Gene loci information

Transcript annotation

  • This transcript has been annotated as Transcription initiation factor IIB.

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 g6837 g6837.t2 TTS g6837.t2 19011135 19011135
chr_2 g6837 g6837.t2 isoform g6837.t2 19011180 19012148
chr_2 g6837 g6837.t2 exon g6837.t2.exon1 19011180 19011236
chr_2 g6837 g6837.t2 cds g6837.t2.CDS1 19011222 19011236
chr_2 g6837 g6837.t2 exon g6837.t2.exon2 19011442 19012148
chr_2 g6837 g6837.t2 cds g6837.t2.CDS2 19011442 19011987
chr_2 g6837 g6837.t2 TSS g6837.t2 19013035 19013035

Sequences

>g6837.t2 Gene=g6837 Length=764
AGATTGATGTTGATTATTTCTTAATATATTTTATTTGCTTCATCAGAGTAATTGACGTTG
GTTCAGAATGGAGAACATTTAGTAATGAAAAAGCAGGAGTTGATCCATCTCGTGTTGGTG
GACCAGAAAATCCTCTTTTAAGTGGAGGTGATCTTTCAACAATGATTGGACCAGGAACTG
GTGCTGCTTCATTCGATTCATTTGGATCTGCAAAATATCAAAATAGACGAACTATGAGTA
GTTCTGATCGTGCTTTAATCACAGCATTCAAAGAAATAAGTTCTATGGCAGATCGCATCA
ATTTGCCTAAAACTATCGTGGATAGAGCTAATAATTTATTCAAACAAGTACATGATGGAA
AAAGTCTTAAAGGTCGTTCAAATGATGCAAAAGCCTCCGCGTGTTTATATATTGCTTGTC
GCCAAGAAGGAGTTCCTCGTACTTTTAAAGAAATCTGTGCGATTAGTAGAGTGAGCAAGA
AAGAAATTGGACGATGCTTTAAACTGACATTAAAAGCACTTGCCACTTCTGTTGATCTCA
TCACAACGGCCGATTTTATGTCTAGATTTTGTGCAAATTTGGTACTGCCTAATTATGTTC
AGCGAGCTGCAACTCATATTGCGCGAAAAGCTGTTGAAATGGATATTGTTGCAGGAAGAT
CACCTATTTCAGTGGCTGCTGCAGCAATTTATATGGCATCACAAGCACTGTTTGAAAAAT
AATTTCGTGATGAATTCTTCTTTAAGTCTTATAAAATGTATTTT

>g6837.t2 Gene=g6837 Length=186
MIGPGTGAASFDSFGSAKYQNRRTMSSSDRALITAFKEISSMADRINLPKTIVDRANNLF
KQVHDGKSLKGRSNDAKASACLYIACRQEGVPRTFKEICAISRVSKKEIGRCFKLTLKAL
ATSVDLITTADFMSRFCANLVLPNYVQRAATHIARKAVEMDIVAGRSPISVAAAAIYMAS
QALFEK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g6837.t2 CDD cd00043 CYCLIN 32 115 2.16684E-13
14 g6837.t2 CDD cd00043 CYCLIN 126 180 1.07344E-7
11 g6837.t2 Gene3D G3DSA:1.10.472.10 - 31 127 6.2E-41
12 g6837.t2 Gene3D G3DSA:1.10.472.10 - 128 185 3.4E-16
3 g6837.t2 PANTHER PTHR11618 TRANSCRIPTION INITIATION FACTOR IIB-RELATED 15 182 1.8E-50
4 g6837.t2 PANTHER PTHR11618:SF13 TRANSCRIPTION INITIATION FACTOR IIB 15 182 1.8E-50
8 g6837.t2 PRINTS PR00685 Transcription initiation factor IIB signature 79 98 1.5E-35
6 g6837.t2 PRINTS PR00685 Transcription initiation factor IIB signature 105 120 1.5E-35
7 g6837.t2 PRINTS PR00685 Transcription initiation factor IIB signature 132 150 1.5E-35
5 g6837.t2 PRINTS PR00685 Transcription initiation factor IIB signature 166 182 1.5E-35
2 g6837.t2 Pfam PF00382 Transcription factor TFIIB repeat 39 109 1.1E-27
1 g6837.t2 Pfam PF00382 Transcription factor TFIIB repeat 133 182 1.5E-17
16 g6837.t2 ProSitePatterns PS00782 Transcription factor TFIIB repeat signature. 71 86 -
15 g6837.t2 ProSitePatterns PS00782 Transcription factor TFIIB repeat signature. 165 180 -
17 g6837.t2 SMART SM00385 cyclin_7 37 118 2.4E-10
10 g6837.t2 SUPERFAMILY SSF47954 Cyclin-like 32 122 6.28E-26
9 g6837.t2 SUPERFAMILY SSF47954 Cyclin-like 127 182 3.21E-16

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:0017025 TBP-class protein binding MF
GO:0070897 transcription preinitiation complex assembly BP
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.

Raw TPM values