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.t8 TTS g6837.t8 19011135 19011135
chr_2 g6837 g6837.t8 isoform g6837.t8 19011283 19012928
chr_2 g6837 g6837.t8 exon g6837.t8.exon1 19011283 19012160
chr_2 g6837 g6837.t8 cds g6837.t8.CDS1 19011283 19012160
chr_2 g6837 g6837.t8 exon g6837.t8.exon2 19012771 19012823
chr_2 g6837 g6837.t8 cds g6837.t8.CDS2 19012771 19012823
chr_2 g6837 g6837.t8 exon g6837.t8.exon3 19012912 19012928
chr_2 g6837 g6837.t8 cds g6837.t8.CDS3 19012912 19012928
chr_2 g6837 g6837.t8 TSS g6837.t8 19013035 19013035

Sequences

>g6837.t8 Gene=g6837 Length=948
ATGGCAAGCACTTCAAACTTTAAGGACAGAGTGGTTTGTGTACATCATCCAGATGCTCCT
TTAATTGAAGAATATGCATCAAAGATTGATGTTGATTATTTCTTAATATATTTTATTTGC
TTCATCAGAGTAATTGACGTTGGTTCAGAATGGAGAACATTTAGTAATGAAAAAGCAGGA
GTTGATCCATCTCGTGTTGGTGGACCAGAAAATCCTCTTTTAAGTGGAGGTGATCTTTCA
ACAATGATTGGACCAGGAACTGGTGCTGCTTCATTCGATTCATTTGGATCTGCAAAATAT
CAAAATAGACGAACTATGAGTAGTTCTGATCGTGCTTTAATCACAGCATTCAAAGAAATA
AGTTCTATGGCAGATCGCATCAATTTGCCTAAAACTATCGTGGATAGAGCTAATAATTTA
TTCAAACAAGTACATGATGGAAAAAGTCTTAAAGGTCGTTCAAATGATGCAAAAGCCTCC
GCGTGTTTATATATTGCTTGTCGCCAAGAAGGAGTTCCTCGTACTTTTAAAGAAATCTGT
GCGATTAGTAGAGTGAGCAAGAAAGAAATTGGACGATGCTTTAAACTGACATTAAAAGCA
CTTGCCACTTCTGTTGATCTCATCACAACGGCCGATTTTATGTCTAGATTTTGTGCAAAT
TTGGTACTGCCTAATTATGTTCAGCGAGCTGCAACTCATATTGCGCGAAAAGCTGTTGAA
ATGGATATTGTTGCAGGAAGATCACCTATTTCAGTGGCTGCTGCAGCAATTTATATGGCA
TCACAAGCATCTGAAAATAAAAAGACACACAAGGAAATTGGCGATATTGCGGGTGTAGCA
GAAGCAACAATTCGTCAATCGTACAAATTAATGTATGGACATGCAAAAGCATTATTTCCT
GAAGACTTTCCATTTGCAACTCCAATTGAACAGCTTCCGCTGTTGTAA

>g6837.t8 Gene=g6837 Length=315
MASTSNFKDRVVCVHHPDAPLIEEYASKIDVDYFLIYFICFIRVIDVGSEWRTFSNEKAG
VDPSRVGGPENPLLSGGDLSTMIGPGTGAASFDSFGSAKYQNRRTMSSSDRALITAFKEI
SSMADRINLPKTIVDRANNLFKQVHDGKSLKGRSNDAKASACLYIACRQEGVPRTFKEIC
AISRVSKKEIGRCFKLTLKALATSVDLITTADFMSRFCANLVLPNYVQRAATHIARKAVE
MDIVAGRSPISVAAAAIYMASQASENKKTHKEIGDIAGVAEATIRQSYKLMYGHAKALFP
EDFPFATPIEQLPLL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g6837.t8 CDD cd00043 CYCLIN 113 196 2.24881E-13
16 g6837.t8 CDD cd00043 CYCLIN 207 292 1.7255E-12
14 g6837.t8 Gene3D G3DSA:1.10.472.170 - 39 201 2.4E-54
15 g6837.t8 Gene3D G3DSA:1.10.472.10 - 209 314 1.9E-32
3 g6837.t8 PANTHER PTHR11618 TRANSCRIPTION INITIATION FACTOR IIB-RELATED 44 296 6.1E-70
4 g6837.t8 PANTHER PTHR11618:SF13 TRANSCRIPTION INITIATION FACTOR IIB 44 296 6.1E-70
11 g6837.t8 PRINTS PR00685 Transcription initiation factor IIB signature 48 61 6.1E-61
5 g6837.t8 PRINTS PR00685 Transcription initiation factor IIB signature 62 83 6.1E-61
7 g6837.t8 PRINTS PR00685 Transcription initiation factor IIB signature 160 179 6.1E-61
9 g6837.t8 PRINTS PR00685 Transcription initiation factor IIB signature 186 201 6.1E-61
8 g6837.t8 PRINTS PR00685 Transcription initiation factor IIB signature 213 231 6.1E-61
10 g6837.t8 PRINTS PR00685 Transcription initiation factor IIB signature 247 263 6.1E-61
6 g6837.t8 PRINTS PR00685 Transcription initiation factor IIB signature 279 293 6.1E-61
2 g6837.t8 Pfam PF00382 Transcription factor TFIIB repeat 120 190 3.1E-27
1 g6837.t8 Pfam PF00382 Transcription factor TFIIB repeat 214 284 6.0E-25
18 g6837.t8 ProSitePatterns PS00782 Transcription factor TFIIB repeat signature. 152 167 -
19 g6837.t8 ProSitePatterns PS00782 Transcription factor TFIIB repeat signature. 246 261 -
21 g6837.t8 SMART SM00385 cyclin_7 118 199 2.4E-10
20 g6837.t8 SMART SM00385 cyclin_7 212 293 1.2E-10
12 g6837.t8 SUPERFAMILY SSF47954 Cyclin-like 113 203 1.46E-25
13 g6837.t8 SUPERFAMILY SSF47954 Cyclin-like 208 314 2.89E-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. There were no conditions that were differentially expressed