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.t3 TSS g5386.t3 9313412 9313412
chr_2 g5386 g5386.t3 isoform g5386.t3 9313648 9314575
chr_2 g5386 g5386.t3 exon g5386.t3.exon1 9313648 9314575
chr_2 g5386 g5386.t3 cds g5386.t3.CDS1 9314102 9314575
chr_2 g5386 g5386.t3 TTS g5386.t3 9314608 9314608

Sequences

>g5386.t3 Gene=g5386 Length=928
TCTTTCTCAATTACTTTGGATGGACAACCGGTTGTATGCTTTTTGTTTTTCAAACATTTC
TCTAAAACAAAAACAGCTTAATTTAAGCAATGAAAAGTACATTATTCCTTAATAAATTGC
TTATCTTTTGTTATGCATTTAATTGCTTAAAAAATGGAAATTTTTTAATCGTTTATTTTG
CTTTAATACCGAAAGAAACTGATCGTAATAGATCAAATGAATTATTTAATGATCCAATAA
TTCATTTAGAATCAGTACTTAAAAAGCATATATAGTCAAATGACCCTTAATCTACAAAAT
TCACACTTACAGTTTTTACATTTTATAGATCCCACAACAGATCCCGACTAGTTCAATTCA
ACAAGCACCTTCAGGTCCACAAGAGGCAATAAATTCAATAAAAATTCAAAATTGTGTTGC
AAGTGTATCTCTTGGATGTGAGCTAAATCTTCAAATGATAAATTATCGTACACGAAATTC
AGAATACAATCCACAAAGATTTCATGGAGTAGTGATGAGAATTAGAGAACCAAGATGTAC
AGCTTTAATATTTCGATCTGGAAAATTAGTATGCACAGGTGCTAGAAATGAAGGTGATGC
ACATTTAGCTGCAAGAAAATTTGCTAGAATAATTCAAAAATTAGGTCATGATGTAAAATT
TATCGACTTTAAAGTGCAAAATTTAGTCGCTACCGTTGATCTTCGATTTCCAATTCGTTT
AGAAAATCTAAATCAAGTACATGGACAATTTTCATCCTATGAGCCTGAACTGTTTCCAGG
ACTTATATATCGAATGGTTCGACCTCGAGTTGTTCTTTTAATTTTTGTAAATGGTAAAAT
TGTGTTCACCGGCGCAAAATCAAATCAAGATATTGCCGAGAGCTTAGAGAATATTTATCC
AATTCTGCAAAGTTTTAAGAAAAATTAA

>g5386.t3 Gene=g5386 Length=157
MINYRTRNSEYNPQRFHGVVMRIREPRCTALIFRSGKLVCTGARNEGDAHLAARKFARII
QKLGHDVKFIDFKVQNLVATVDLRFPIRLENLNQVHGQFSSYEPELFPGLIYRMVRPRVV
LLIFVNGKIVFTGAKSNQDIAESLENIYPILQSFKKN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g5386.t3 CDD cd04516 TBP_eukaryotes 1 154 4.37505E-97
14 g5386.t3 Gene3D G3DSA:3.30.310.10 - 1 70 1.5E-32
13 g5386.t3 Gene3D G3DSA:3.30.310.10 - 71 157 9.7E-37
3 g5386.t3 PANTHER PTHR10126:SF41 TBP-RELATED FACTOR 2 157 2.4E-96
4 g5386.t3 PANTHER PTHR10126 TATA-BOX BINDING PROTEIN 2 157 2.4E-96
6 g5386.t3 PRINTS PR00686 Transcription initiation factor TFIID signature 8 27 9.4E-49
7 g5386.t3 PRINTS PR00686 Transcription initiation factor TFIID signature 27 45 9.4E-49
8 g5386.t3 PRINTS PR00686 Transcription initiation factor TFIID signature 74 90 9.4E-49
5 g5386.t3 PRINTS PR00686 Transcription initiation factor TFIID signature 98 113 9.4E-49
9 g5386.t3 PRINTS PR00686 Transcription initiation factor TFIID signature 117 133 9.4E-49
2 g5386.t3 Pfam PF00352 Transcription factor TFIID (or TATA-binding protein, TBP) 5 62 1.3E-22
1 g5386.t3 Pfam PF00352 Transcription factor TFIID (or TATA-binding protein, TBP) 71 153 2.9E-30
12 g5386.t3 ProSitePatterns PS00351 Transcription factor TFIID repeat signature. 102 151 -
10 g5386.t3 SUPERFAMILY SSF55945 TATA-box binding protein-like 3 73 1.22E-25
11 g5386.t3 SUPERFAMILY SSF55945 TATA-box binding protein-like 66 155 1.21E-30

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5386/g5386.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5386.t3.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

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. There were no conditions that were differentially expressed