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.t9 TTS g6837.t9 19011135 19011135
chr_2 g6837 g6837.t9 isoform g6837.t9 19011283 19012928
chr_2 g6837 g6837.t9 exon g6837.t9.exon1 19011283 19012102
chr_2 g6837 g6837.t9 cds g6837.t9.CDS1 19011283 19012102
chr_2 g6837 g6837.t9 exon g6837.t9.exon2 19012596 19012650
chr_2 g6837 g6837.t9 cds g6837.t9.CDS2 19012596 19012633
chr_2 g6837 g6837.t9 exon g6837.t9.exon3 19012767 19012823
chr_2 g6837 g6837.t9 exon g6837.t9.exon4 19012912 19012928
chr_2 g6837 g6837.t9 TSS g6837.t9 19013035 19013035

Sequences

>g6837.t9 Gene=g6837 Length=949
ATGGCAAGCACTTCAAACTTTAAGGACAGAGTGGTTTGTGTACATCATCCAGATGCTCCT
TTAATTGAAGGTATATTATCGAGCTGGTGATATGATTTGTTCGGAATGTGGATTAATAGT
TGGTGACAGAGTAATTGACGTTGGTTCAGAATGGAGAACATTTAGTAATGAAAAAGCAGG
AGTTGATCCATCTCGTGTTGGTGGACCAGAAAATCCTCTTTTAAGTGGAGGTGATCTTTC
AACAATGATTGGACCAGGAACTGGTGCTGCTTCATTCGATTCATTTGGATCTGCAAAATA
TCAAAATAGACGAACTATGAGTAGTTCTGATCGTGCTTTAATCACAGCATTCAAAGAAAT
AAGTTCTATGGCAGATCGCATCAATTTGCCTAAAACTATCGTGGATAGAGCTAATAATTT
ATTCAAACAAGTACATGATGGAAAAAGTCTTAAAGGTCGTTCAAATGATGCAAAAGCCTC
CGCGTGTTTATATATTGCTTGTCGCCAAGAAGGAGTTCCTCGTACTTTTAAAGAAATCTG
TGCGATTAGTAGAGTGAGCAAGAAAGAAATTGGACGATGCTTTAAACTGACATTAAAAGC
ACTTGCCACTTCTGTTGATCTCATCACAACGGCCGATTTTATGTCTAGATTTTGTGCAAA
TTTGGTACTGCCTAATTATGTTCAGCGAGCTGCAACTCATATTGCGCGAAAAGCTGTTGA
AATGGATATTGTTGCAGGAAGATCACCTATTTCAGTGGCTGCTGCAGCAATTTATATGGC
ATCACAAGCATCTGAAAATAAAAAGACACACAAGGAAATTGGCGATATTGCGGGTGTAGC
AGAAGCAACAATTCGTCAATCGTACAAATTAATGTATGGACATGCAAAAGCATTATTTCC
TGAAGACTTTCCATTTGCAACTCCAATTGAACAGCTTCCGCTGTTGTAA

>g6837.t9 Gene=g6837 Length=285
MICSECGLIVGDRVIDVGSEWRTFSNEKAGVDPSRVGGPENPLLSGGDLSTMIGPGTGAA
SFDSFGSAKYQNRRTMSSSDRALITAFKEISSMADRINLPKTIVDRANNLFKQVHDGKSL
KGRSNDAKASACLYIACRQEGVPRTFKEICAISRVSKKEIGRCFKLTLKALATSVDLITT
ADFMSRFCANLVLPNYVQRAATHIARKAVEMDIVAGRSPISVAAAAIYMASQASENKKTH
KEIGDIAGVAEATIRQSYKLMYGHAKALFPEDFPFATPIEQLPLL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g6837.t9 CDD cd00043 CYCLIN 83 166 8.53776E-14
17 g6837.t9 CDD cd00043 CYCLIN 177 262 7.45295E-13
15 g6837.t9 Gene3D G3DSA:1.10.472.170 - 1 171 1.4E-62
16 g6837.t9 Gene3D G3DSA:1.10.472.10 - 179 284 1.5E-32
3 g6837.t9 PANTHER PTHR11618 TRANSCRIPTION INITIATION FACTOR IIB-RELATED 1 266 4.9E-77
4 g6837.t9 PANTHER PTHR11618:SF13 TRANSCRIPTION INITIATION FACTOR IIB 1 266 4.9E-77
8 g6837.t9 PRINTS PR00685 Transcription initiation factor IIB signature 18 31 3.5E-61
11 g6837.t9 PRINTS PR00685 Transcription initiation factor IIB signature 32 53 3.5E-61
10 g6837.t9 PRINTS PR00685 Transcription initiation factor IIB signature 130 149 3.5E-61
9 g6837.t9 PRINTS PR00685 Transcription initiation factor IIB signature 156 171 3.5E-61
5 g6837.t9 PRINTS PR00685 Transcription initiation factor IIB signature 183 201 3.5E-61
7 g6837.t9 PRINTS PR00685 Transcription initiation factor IIB signature 217 233 3.5E-61
6 g6837.t9 PRINTS PR00685 Transcription initiation factor IIB signature 249 263 3.5E-61
1 g6837.t9 Pfam PF00382 Transcription factor TFIIB repeat 90 160 2.6E-27
2 g6837.t9 Pfam PF00382 Transcription factor TFIIB repeat 184 254 5.0E-25
20 g6837.t9 ProSitePatterns PS00782 Transcription factor TFIIB repeat signature. 122 137 -
19 g6837.t9 ProSitePatterns PS00782 Transcription factor TFIIB repeat signature. 216 231 -
22 g6837.t9 SMART SM00385 cyclin_7 88 169 2.4E-10
21 g6837.t9 SMART SM00385 cyclin_7 182 263 1.2E-10
14 g6837.t9 SUPERFAMILY SSF57783 Zinc beta-ribbon 1 27 6.97E-8
13 g6837.t9 SUPERFAMILY SSF47954 Cyclin-like 83 173 1.26E-25
12 g6837.t9 SUPERFAMILY SSF47954 Cyclin-like 178 284 2.34E-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. There were no conditions that were differentially expressed