General information for g2413.t22
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as General transcription factor IIF subunit 2.
Parent gene
- The parent gene g2413 is located on chr_3: 17778141..17780592 (- strand)
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.t22 | TTS | g2413.t22 | 17778075 | 17778075 |
| chr_3 | g2413 | g2413.t22 | isoform | g2413.t22 | 17778141 | 17780592 |
| chr_3 | g2413 | g2413.t22 | exon | g2413.t22.exon1 | 17778141 | 17778667 |
| chr_3 | g2413 | g2413.t22 | cds | g2413.t22.CDS1 | 17778141 | 17778667 |
| chr_3 | g2413 | g2413.t22 | exon | g2413.t22.exon2 | 17778723 | 17778905 |
| chr_3 | g2413 | g2413.t22 | cds | g2413.t22.CDS2 | 17778723 | 17778905 |
| chr_3 | g2413 | g2413.t22 | exon | g2413.t22.exon3 | 17778965 | 17779134 |
| chr_3 | g2413 | g2413.t22 | cds | g2413.t22.CDS3 | 17778965 | 17779076 |
| chr_3 | g2413 | g2413.t22 | exon | g2413.t22.exon4 | 17779405 | 17779676 |
| chr_3 | g2413 | g2413.t22 | exon | g2413.t22.exon5 | 17780485 | 17780592 |
| chr_3 | g2413 | g2413.t22 | TSS | g2413.t22 | NA | NA |
Sequences
>g2413.t22 Gene=g2413 Length=1260
GCTGATGCTTAAATTTCTACAACTAAACAACAAAAAAAAAGTATGAAGAATTGATGTTTC
AACACATACATATATGTAAATGCATGAATGTGACTTTATTAAGAAAAGCCTGTTTAACAT
TTTATGTGTAACTCAATAATAAACCCTTTACAATGAATGCTAAATACCAAAACACAGAAC
CATTCAGTACTGATGAGCATAAAAACATTGAAACAAAGAAACATAAACAATGAGTGCTGA
GCACTGATACACAAAAAACATTAAAACAATACTTTCATAAAATTTGATTTTACACTCCTA
TATATGTTGTTAAACTATGTTTGTTTTTTGAAAATTATTCTTTTAAAAAACATAAAATGC
GTCAAGAGTATTATTTTACTATTTTCAAAAAAAATCAAAAGCTATCTAAAGACGTAAACA
AAAAATATTAAATTGAAAATGTCAAAACACGAGGAAGTCAAGCAAGAGAAGGAGTTAGAT
GTTGCAAATGCAAACCGTGGTGTATGGCTTGTAAAGGTACCGAAATATATTGCAAAAAAA
TGGGAACGAGTTAATGGTGATGTTGAAGTAGGAAAACTAAAAATAGTGAAATATCCGGGT
CAAAAATCACAAGTATCATTATCATTGTCAGAAGCAACTTTAAAAATTGATACTGATGAA
GAAATTCCAAAAGATCATAGGTTTGACGTATTGGCTGTGAATAAACAAACTCTTGGTGTT
TTTAGTCAAAATATTGATCCAGATAAATCTGACAAAATTTATATGGAAGGTACAATAGTT
GAGAAATTAGAATGTCGTCCTTATGCTGACACCACTTACATGAAACTTAAAGCAATGTCA
ATTAGAAATGCATCGCTTCCCAAACGTCGTGTTGAACAATTAGATACTGTTGTGACTACA
TTTAAACCAGTCTCTGACCATAAACATAATATCGAGTATGAGAATAAGAAAAAGAACGAT
GGGAAGAAATCTCGTGCAGATAAAAATGCTGTTATGGATGTCTTATTTAATGCATTCGAA
AAACATCAGTATTACAATATCAAAGATCTTGTTACAATCACAAATCAACCAATTTCATAC
TTGAAAGAAATTCTCAAAGAAATATGCGAATATAGTGTGAAGAATCCTCATAAAAATACA
TGGCATTTGAAAGCAGAATATAGGCATTATTCTGAAGAGAAAAAGGATAAAAAGGCTGAT
ACTAAAGATGAAGGAACTGATGACAAAATGAGCGATAGCGATGATGACGATGACTTTTAG
>g2413.t22 Gene=g2413 Length=273
MSKHEEVKQEKELDVANANRGVWLVKVPKYIAKKWERVNGDVEVGKLKIVKYPGQKSQVS
LSLSEATLKIDTDEEIPKDHRFDVLAVNKQTLGVFSQNIDPDKSDKIYMEGTIVEKLECR
PYADTTYMKLKAMSIRNASLPKRRVEQLDTVVTTFKPVSDHKHNIEYENKKKNDGKKSRA
DKNAVMDVLFNAFEKHQYYNIKDLVTITNQPISYLKEILKEICEYSVKNPHKNTWHLKAE
YRHYSEEKKDKKADTKDEGTDDKMSDSDDDDDF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g2413.t22 | CDD | cd07980 | TFIIF_beta | 10 | 121 | 8.30203E-28 |
| 9 | g2413.t22 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 177 | 245 | 3.7E-31 |
| 7 | g2413.t22 | MobiDBLite | mobidb-lite | consensus disorder prediction | 245 | 273 | - |
| 8 | g2413.t22 | MobiDBLite | mobidb-lite | consensus disorder prediction | 245 | 262 | - |
| 3 | g2413.t22 | PANTHER | PTHR10445:SF0 | GENERAL TRANSCRIPTION FACTOR IIF SUBUNIT 2 | 5 | 253 | 3.6E-68 |
| 4 | g2413.t22 | PANTHER | PTHR10445 | GENERAL TRANSCRIPTION FACTOR IIF SUBUNIT 2 | 5 | 253 | 3.6E-68 |
| 10 | g2413.t22 | PIRSF | PIRSF015849 | TFIIF-beta | 1 | 254 | 1.1E-92 |
| 1 | g2413.t22 | Pfam | PF17683 | TFIIF, beta subunit N-terminus | 19 | 102 | 9.9E-17 |
| 2 | g2413.t22 | Pfam | PF02270 | TFIIF, beta subunit HTH domain | 179 | 242 | 5.9E-23 |
| 5 | g2413.t22 | SUPERFAMILY | SSF50916 | Rap30/74 interaction domains | 9 | 122 | 2.88E-29 |
| 6 | g2413.t22 | 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
- This transcript has been annotated with K03139 (transcription initiation factor TFIIF subunit beta [EC:5.6.2.-])
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.
