General information for g3997.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Transcription initiation factor IIA subunit 2.
Parent gene
- The parent gene g3997 is located on chr_3: 29411890..29412362 (- 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 | g3997 | g3997.t1 | isoform | g3997.t1 | 29411890 | 29412362 |
| chr_3 | g3997 | g3997.t1 | exon | g3997.t1.exon1 | 29411890 | 29412004 |
| chr_3 | g3997 | g3997.t1 | cds | g3997.t1.CDS1 | 29411890 | 29412004 |
| chr_3 | g3997 | g3997.t1 | exon | g3997.t1.exon2 | 29412063 | 29412183 |
| chr_3 | g3997 | g3997.t1 | cds | g3997.t1.CDS2 | 29412063 | 29412183 |
| chr_3 | g3997 | g3997.t1 | exon | g3997.t1.exon3 | 29412257 | 29412362 |
| chr_3 | g3997 | g3997.t1 | cds | g3997.t1.CDS3 | 29412257 | 29412362 |
| chr_3 | g3997 | g3997.t1 | TSS | g3997.t1 | 29412420 | 29412420 |
| chr_3 | g3997 | g3997.t1 | TTS | g3997.t1 | NA | NA |
Sequences
>g3997.t1 Gene=g3997 Length=342
ATGTCTTATCAACTTTATAGAAATACAACTATTGGCAACACATTGCAAGAAAGTTTAGAT
GAATTGATTTCATATGGACAGATAACGCCACAGTTAGCCTTAAGAGTGCTCATACAATTT
GACAAATCTATCAATTCTGCATTATCTAATAAAGTTAAGTCAAGAATAACATTTAAAGCA
TCAAAATTAAACACATATCGATTTTGTGACAATGTTTGGACTCTCATGCTTAATGATGTT
GAATTTCGAGAGGTTCATGAATTTGCCAAAGTTGATAAAATTAAGATTGTAGCGTGTGAT
GGAAAATCGACTTACAATAATGATACTGAAAAAAACAATTGA
>g3997.t1 Gene=g3997 Length=113
MSYQLYRNTTIGNTLQESLDELISYGQITPQLALRVLIQFDKSINSALSNKVKSRITFKA
SKLNTYRFCDNVWTLMLNDVEFREVHEFAKVDKIKIVACDGKSTYNNDTEKNN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g3997.t1 | CDD | cd10145 | TFIIA_gamma_N | 2 | 50 | 0 |
| 10 | g3997.t1 | CDD | cd10014 | TFIIA_gamma_C | 56 | 102 | 0 |
| 7 | g3997.t1 | Gene3D | G3DSA:1.10.287.190 | - | 2 | 53 | 0 |
| 8 | g3997.t1 | Gene3D | G3DSA:2.30.18.10 | Transcription factor IIA (TFIIA) | 54 | 110 | 0 |
| 3 | g3997.t1 | PANTHER | PTHR10966:SF5 | TRANSCRIPTION INITIATION FACTOR IIA SUBUNIT 2 | 1 | 110 | 0 |
| 4 | g3997.t1 | PANTHER | PTHR10966 | TRANSCRIPTION INITIATION FACTOR IIA SUBUNIT 2 | 1 | 110 | 0 |
| 9 | g3997.t1 | PIRSF | PIRSF009415 | TFIIA_gamma_hum | 1 | 107 | 0 |
| 2 | g3997.t1 | Pfam | PF02268 | Transcription initiation factor IIA, gamma subunit, helical domain | 2 | 48 | 0 |
| 1 | g3997.t1 | Pfam | PF02751 | Transcription initiation factor IIA, gamma subunit | 62 | 101 | 0 |
| 6 | g3997.t1 | SUPERFAMILY | SSF47396 | Transcription factor IIA (TFIIA), alpha-helical domain | 3 | 53 | 0 |
| 5 | g3997.t1 | SUPERFAMILY | SSF50784 | Transcription factor IIA (TFIIA), beta-barrel domain | 51 | 102 | 0 |
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:0005672 | transcription factor TFIIA complex | CC |
| GO:0006367 | transcription initiation from RNA polymerase II promoter | BP |
KEGG
Orthology
- This transcript has been annotated with K03123 (transcription initiation factor TFIIA small subunit)
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.
