General information for g12007.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as General transcription factor IIE subunit 1.
Parent gene
- The parent gene g12007 is located on chr_1: 20304962..20306578 (- 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 | g12007 | g12007.t2 | TTS | g12007.t2 | 20303498 | 20303498 |
| chr_1 | g12007 | g12007.t2 | isoform | g12007.t2 | 20303535 | 20304962 |
| chr_1 | g12007 | g12007.t2 | exon | g12007.t2.exon1 | 20303535 | 20303728 |
| chr_1 | g12007 | g12007.t2 | cds | g12007.t2.CDS1 | 20303535 | 20303728 |
| chr_1 | g12007 | g12007.t2 | exon | g12007.t2.exon2 | 20303798 | 20304962 |
| chr_1 | g12007 | g12007.t2 | cds | g12007.t2.CDS2 | 20303798 | 20304734 |
| chr_1 | g12007 | g12007.t2 | TSS | g12007.t2 | 20305027 | 20305027 |
Sequences
>g12007.t2 Gene=g12007 Length=1359
ATGAGTAATAATCAAGAATTAGTTTATGAAATTCCTAGTTCATTGAAACAATTAGCTCGT
CTTGTGGTTCGCGGTTTTTATACAATTGAAGATGCATTGATAGTTGATATGCTTGTAAGA
AATCCATGTATGAAGGTAAATAAATTTTCTAATATCTTTAAATACAAATATTAATTTGTT
AAATTATAGGAAGACGATATAGCTGAACTTCTTAAATTTGAGAAAAAGATGCTACGAGCC
AGATTAACGCTTTTAAAAAACGATAAATTTATGCAAGCAAGATTAAAAATGGAAACTGGA
GTAGACGGAAAAGCACATAAAGTGAATTATTACTTTATCAATTATAAAACTTTCGTTAAT
GTTATTAAATATAAATTGGATTTAATGAGAAAGAGACTTGAAACAGAGGAAAGAGACGCA
ACTGCTCGAGCTAATTTTAAATGCACAAATTGCTCAAAACCTTTTACTGATCTTGAAGTT
GATCAATTATTTGACCTTAATACTGGTGAATTAAGATGTACCTATTGTGGGAGTTTAGTA
GAAGAAGATATGGCAGCAATGCCGCGAACAGATTCTCGATTAATGCTCGCAAAATTCAAT
GAGCAATTAGAACCACTTTATGATCTTTTAAAGCAAGCCGAAGGTATAAAATTGGCTCCT
GAAGTTTTGGAACCACAGCCAATTGATATCGATGTAATTCGTGGAATAACTAAGCCATCT
GAAATGATGCATAATGAAGTGTGGTCAGGTGAAGCAACAAGATCAACATCAGGTTTCATG
AATGAAGAGGCAAAGGTTAATGTGACAATTGGAGAGATTGATACAGTTGATCAAAGTGCT
CAAAAGAAAGAACGACCTGTTTGGATGACTGAAAGTACTGTGGTTTCTAAAGATGCTGAA
CAGGATGCTGAGTCAATGCTTGAAAAAGTAGCTCAAAGTGCAGTACAAGCAAGTTCATGG
CAAACACCAGCACCAGCTATCACAACCACATCTAAAAATAAGAAAGAAACTGAAGAAAAT
ATCATGTCTGTTCTTTTAGCACATGAAAAACAAACGACTAAAGCTAATAATGATGCCGTA
AGGAACCTCAATAATCAAGACGATTCCAGTGGTGGTGGTGACTCGAGCGGAGATGATGAT
GATGAAATCGATCGAACTGAAATTCCAAACATTGAGCTTGAAATTATGAATGAAGATGAA
GAATCGGATGAAGAAGATGTACCTAAAGTGATGATTGGGAACAAATCTTATCCTGTAACA
GAAGTCATGGATAATACAGAATTAATAGCTAAAATGACACCTCATGAAAAAGCGCAATAC
ATTCAAATTTATCAAGAATATTTTGAGCATCTGTATTAA
>g12007.t2 Gene=g12007 Length=376
MLRARLTLLKNDKFMQARLKMETGVDGKAHKVNYYFINYKTFVNVIKYKLDLMRKRLETE
ERDATARANFKCTNCSKPFTDLEVDQLFDLNTGELRCTYCGSLVEEDMAAMPRTDSRLML
AKFNEQLEPLYDLLKQAEGIKLAPEVLEPQPIDIDVIRGITKPSEMMHNEVWSGEATRST
SGFMNEEAKVNVTIGEIDTVDQSAQKKERPVWMTESTVVSKDAEQDAESMLEKVAQSAVQ
ASSWQTPAPAITTTSKNKKETEENIMSVLLAHEKQTTKANNDAVRNLNNQDDSSGGGDSS
GDDDDEIDRTEIPNIELEIMNEDEESDEEDVPKVMIGNKSYPVTEVMDNTELIAKMTPHE
KAQYIQIYQEYFEHLY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g12007.t2 | Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain | 56 | 117 | 1.4E-25 |
| 8 | g12007.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 239 | 260 | - |
| 9 | g12007.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 239 | 255 | - |
| 7 | g12007.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 282 | 296 | - |
| 10 | g12007.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 282 | 308 | - |
| 4 | g12007.t2 | PANTHER | PTHR13097 | TRANSCRIPTION INITIATION FACTOR IIE, ALPHA SUBUNIT | 1 | 327 | 5.8E-53 |
| 2 | g12007.t2 | Pfam | PF02002 | TFIIE alpha subunit | 2 | 64 | 2.8E-8 |
| 3 | g12007.t2 | Pfam | PF08271 | TFIIB zinc-binding | 70 | 107 | 2.2E-7 |
| 1 | g12007.t2 | Pfam | PF11521 | C-terminal general transcription factor TFIIE alpha | 299 | 376 | 3.2E-15 |
| 12 | g12007.t2 | ProSiteProfiles | PS51344 | TFE/IIEalpha-type HTH domain profile. | 1 | 47 | 11.193 |
| 6 | g12007.t2 | SMART | SM00531 | tfiie3 | 1 | 118 | 1.7E-26 |
| 5 | g12007.t2 | SUPERFAMILY | SSF57783 | Zinc beta-ribbon | 56 | 116 | 1.96E-19 |
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: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.
