Gene loci information

Transcript annotation

  • This transcript has been annotated as General transcription factor IIF 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_3 g2413 g2413.t1 TTS g2413.t1 17778075 17778075
chr_3 g2413 g2413.t1 isoform g2413.t1 17778141 17779076
chr_3 g2413 g2413.t1 exon g2413.t1.exon1 17778141 17778667
chr_3 g2413 g2413.t1 cds g2413.t1.CDS1 17778141 17778667
chr_3 g2413 g2413.t1 exon g2413.t1.exon2 17778723 17778905
chr_3 g2413 g2413.t1 cds g2413.t1.CDS2 17778723 17778905
chr_3 g2413 g2413.t1 exon g2413.t1.exon3 17778965 17779076
chr_3 g2413 g2413.t1 cds g2413.t1.CDS3 17778965 17779076
chr_3 g2413 g2413.t1 TSS g2413.t1 17779135 17779135

Sequences

>g2413.t1 Gene=g2413 Length=822
ATGTCAAAACACGAGGAAGTCAAGCAAGAGAAGGAGTTAGATGTTGCAAATGCAAACCGT
GGTGTATGGCTTGTAAAGGTACCGAAATATATTGCAAAAAAATGGGAACGAGTTAATGGT
GATGTTGAAGTAGGAAAACTAAAAATAGTGAAATATCCGGGTCAAAAATCACAAGTATCA
TTATCATTGTCAGAAGCAACTTTAAAAATTGATACTGATGAAGAAATTCCAAAAGATCAT
AGGTTTGACGTATTGGCTGTGAATAAACAAACTCTTGGTGTTTTTAGTCAAAATATTGAT
CCAGATAAATCTGACAAAATTTATATGGAAGGTACAATAGTTGAGAAATTAGAATGTCGT
CCTTATGCTGACACCACTTACATGAAACTTAAAGCAATGTCAATTAGAAATGCATCGCTT
CCCAAACGTCGTGTTGAACAATTAGATACTGTTGTGACTACATTTAAACCAGTCTCTGAC
CATAAACATAATATCGAGTATGAGAATAAGAAAAAGAACGATGGGAAGAAATCTCGTGCA
GATAAAAATGCTGTTATGGATGTCTTATTTAATGCATTCGAAAAACATCAGTATTACAAT
ATCAAAGATCTTGTTACAATCACAAATCAACCAATTTCATACTTGAAAGAAATTCTCAAA
GAAATATGCGAATATAGTGTGAAGAATCCTCATAAAAATACATGGCATTTGAAAGCAGAA
TATAGGCATTATTCTGAAGAGAAAAAGGATAAAAAGGCTGATACTAAAGATGAAGGAACT
GATGACAAAATGAGCGATAGCGATGATGACGATGACTTTTAG

>g2413.t1 Gene=g2413 Length=273
MSKHEEVKQEKELDVANANRGVWLVKVPKYIAKKWERVNGDVEVGKLKIVKYPGQKSQVS
LSLSEATLKIDTDEEIPKDHRFDVLAVNKQTLGVFSQNIDPDKSDKIYMEGTIVEKLECR
PYADTTYMKLKAMSIRNASLPKRRVEQLDTVVTTFKPVSDHKHNIEYENKKKNDGKKSRA
DKNAVMDVLFNAFEKHQYYNIKDLVTITNQPISYLKEILKEICEYSVKNPHKNTWHLKAE
YRHYSEEKKDKKADTKDEGTDDKMSDSDDDDDF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g2413.t1 CDD cd07980 TFIIF_beta 10 121 8.30203E-28
9 g2413.t1 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 177 245 3.7E-31
7 g2413.t1 MobiDBLite mobidb-lite consensus disorder prediction 245 273 -
8 g2413.t1 MobiDBLite mobidb-lite consensus disorder prediction 245 262 -
3 g2413.t1 PANTHER PTHR10445:SF0 GENERAL TRANSCRIPTION FACTOR IIF SUBUNIT 2 5 253 3.6E-68
4 g2413.t1 PANTHER PTHR10445 GENERAL TRANSCRIPTION FACTOR IIF SUBUNIT 2 5 253 3.6E-68
10 g2413.t1 PIRSF PIRSF015849 TFIIF-beta 1 254 1.1E-92
1 g2413.t1 Pfam PF17683 TFIIF, beta subunit N-terminus 19 102 9.9E-17
2 g2413.t1 Pfam PF02270 TFIIF, beta subunit HTH domain 179 242 5.9E-23
5 g2413.t1 SUPERFAMILY SSF50916 Rap30/74 interaction domains 9 122 2.88E-29
6 g2413.t1 SUPERFAMILY SSF46785 Winged helix DNA-binding domain 179 244 1.71E-22

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:0005674 transcription factor TFIIF complex CC
GO:0006367 transcription initiation from RNA polymerase II promoter BP
GO:0006366 transcription by RNA polymerase II 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