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.t1 TTS g6837.t1 19011135 19011135
chr_2 g6837 g6837.t1 isoform g6837.t1 19011283 19012928
chr_2 g6837 g6837.t1 exon g6837.t1.exon1 19011283 19012102
chr_2 g6837 g6837.t1 cds g6837.t1.CDS1 19011283 19012102
chr_2 g6837 g6837.t1 exon g6837.t1.exon2 19012596 19012650
chr_2 g6837 g6837.t1 cds g6837.t1.CDS2 19012596 19012650
chr_2 g6837 g6837.t1 exon g6837.t1.exon3 19012771 19012823
chr_2 g6837 g6837.t1 cds g6837.t1.CDS3 19012771 19012823
chr_2 g6837 g6837.t1 exon g6837.t1.exon4 19012912 19012928
chr_2 g6837 g6837.t1 cds g6837.t1.CDS4 19012912 19012928
chr_2 g6837 g6837.t1 TSS g6837.t1 19013035 19013035

Sequences

>g6837.t1 Gene=g6837 Length=945
ATGGCAAGCACTTCAAACTTTAAGGACAGAGTGGTTTGTGTACATCATCCAGATGCTCCT
TTAATTGAAGATTATCGAGCTGGTGATATGATTTGTTCGGAATGTGGATTAATAGTTGGT
GACAGAGTAATTGACGTTGGTTCAGAATGGAGAACATTTAGTAATGAAAAAGCAGGAGTT
GATCCATCTCGTGTTGGTGGACCAGAAAATCCTCTTTTAAGTGGAGGTGATCTTTCAACA
ATGATTGGACCAGGAACTGGTGCTGCTTCATTCGATTCATTTGGATCTGCAAAATATCAA
AATAGACGAACTATGAGTAGTTCTGATCGTGCTTTAATCACAGCATTCAAAGAAATAAGT
TCTATGGCAGATCGCATCAATTTGCCTAAAACTATCGTGGATAGAGCTAATAATTTATTC
AAACAAGTACATGATGGAAAAAGTCTTAAAGGTCGTTCAAATGATGCAAAAGCCTCCGCG
TGTTTATATATTGCTTGTCGCCAAGAAGGAGTTCCTCGTACTTTTAAAGAAATCTGTGCG
ATTAGTAGAGTGAGCAAGAAAGAAATTGGACGATGCTTTAAACTGACATTAAAAGCACTT
GCCACTTCTGTTGATCTCATCACAACGGCCGATTTTATGTCTAGATTTTGTGCAAATTTG
GTACTGCCTAATTATGTTCAGCGAGCTGCAACTCATATTGCGCGAAAAGCTGTTGAAATG
GATATTGTTGCAGGAAGATCACCTATTTCAGTGGCTGCTGCAGCAATTTATATGGCATCA
CAAGCATCTGAAAATAAAAAGACACACAAGGAAATTGGCGATATTGCGGGTGTAGCAGAA
GCAACAATTCGTCAATCGTACAAATTAATGTATGGACATGCAAAAGCATTATTTCCTGAA
GACTTTCCATTTGCAACTCCAATTGAACAGCTTCCGCTGTTGTAA

>g6837.t1 Gene=g6837 Length=314
MASTSNFKDRVVCVHHPDAPLIEDYRAGDMICSECGLIVGDRVIDVGSEWRTFSNEKAGV
DPSRVGGPENPLLSGGDLSTMIGPGTGAASFDSFGSAKYQNRRTMSSSDRALITAFKEIS
SMADRINLPKTIVDRANNLFKQVHDGKSLKGRSNDAKASACLYIACRQEGVPRTFKEICA
ISRVSKKEIGRCFKLTLKALATSVDLITTADFMSRFCANLVLPNYVQRAATHIARKAVEM
DIVAGRSPISVAAAAIYMASQASENKKTHKEIGDIAGVAEATIRQSYKLMYGHAKALFPE
DFPFATPIEQLPLL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g6837.t1 CDD cd00043 CYCLIN 112 195 1.05264E-13
20 g6837.t1 CDD cd00043 CYCLIN 206 291 8.78345E-13
17 g6837.t1 Gene3D G3DSA:1.10.472.170 - 11 200 2.5E-67
18 g6837.t1 Gene3D G3DSA:1.10.472.10 - 208 313 1.9E-32
4 g6837.t1 PANTHER PTHR11618 TRANSCRIPTION INITIATION FACTOR IIB-RELATED 13 295 6.1E-80
5 g6837.t1 PANTHER PTHR11618:SF13 TRANSCRIPTION INITIATION FACTOR IIB 13 295 6.1E-80
9 g6837.t1 PRINTS PR00685 Transcription initiation factor IIB signature 25 45 1.4E-72
11 g6837.t1 PRINTS PR00685 Transcription initiation factor IIB signature 47 60 1.4E-72
8 g6837.t1 PRINTS PR00685 Transcription initiation factor IIB signature 61 82 1.4E-72
6 g6837.t1 PRINTS PR00685 Transcription initiation factor IIB signature 159 178 1.4E-72
10 g6837.t1 PRINTS PR00685 Transcription initiation factor IIB signature 185 200 1.4E-72
13 g6837.t1 PRINTS PR00685 Transcription initiation factor IIB signature 212 230 1.4E-72
7 g6837.t1 PRINTS PR00685 Transcription initiation factor IIB signature 246 262 1.4E-72
12 g6837.t1 PRINTS PR00685 Transcription initiation factor IIB signature 278 292 1.4E-72
3 g6837.t1 Pfam PF08271 TFIIB zinc-binding 12 53 1.8E-11
1 g6837.t1 Pfam PF00382 Transcription factor TFIIB repeat 119 189 3.1E-27
2 g6837.t1 Pfam PF00382 Transcription factor TFIIB repeat 213 283 6.0E-25
21 g6837.t1 ProSitePatterns PS00782 Transcription factor TFIIB repeat signature. 151 166 -
22 g6837.t1 ProSitePatterns PS00782 Transcription factor TFIIB repeat signature. 245 260 -
25 g6837.t1 ProSiteProfiles PS51134 Zinc finger TFIIB-type profile. 9 40 8.653
23 g6837.t1 SMART SM00385 cyclin_7 117 198 2.4E-10
24 g6837.t1 SMART SM00385 cyclin_7 211 292 1.2E-10
16 g6837.t1 SUPERFAMILY SSF57783 Zinc beta-ribbon 9 56 1.11E-14
15 g6837.t1 SUPERFAMILY SSF47954 Cyclin-like 112 202 1.44E-25
14 g6837.t1 SUPERFAMILY SSF47954 Cyclin-like 207 313 2.85E-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