General information for g12007.t3
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.t3 | TTS | g12007.t3 | 20303498 | 20303498 |
| chr_1 | g12007 | g12007.t3 | isoform | g12007.t3 | 20303535 | 20304962 |
| chr_1 | g12007 | g12007.t3 | exon | g12007.t3.exon1 | 20303535 | 20304773 |
| chr_1 | g12007 | g12007.t3 | cds | g12007.t3.CDS1 | 20303535 | 20304734 |
| chr_1 | g12007 | g12007.t3 | exon | g12007.t3.exon2 | 20304836 | 20304962 |
| chr_1 | g12007 | g12007.t3 | TSS | g12007.t3 | 20305027 | 20305027 |
Sequences
>g12007.t3 Gene=g12007 Length=1366
ATGAGTAATAATCAAGAATTAGTTTATGAAATTCCTAGTTCATTGAAACAATTAGCTCGT
CTTGTGGTTCGCGGTTTTTATACAATTGAAGATGCATTGATAGTTGATATGCTTGTAAGA
AATCCATGAAGACGATATAGCTGAACTTCTTAAATTTGAGAAAAAGATGCTACGAGCCAG
ATTAACGCTTTTAAAAAACGATAAATTTATGCAAGCAAGATTAAAAATGGAAACTGGAGT
AGACGGAAAAGCACATAAAGTGAATTATTACTTTATCAATTATAAAACTTTCGTTAATGT
TATTAAATATAAATTGGATTTAATGAGAAAGAGACTTGAAACAGAGGAAAGAGACGCAAC
TGCTCGAGCTAATTTTAAATGCACAAATTGCTCAAAACCTTTTACTGATCTTGAAGTTGA
TCAATTATTTGACCTTAATACTGGTGAATTAAGATGTACCTATTGTGGGAGTTTAGTAGA
AGAAGATATGGCAGCAATGCCGCGAACAGATTCTCGATTAATGCTCGCAAAATTCAATGA
GCAATTAGAACCACTTTATGATCTTTTAAAGCAAGCCGAAGGTATAAAATTGGCTCCTGA
AGTTTTGGAACCACAGCCAATTGATATCGATGTAATTCGTGGAATAACTAAGCCATCTGA
AATGATGCATAATGAAGTGTGGTCAGGTGAAGCAACAAGATCAACATCAGGTTTCATGAA
TGAAGAGGCAAAGGTTAATGTGACAATTGGAGAGATTGATACAGTTGATCAAAGTGCTCA
AAAGAAAGAACGACCTGTTTGGATGACTGAAAGTACTGTGGTTTCTAAAGATGCTGAACA
GGATGCTGAGTCAATGCTTGAAAAAGTAGCTCAAAGTGCAGTACAAGCAAGTTCATGGCA
AACACCAGCACCAGCTATCACAACCACATCTAAAAATAAGAAAGAAACTGAAGAAAATAT
CATGTCTGTTCTTTTAGCACATGAAAAACAAACGACTAAAGCTAATAATGATGCCGTAAG
GAACCTCAATAATCAAGACGATTCCAGTGGTGGTGGTGACTCGAGCGGAGATGATGATGA
TGAAATCGATCGAACTGAAATTCGTAAGTTGATAAGTTATTTCATACAAATTAACAATTT
TATATCTATATCTATTTGTATTATTGTTTTAGCAAACATTGAGCTTGAAATTATGAATGA
AGATGAAGAATCGGATGAAGAAGATGTACCTAAAGTGATGATTGGGAACAAATCTTATCC
TGTAACAGAAGTCATGGATAATACAGAATTAATAGCTAAAATGACACCTCATGAAAAAGC
GCAATACATTCAAATTTATCAAGAATATTTTGAGCATCTGTATTAA
>g12007.t3 Gene=g12007 Length=399
MLRARLTLLKNDKFMQARLKMETGVDGKAHKVNYYFINYKTFVNVIKYKLDLMRKRLETE
ERDATARANFKCTNCSKPFTDLEVDQLFDLNTGELRCTYCGSLVEEDMAAMPRTDSRLML
AKFNEQLEPLYDLLKQAEGIKLAPEVLEPQPIDIDVIRGITKPSEMMHNEVWSGEATRST
SGFMNEEAKVNVTIGEIDTVDQSAQKKERPVWMTESTVVSKDAEQDAESMLEKVAQSAVQ
ASSWQTPAPAITTTSKNKKETEENIMSVLLAHEKQTTKANNDAVRNLNNQDDSSGGGDSS
GDDDDEIDRTEIRKLISYFIQINNFISISICIIVLANIELEIMNEDEESDEEDVPKVMIG
NKSYPVTEVMDNTELIAKMTPHEKAQYIQIYQEYFEHLY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g12007.t3 | Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain | 56 | 117 | 1.6E-25 |
| 11 | g12007.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 240 | 255 | - |
| 14 | g12007.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 240 | 259 | - |
| 12 | g12007.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 282 | 296 | - |
| 13 | g12007.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 282 | 305 | - |
| 4 | g12007.t3 | PANTHER | PTHR13097 | TRANSCRIPTION INITIATION FACTOR IIE, ALPHA SUBUNIT | 1 | 300 | 7.6E-53 |
| 2 | g12007.t3 | Pfam | PF02002 | TFIIE alpha subunit | 2 | 64 | 3.0E-8 |
| 3 | g12007.t3 | Pfam | PF08271 | TFIIB zinc-binding | 70 | 107 | 2.4E-7 |
| 1 | g12007.t3 | Pfam | PF11521 | C-terminal general transcription factor TFIIE alpha | 340 | 399 | 1.9E-12 |
| 7 | g12007.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 314 | - |
| 9 | g12007.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 315 | 336 | - |
| 8 | g12007.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 337 | 399 | - |
| 15 | g12007.t3 | ProSiteProfiles | PS51344 | TFE/IIEalpha-type HTH domain profile. | 1 | 47 | 11.193 |
| 10 | g12007.t3 | SMART | SM00531 | tfiie3 | 1 | 118 | 1.7E-26 |
| 5 | g12007.t3 | SUPERFAMILY | SSF57783 | Zinc beta-ribbon | 56 | 116 | 2.13E-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.
