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.t5 TTS g6837.t5 19011135 19011135
chr_2 g6837 g6837.t5 isoform g6837.t5 19011283 19012928
chr_2 g6837 g6837.t5 exon g6837.t5.exon1 19011283 19012102
chr_2 g6837 g6837.t5 cds g6837.t5.CDS1 19011283 19012102
chr_2 g6837 g6837.t5 exon g6837.t5.exon2 19012596 19012650
chr_2 g6837 g6837.t5 cds g6837.t5.CDS2 19012596 19012650
chr_2 g6837 g6837.t5 exon g6837.t5.exon3 19012771 19012928
chr_2 g6837 g6837.t5 cds g6837.t5.CDS3 19012771 19012861
chr_2 g6837 g6837.t5 TSS g6837.t5 19013035 19013035

Sequences

>g6837.t5 Gene=g6837 Length=1033
ATGGCAAGCACTTCAAAGTGAGTATGAACAACATGATTATGAGTTACAGATAATATAAAT
ATTCAAAATGATGAAATTAATAAATATTTTTATAAACTTTTATAGCTTTAAGGACAGAGT
GGTTTGTGTACATCATCCAGATGCTCCTTTAATTGAAGATTATCGAGCTGGTGATATGAT
TTGTTCGGAATGTGGATTAATAGTTGGTGACAGAGTAATTGACGTTGGTTCAGAATGGAG
AACATTTAGTAATGAAAAAGCAGGAGTTGATCCATCTCGTGTTGGTGGACCAGAAAATCC
TCTTTTAAGTGGAGGTGATCTTTCAACAATGATTGGACCAGGAACTGGTGCTGCTTCATT
CGATTCATTTGGATCTGCAAAATATCAAAATAGACGAACTATGAGTAGTTCTGATCGTGC
TTTAATCACAGCATTCAAAGAAATAAGTTCTATGGCAGATCGCATCAATTTGCCTAAAAC
TATCGTGGATAGAGCTAATAATTTATTCAAACAAGTACATGATGGAAAAAGTCTTAAAGG
TCGTTCAAATGATGCAAAAGCCTCCGCGTGTTTATATATTGCTTGTCGCCAAGAAGGAGT
TCCTCGTACTTTTAAAGAAATCTGTGCGATTAGTAGAGTGAGCAAGAAAGAAATTGGACG
ATGCTTTAAACTGACATTAAAAGCACTTGCCACTTCTGTTGATCTCATCACAACGGCCGA
TTTTATGTCTAGATTTTGTGCAAATTTGGTACTGCCTAATTATGTTCAGCGAGCTGCAAC
TCATATTGCGCGAAAAGCTGTTGAAATGGATATTGTTGCAGGAAGATCACCTATTTCAGT
GGCTGCTGCAGCAATTTATATGGCATCACAAGCATCTGAAAATAAAAAGACACACAAGGA
AATTGGCGATATTGCGGGTGTAGCAGAAGCAACAATTCGTCAATCGTACAAATTAATGTA
TGGACATGCAAAAGCATTATTTCCTGAAGACTTTCCATTTGCAACTCCAATTGAACAGCT
TCCGCTGTTGTAA

>g6837.t5 Gene=g6837 Length=321
MMKLINIFINFYSFKDRVVCVHHPDAPLIEDYRAGDMICSECGLIVGDRVIDVGSEWRTF
SNEKAGVDPSRVGGPENPLLSGGDLSTMIGPGTGAASFDSFGSAKYQNRRTMSSSDRALI
TAFKEISSMADRINLPKTIVDRANNLFKQVHDGKSLKGRSNDAKASACLYIACRQEGVPR
TFKEICAISRVSKKEIGRCFKLTLKALATSVDLITTADFMSRFCANLVLPNYVQRAATHI
ARKAVEMDIVAGRSPISVAAAAIYMASQASENKKTHKEIGDIAGVAEATIRQSYKLMYGH
AKALFPEDFPFATPIEQLPLL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g6837.t5 CDD cd00043 CYCLIN 119 202 1.96162E-13
20 g6837.t5 CDD cd00043 CYCLIN 213 298 1.5762E-12
17 g6837.t5 Gene3D G3DSA:1.10.472.170 - 18 207 2.7E-67
18 g6837.t5 Gene3D G3DSA:1.10.472.10 - 215 320 2.0E-32
4 g6837.t5 PANTHER PTHR11618 TRANSCRIPTION INITIATION FACTOR IIB-RELATED 20 302 6.6E-80
5 g6837.t5 PANTHER PTHR11618:SF13 TRANSCRIPTION INITIATION FACTOR IIB 20 302 6.6E-80
8 g6837.t5 PRINTS PR00685 Transcription initiation factor IIB signature 32 52 1.7E-72
9 g6837.t5 PRINTS PR00685 Transcription initiation factor IIB signature 54 67 1.7E-72
13 g6837.t5 PRINTS PR00685 Transcription initiation factor IIB signature 68 89 1.7E-72
6 g6837.t5 PRINTS PR00685 Transcription initiation factor IIB signature 166 185 1.7E-72
7 g6837.t5 PRINTS PR00685 Transcription initiation factor IIB signature 192 207 1.7E-72
12 g6837.t5 PRINTS PR00685 Transcription initiation factor IIB signature 219 237 1.7E-72
10 g6837.t5 PRINTS PR00685 Transcription initiation factor IIB signature 253 269 1.7E-72
11 g6837.t5 PRINTS PR00685 Transcription initiation factor IIB signature 285 299 1.7E-72
3 g6837.t5 Pfam PF08271 TFIIB zinc-binding 19 60 1.8E-11
2 g6837.t5 Pfam PF00382 Transcription factor TFIIB repeat 126 196 3.2E-27
1 g6837.t5 Pfam PF00382 Transcription factor TFIIB repeat 220 290 6.2E-25
22 g6837.t5 ProSitePatterns PS00782 Transcription factor TFIIB repeat signature. 158 173 -
21 g6837.t5 ProSitePatterns PS00782 Transcription factor TFIIB repeat signature. 252 267 -
25 g6837.t5 ProSiteProfiles PS51134 Zinc finger TFIIB-type profile. 16 47 8.653
24 g6837.t5 SMART SM00385 cyclin_7 124 205 2.4E-10
23 g6837.t5 SMART SM00385 cyclin_7 218 299 1.2E-10
16 g6837.t5 SUPERFAMILY SSF57783 Zinc beta-ribbon 14 63 8.25E-15
14 g6837.t5 SUPERFAMILY SSF47954 Cyclin-like 119 209 1.51E-25
15 g6837.t5 SUPERFAMILY SSF47954 Cyclin-like 214 320 3.02E-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

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