E-55
6 g5386.t1 PRINTS PR00686 Transcription initiation factor TFIID signature 66 85 2.2E-55
11 g5386.t1 PRINTS PR00686 Transcription initiation factor TFIID signature 85 103 2.2E-55
8 g5386.t1 PRINTS PR00686 Transcription initiation factor TFIID signature 132 148 2.2E-55
7 g5386.t1 PRINTS PR00686 Transcription initiation factor TFIID signature 156 171 2.2E-55
10 g5386.t1 PRINTS PR00686 Transcription initiation factor TFIID signature 175 191 2.2E-55
1 g5386.t1 Pfam PF00352 Transcription factor TFIID (or TATA-binding protein, TBP) 40 120 1.1E-31
2 g5386.t1 Pfam PF00352 Transcription factor TFIID (or TATA-binding protein, TBP) 129 211 6.2E-30
17 g5386.t1 ProSitePatterns PS00351 Transcription factor TFIID repeat signature. 160 209 -
12 g5386.t1 SUPERFAMILY SSF55945 TATA-box binding protein-like 37 132 2.98E-34
13 g5386.t1 SUPERFAMILY SSF55945 TATA-box binding protein-like 124 213 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.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5386.t1.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