General information for g11011.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Transcription initiation factor IIA subunit 1.
Parent gene
- The parent gene g11011 is located on chr_1: 13393959..13395233 (- 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_1 | g11011 | g11011.t4 | TTS | g11011.t4 | 13393136 | 13393136 |
| chr_1 | g11011 | g11011.t4 | isoform | g11011.t4 | 13393959 | 13395233 |
| chr_1 | g11011 | g11011.t4 | exon | g11011.t4.exon1 | 13393959 | 13394496 |
| chr_1 | g11011 | g11011.t4 | cds | g11011.t4.CDS1 | 13393960 | 13394496 |
| chr_1 | g11011 | g11011.t4 | exon | g11011.t4.exon2 | 13394716 | 13394922 |
| chr_1 | g11011 | g11011.t4 | cds | g11011.t4.CDS2 | 13394716 | 13394922 |
| chr_1 | g11011 | g11011.t4 | exon | g11011.t4.exon3 | 13395204 | 13395233 |
| chr_1 | g11011 | g11011.t4 | cds | g11011.t4.CDS3 | 13395204 | 13395233 |
| chr_1 | g11011 | g11011.t4 | TSS | g11011.t4 | 13395335 | 13395335 |
Sequences
>g11011.t4 Gene=g11011 Length=775
ATGGCTCAAACCTCTGCATCATCGTCGGTGCTCAAATTATATCAACTTGTAATTGAGGAT
GTTGTTGCAAATGTACGCGATGCCTTTCTCGACGAAGGAGTCGATGAACAAGTGCTACAG
GAAATGAAACAAATCTGGACAAATCGACTGATGGCCAGTAAAGCGGTTGAAGTGACGCCA
GAACCACAAGCTCCTCCAACAGGCAATCAGCCTGCAATACTGGCGAATAATCCTAAGGCA
AATGGAACAAAGTCTAAAAAGGCAGCAGCAGCAGAGCTCAAAAATTCGGCAGCATCTGTC
AATGGAAATGTAAAAAGTAATGTCCCTCCTCTTGCAGCTTCTGCACCAAAAAATACAGCA
AACACATCTGTAAAAAATCAACAGCAGACTACAAATGTCATTAAAACAGAACCAGGTCAA
TCAACGACATCTGCATCTGTTGCCTCTACATCAGCAACAAATTCAACAACGTCTGCACCA
TCGTCTTCATCATCTACCATTGCTGCAGCATCACAAAATGGTCCACCAGCTCTACAACAA
ACCACTTTAGATCCAAATAAGCTCATACCAATTCAAATTACACTTCCTCCACAACCTCCC
AATGAAACTGAAAACCGAGTATTGACTATTAAAGTGCCAGCTCGAGCAATTCAAGAAAAT
CAACTGCAACAGGTCATCACAGGTGAAATCATAACATCAATAATGCCTCTTCAACCAAGT
GTGGCATCAGCTGTTCTTCAACAACATGTGACATCTGTTTTAAACACGATGTATG
>g11011.t4 Gene=g11011 Length=258
MAQTSASSSVLKLYQLVIEDVVANVRDAFLDEGVDEQVLQEMKQIWTNRLMASKAVEVTP
EPQAPPTGNQPAILANNPKANGTKSKKAAAAELKNSAASVNGNVKSNVPPLAASAPKNTA
NTSVKNQQQTTNVIKTEPGQSTTSASVASTSATNSTTSAPSSSSSTIAAASQNGPPALQQ
TTLDPNKLIPIQITLPPQPPNETENRVLTIKVPARAIQENQLQQVITGEIITSIMPLQPS
VASAVLQQHVTSVLNTMY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g11011.t4 | CDD | cd07976 | TFIIA_alpha_beta_like | 10 | 102 | 6.2822E-25 |
| 7 | g11011.t4 | Gene3D | G3DSA:1.10.287.100 | - | 2 | 57 | 2.1E-24 |
| 6 | g11011.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 115 | 176 | - |
| 2 | g11011.t4 | PANTHER | PTHR12694 | TRANSCRIPTION INITIATION FACTOR IIA SUBUNIT 1 | 7 | 179 | 5.3E-19 |
| 3 | g11011.t4 | PANTHER | PTHR12694:SF8 | TRANSCRIPTION INITIATION FACTOR IIA SUBUNIT 1 | 7 | 179 | 5.3E-19 |
| 1 | g11011.t4 | Pfam | PF03153 | Transcription factor IIA, alpha/beta subunit | 13 | 223 | 3.8E-24 |
| 5 | g11011.t4 | SMART | SM01371 | TFIIA_2 | 12 | 258 | 3.0E-5 |
| 4 | g11011.t4 | SUPERFAMILY | SSF47396 | Transcription factor IIA (TFIIA), alpha-helical domain | 9 | 51 | 1.88E-13 |
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 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.
