General information for g2413.t20
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.t20 | TTS | g2413.t20 | 17778075 | 17778075 |
| chr_3 | g2413 | g2413.t20 | isoform | g2413.t20 | 17778141 | 17779076 |
| chr_3 | g2413 | g2413.t20 | exon | g2413.t20.exon1 | 17778141 | 17778667 |
| chr_3 | g2413 | g2413.t20 | cds | g2413.t20.CDS1 | 17778141 | 17778638 |
| chr_3 | g2413 | g2413.t20 | exon | g2413.t20.exon2 | 17778723 | 17779076 |
| chr_3 | g2413 | g2413.t20 | TSS | g2413.t20 | 17779135 | 17779135 |
Sequences
>g2413.t20 Gene=g2413 Length=881
ATGTCAAAACACGAGGAAGTCAAGCAAGAGAAGGAGTTAGATGTTGCAAATGCAAACCGT
GGTGTATGGCTTGTAAAGGTACCGAAATATATTGCAAAAAAATGGGAACGAGGTAAAATT
ATGAAATTCTTGATTTAAAATCTTTTTAAAAAAAATTTATAAATGTTTCAGTTAATGGTG
ATGTTGAAGTAGGAAAACTAAAAATAGTGAAATATCCGGGTCAAAAATCACAAGTATCAT
TATCATTGTCAGAAGCAACTTTAAAAATTGATACTGATGAAGAAATTCCAAAAGATCATA
GGTTTGACGTATTGGCTGTGAATAAACAAACTCTTGGTGTTTTTAGTCAAAATATTGATC
CAGATAAATCTGACAAAATTTATATGGAAGGTACAATAGTTGAGAAATTAGAATGTCGTC
CTTATGCTGACACCACTTACATGAAACTTAAAGCAATGTCAATTAGAAATGCATCGCTTC
CCAAACGTCGTGTTGAACAATTAGATACTGTTGTGACTACATTTAAACCAGTCTCTGACC
ATAAACATAATATCGAGTATGAGAATAAGAAAAAGAACGATGGGAAGAAATCTCGTGCAG
ATAAAAATGCTGTTATGGATGTCTTATTTAATGCATTCGAAAAACATCAGTATTACAATA
TCAAAGATCTTGTTACAATCACAAATCAACCAATTTCATACTTGAAAGAAATTCTCAAAG
AAATATGCGAATATAGTGTGAAGAATCCTCATAAAAATACATGGCATTTGAAAGCAGAAT
ATAGGCATTATTCTGAAGAGAAAAAGGATAAAAAGGCTGATACTAAAGATGAAGGAACTG
ATGACAAAATGAGCGATAGCGATGATGACGATGACTTTTAG
>g2413.t20 Gene=g2413 Length=165
MEGTIVEKLECRPYADTTYMKLKAMSIRNASLPKRRVEQLDTVVTTFKPVSDHKHNIEYE
NKKKNDGKKSRADKNAVMDVLFNAFEKHQYYNIKDLVTITNQPISYLKEILKEICEYSVK
NPHKNTWHLKAEYRHYSEEKKDKKADTKDEGTDDKMSDSDDDDDF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g2413.t20 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 69 | 137 | 1.3E-31 |
| 5 | g2413.t20 | MobiDBLite | mobidb-lite | consensus disorder prediction | 137 | 154 | - |
| 6 | g2413.t20 | MobiDBLite | mobidb-lite | consensus disorder prediction | 137 | 165 | - |
| 2 | g2413.t20 | PANTHER | PTHR10445:SF0 | GENERAL TRANSCRIPTION FACTOR IIF SUBUNIT 2 | 1 | 145 | 1.2E-44 |
| 3 | g2413.t20 | PANTHER | PTHR10445 | GENERAL TRANSCRIPTION FACTOR IIF SUBUNIT 2 | 1 | 145 | 1.2E-44 |
| 1 | g2413.t20 | Pfam | PF02270 | TFIIF, beta subunit HTH domain | 71 | 134 | 2.2E-23 |
| 4 | g2413.t20 | SUPERFAMILY | SSF46785 | Winged helix DNA-binding domain | 71 | 136 | 5.98E-23 |
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 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.
