Gene loci information

Transcript annotation

  • This transcript has been annotated as General transcription factor IIE subunit 2.

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_1 g10487 g10487.t4 TSS g10487.t4 10144336 10144336
chr_1 g10487 g10487.t4 isoform g10487.t4 10144405 10145417
chr_1 g10487 g10487.t4 exon g10487.t4.exon1 10144405 10144800
chr_1 g10487 g10487.t4 cds g10487.t4.CDS1 10144702 10144800
chr_1 g10487 g10487.t4 exon g10487.t4.exon2 10144854 10145417
chr_1 g10487 g10487.t4 cds g10487.t4.CDS2 10144854 10145417
chr_1 g10487 g10487.t4 TTS g10487.t4 10145554 10145554

Sequences

>g10487.t4 Gene=g10487 Length=960
ATGGATGCAGCACTTCTTAGAGAAAGAGAAGCGTTTAAGAAAAGAGCTTTAGCTACTCCT
ACGTAAGTACAAATTGTTACAATCACAATTAAACGGTAAATAATTTTTATTTCGCAAAAC
TTTAGAGTTGAAAAAAAATTACAAAAAGAATCAGCAAAATCATCATCAAGCAGCAAAAAA
CCATTACAGCCATGGGAATCAAAAGCACCGAAAGAACCAAGAGAGCCTATGAACTACAAA
ACTATGACCGGTAGTTCTAATAAAAGATTCGCAATTCTTACAAAAATAGTAAATTACATG
AAAGAAAAACATCTTAGTGGTGATGATCATCCAATTACGATAGAAGAAATTCTTGATGAA
ACAAATCAATTAGATATTGGATCATCAACTAAAACATGGCTTATGACAGAAGCTCTTCCA
AACAATCCCAAACTGGAACAGCCAGAATTAGGAAGATTTCAATTTAAACCTATGTATAGA
ATTAAGGATGGTAAGAGTTTAGTAAGACTACTCAAACAACATGATCTGAAAGGTCTTGGT
GGTATTTTACTTGATGACGTACAAGAATCACTGCCAAATTGTGATAAACTATTAAAAAAT
CGTGCATCGGAAATTATTTTCATTACACGACCAATTGATAAGAAAAAGATTCTATTCTAT
AATGATCGTACAGCAAATTTCCAAATCGATGAAGAATTTCAGAAGCTCTGGAGATCAGCA
ACAGTTGATGCAATGGATGATAATAAAATTGAAGAGTATTTAGAAAAACAAGGCATTCGT
TCAATGCAAGACCATGGTATTAGAAAACAAATGGCACCGAAGAGAAAGAAGCAGCCACTC
AAAAAGCGTCAATTTAAGAGACCACGAGACAATGAACATCTTGCAGACATTCTTGAGACA
TATGAAGATAACACAATCACACAGAAAGGAGATTTACATGCAAAGCAATCGGGATGTTAA

>g10487.t4 Gene=g10487 Length=220
MKEKHLSGDDHPITIEEILDETNQLDIGSSTKTWLMTEALPNNPKLEQPELGRFQFKPMY
RIKDGKSLVRLLKQHDLKGLGGILLDDVQESLPNCDKLLKNRASEIIFITRPIDKKKILF
YNDRTANFQIDEEFQKLWRSATVDAMDDNKIEEYLEKQGIRSMQDHGIRKQMAPKRKKQP
LKKRQFKRPRDNEHLADILETYEDNTITQKGDLHAKQSGC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g10487.t4 CDD cd07977 TFIIE_beta_winged_helix 1 63 1.31874E-16
8 g10487.t4 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 1 63 4.8E-23
6 g10487.t4 MobiDBLite mobidb-lite consensus disorder prediction 163 194 -
7 g10487.t4 MobiDBLite mobidb-lite consensus disorder prediction 171 185 -
3 g10487.t4 PANTHER PTHR12716:SF8 TRANSCRIPTION INITIATION FACTOR IIE SUBUNIT BETA 6 203 1.8E-46
4 g10487.t4 PANTHER PTHR12716 TRANSCRIPTION INITIATION FACTOR IIE, BETA SUBUNIT 6 203 1.8E-46
1 g10487.t4 Pfam PF02186 TFIIE beta subunit core domain 4 62 3.7E-13
2 g10487.t4 Pfam PF18121 TFA2 Winged helix domain 2 65 122 4.8E-7
9 g10487.t4 ProSiteProfiles PS51351 TFIIE beta central core DNA-binding domain profile. 1 63 12.038
5 g10487.t4 SUPERFAMILY SSF46785 Winged helix DNA-binding domain 1 63 1.01E-19

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:0005673 transcription factor TFIIE complex CC
GO:0006367 transcription initiation from RNA polymerase II promoter 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