General information for g10814.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as General transcription factor IIF subunit 1.
Parent gene
- The parent gene g10814 is located on chr_1: 12109342..12111929 (- 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 | g10814 | g10814.t3 | isoform | g10814.t3 | 12109342 | 12110462 |
| chr_1 | g10814 | g10814.t3 | exon | g10814.t3.exon1 | 12109342 | 12109950 |
| chr_1 | g10814 | g10814.t3 | cds | g10814.t3.CDS1 | 12109444 | 12109950 |
| chr_1 | g10814 | g10814.t3 | exon | g10814.t3.exon2 | 12110022 | 12110369 |
| chr_1 | g10814 | g10814.t3 | cds | g10814.t3.CDS2 | 12110022 | 12110369 |
| chr_1 | g10814 | g10814.t3 | exon | g10814.t3.exon3 | 12110442 | 12110462 |
| chr_1 | g10814 | g10814.t3 | cds | g10814.t3.CDS3 | 12110442 | 12110462 |
| chr_1 | g10814 | g10814.t3 | TSS | g10814.t3 | 12110595 | 12110595 |
| chr_1 | g10814 | g10814.t3 | TTS | g10814.t3 | NA | NA |
Sequences
>g10814.t3 Gene=g10814 Length=978
ATGCATAAACCAGGACAAATCAATAATCCTAATTCTTCTTCTACACCAACGCCAATAATT
ACTGAGTATTCAATAAGAGTACCCAAAAATCTTAAGAGCAAGCATCATATTATGAGATTT
AATTACAATCTAAAAGTAGATTTTTCGCAATGGAAAAATGTTCGTATGGAAAGAGAAAAT
AATATGAGAGAATTCAAGACAATGGAAGAAGAGCTACCGAAATTTGGTGCCGGTTCAGAA
TATAATCGTGATCAAAAAGAGGAAGCACGTCGCAAGAAGTTTGGAATTATTGCAAAAAAG
TACAATCCAGAAGCACAACCATGGATTTTAAAAACGTCGAGTGGCAAATCAGGGAAAAAG
TTTCGAGGTATAAGAGAAGGTGGTGTGAGTGAAAATGCAGCTCATTTTGTGTTTACGCAA
ACAAAGGATGGTTCAATTGAGGCTTTTCCACTTCATGAATGGTACAATTTTCAACCAATT
CAAAGATATAAAGCCCTTACTGCTGAAGAAGCAGAAGAAGAATTTGGTCGTCGTCGTAAA
TGTGTAAATTTATGGTCAATGAAAATGCGAATGAAATTAAAGAATAAAGATGATGAGGAA
GCAGAAGATCCTGAAGATAAACCAGTGAAGGGATCAAAAGGTGGTGATAAAAAGAAACTT
ATGATTAGCGAAATGGATGAATGGATGGATTCTGATGATATGAGTTCTAGTGATGATGAT
GAAGATGGTGAAAAGAAAAAGAAAGAGGAAGAAAGTGATGACGATCAAGGTGCCAAGAAC
AAGAAAGGCAAAGGAAAAGCTGCACAAAATGCCAAGAAAAAGAAACGTGACGTGGATGAT
GAAGCATTTGAAGTGAGTTTAAAGAAAATTTTTTAAATGTAAATCTGTAATATTTTAATA
CTTCTTTTGTAGGAATCTGACGATGGTGATGAAGAAGGACGAGAACGTGACTATATTTCA
GACTCGAGTGATAGGTAA
>g10814.t3 Gene=g10814 Length=291
MHKPGQINNPNSSSTPTPIITEYSIRVPKNLKSKHHIMRFNYNLKVDFSQWKNVRMEREN
NMREFKTMEEELPKFGAGSEYNRDQKEEARRKKFGIIAKKYNPEAQPWILKTSSGKSGKK
FRGIREGGVSENAAHFVFTQTKDGSIEAFPLHEWYNFQPIQRYKALTAEEAEEEFGRRRK
CVNLWSMKMRMKLKNKDDEEAEDPEDKPVKGSKGGDKKKLMISEMDEWMDSDDMSSSDDD
EDGEKKKKEEESDDDQGAKNKKGKGKAAQNAKKKKRDVDDEAFEVSLKKIF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g10814.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 194 | 280 | - |
| 7 | g10814.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 194 | 226 | - |
| 5 | g10814.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 240 | 262 | - |
| 2 | g10814.t3 | PANTHER | PTHR13011 | TFIIF-ALPHA | 15 | 285 | 3.6E-63 |
| 3 | g10814.t3 | PANTHER | PTHR13011:SF0 | GENERAL TRANSCRIPTION FACTOR IIF SUBUNIT 1 | 15 | 285 | 3.6E-63 |
| 1 | g10814.t3 | Pfam | PF05793 | Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) | 12 | 284 | 5.2E-96 |
| 4 | g10814.t3 | SUPERFAMILY | SSF50916 | Rap30/74 interaction domains | 17 | 178 | 1.26E-53 |
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:0005634 | nucleus | CC |
| GO:0003677 | DNA binding | MF |
| GO:0032968 | positive regulation of transcription elongation from RNA polymerase II promoter | BP |
| GO:0006367 | transcription initiation from RNA polymerase II promoter | BP |
KEGG
Orthology
- This transcript has been annotated with K03138 (transcription initiation factor TFIIF subunit alpha)
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.
