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.t3 TTS g6837.t3 19011135 19011135
chr_2 g6837 g6837.t3 isoform g6837.t3 19011283 19012092
chr_2 g6837 g6837.t3 exon g6837.t3.exon1 19011283 19012092
chr_2 g6837 g6837.t3 cds g6837.t3.CDS1 19011283 19011987
chr_2 g6837 g6837.t3 TSS g6837.t3 19013035 19013035

Sequences

>g6837.t3 Gene=g6837 Length=810
GTTGGTTCAGAATGGAGAACATTTAGTAATGAAAAAGCAGGAGTTGATCCATCTCGTGTT
GGTGGACCAGAAAATCCTCTTTTAAGTGGAGGTGATCTTTCAACAATGATTGGACCAGGA
ACTGGTGCTGCTTCATTCGATTCATTTGGATCTGCAAAATATCAAAATAGACGAACTATG
AGTAGTTCTGATCGTGCTTTAATCACAGCATTCAAAGAAATAAGTTCTATGGCAGATCGC
ATCAATTTGCCTAAAACTATCGTGGATAGAGCTAATAATTTATTCAAACAAGTACATGAT
GGAAAAAGTCTTAAAGGTCGTTCAAATGATGCAAAAGCCTCCGCGTGTTTATATATTGCT
TGTCGCCAAGAAGGAGTTCCTCGTACTTTTAAAGAAATCTGTGCGATTAGTAGAGTGAGC
AAGAAAGAAATTGGACGATGCTTTAAACTGACATTAAAAGCACTTGCCACTTCTGTTGAT
CTCATCACAACGGCCGATTTTATGTCTAGATTTTGTGCAAATTTGGTACTGCCTAATTAT
GTTCAGCGAGCTGCAACTCATATTGCGCGAAAAGCTGTTGAAATGGATATTGTTGCAGGA
AGATCACCTATTTCAGTGGCTGCTGCAGCAATTTATATGGCATCACAAGCATCTGAAAAT
AAAAAGACACACAAGGAAATTGGCGATATTGCGGGTGTAGCAGAAGCAACAATTCGTCAA
TCGTACAAATTAATGTATGGACATGCAAAAGCATTATTTCCTGAAGACTTTCCATTTGCA
ACTCCAATTGAACAGCTTCCGCTGTTGTAA

>g6837.t3 Gene=g6837 Length=234
MIGPGTGAASFDSFGSAKYQNRRTMSSSDRALITAFKEISSMADRINLPKTIVDRANNLF
KQVHDGKSLKGRSNDAKASACLYIACRQEGVPRTFKEICAISRVSKKEIGRCFKLTLKAL
ATSVDLITTADFMSRFCANLVLPNYVQRAATHIARKAVEMDIVAGRSPISVAAAAIYMAS
QASENKKTHKEIGDIAGVAEATIRQSYKLMYGHAKALFPEDFPFATPIEQLPLL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g6837.t3 CDD cd00043 CYCLIN 32 115 2.80455E-13
14 g6837.t3 CDD cd00043 CYCLIN 126 211 2.10063E-12
13 g6837.t3 Gene3D G3DSA:1.10.472.10 - 31 127 1.1E-40
12 g6837.t3 Gene3D G3DSA:1.10.472.10 - 128 233 9.7E-33
3 g6837.t3 PANTHER PTHR11618 TRANSCRIPTION INITIATION FACTOR IIB-RELATED 15 215 5.0E-62
4 g6837.t3 PANTHER PTHR11618:SF13 TRANSCRIPTION INITIATION FACTOR IIB 15 215 5.0E-62
9 g6837.t3 PRINTS PR00685 Transcription initiation factor IIB signature 79 98 6.9E-42
7 g6837.t3 PRINTS PR00685 Transcription initiation factor IIB signature 105 120 6.9E-42
8 g6837.t3 PRINTS PR00685 Transcription initiation factor IIB signature 132 150 6.9E-42
5 g6837.t3 PRINTS PR00685 Transcription initiation factor IIB signature 166 182 6.9E-42
6 g6837.t3 PRINTS PR00685 Transcription initiation factor IIB signature 198 212 6.9E-42
2 g6837.t3 Pfam PF00382 Transcription factor TFIIB repeat 39 109 1.8E-27
1 g6837.t3 Pfam PF00382 Transcription factor TFIIB repeat 133 203 3.5E-25
17 g6837.t3 ProSitePatterns PS00782 Transcription factor TFIIB repeat signature. 71 86 -
16 g6837.t3 ProSitePatterns PS00782 Transcription factor TFIIB repeat signature. 165 180 -
19 g6837.t3 SMART SM00385 cyclin_7 37 118 2.4E-10
18 g6837.t3 SMART SM00385 cyclin_7 131 212 1.2E-10
10 g6837.t3 SUPERFAMILY SSF47954 Cyclin-like 32 122 7.75E-26
11 g6837.t3 SUPERFAMILY SSF47954 Cyclin-like 127 233 1.49E-31

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