General information for g12007.t1
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.t1 | TTS | g12007.t1 | 20303498 | 20303498 |
| chr_1 | g12007 | g12007.t1 | isoform | g12007.t1 | 20303535 | 20304962 |
| chr_1 | g12007 | g12007.t1 | exon | g12007.t1.exon1 | 20303535 | 20303728 |
| chr_1 | g12007 | g12007.t1 | cds | g12007.t1.CDS1 | 20303535 | 20303728 |
| chr_1 | g12007 | g12007.t1 | exon | g12007.t1.exon2 | 20303798 | 20304773 |
| chr_1 | g12007 | g12007.t1 | cds | g12007.t1.CDS2 | 20303798 | 20304773 |
| chr_1 | g12007 | g12007.t1 | exon | g12007.t1.exon3 | 20304828 | 20304962 |
| chr_1 | g12007 | g12007.t1 | cds | g12007.t1.CDS3 | 20304828 | 20304962 |
| chr_1 | g12007 | g12007.t1 | TSS | g12007.t1 | 20305027 | 20305027 |
Sequences
>g12007.t1 Gene=g12007 Length=1305
ATGAGTAATAATCAAGAATTAGTTTATGAAATTCCTAGTTCATTGAAACAATTAGCTCGT
CTTGTGGTTCGCGGTTTTTATACAATTGAAGATGCATTGATAGTTGATATGCTTGTAAGA
AATCCATGTATGAAGGAAGACGATATAGCTGAACTTCTTAAATTTGAGAAAAAGATGCTA
CGAGCCAGATTAACGCTTTTAAAAAACGATAAATTTATGCAAGCAAGATTAAAAATGGAA
ACTGGAGTAGACGGAAAAGCACATAAAGTGAATTATTACTTTATCAATTATAAAACTTTC
GTTAATGTTATTAAATATAAATTGGATTTAATGAGAAAGAGACTTGAAACAGAGGAAAGA
GACGCAACTGCTCGAGCTAATTTTAAATGCACAAATTGCTCAAAACCTTTTACTGATCTT
GAAGTTGATCAATTATTTGACCTTAATACTGGTGAATTAAGATGTACCTATTGTGGGAGT
TTAGTAGAAGAAGATATGGCAGCAATGCCGCGAACAGATTCTCGATTAATGCTCGCAAAA
TTCAATGAGCAATTAGAACCACTTTATGATCTTTTAAAGCAAGCCGAAGGTATAAAATTG
GCTCCTGAAGTTTTGGAACCACAGCCAATTGATATCGATGTAATTCGTGGAATAACTAAG
CCATCTGAAATGATGCATAATGAAGTGTGGTCAGGTGAAGCAACAAGATCAACATCAGGT
TTCATGAATGAAGAGGCAAAGGTTAATGTGACAATTGGAGAGATTGATACAGTTGATCAA
AGTGCTCAAAAGAAAGAACGACCTGTTTGGATGACTGAAAGTACTGTGGTTTCTAAAGAT
GCTGAACAGGATGCTGAGTCAATGCTTGAAAAAGTAGCTCAAAGTGCAGTACAAGCAAGT
TCATGGCAAACACCAGCACCAGCTATCACAACCACATCTAAAAATAAGAAAGAAACTGAA
GAAAATATCATGTCTGTTCTTTTAGCACATGAAAAACAAACGACTAAAGCTAATAATGAT
GCCGTAAGGAACCTCAATAATCAAGACGATTCCAGTGGTGGTGGTGACTCGAGCGGAGAT
GATGATGATGAAATCGATCGAACTGAAATTCCAAACATTGAGCTTGAAATTATGAATGAA
GATGAAGAATCGGATGAAGAAGATGTACCTAAAGTGATGATTGGGAACAAATCTTATCCT
GTAACAGAAGTCATGGATAATACAGAATTAATAGCTAAAATGACACCTCATGAAAAAGCG
CAATACATTCAAATTTATCAAGAATATTTTGAGCATCTGTATTAA
>g12007.t1 Gene=g12007 Length=434
MSNNQELVYEIPSSLKQLARLVVRGFYTIEDALIVDMLVRNPCMKEDDIAELLKFEKKML
RARLTLLKNDKFMQARLKMETGVDGKAHKVNYYFINYKTFVNVIKYKLDLMRKRLETEER
DATARANFKCTNCSKPFTDLEVDQLFDLNTGELRCTYCGSLVEEDMAAMPRTDSRLMLAK
FNEQLEPLYDLLKQAEGIKLAPEVLEPQPIDIDVIRGITKPSEMMHNEVWSGEATRSTSG
FMNEEAKVNVTIGEIDTVDQSAQKKERPVWMTESTVVSKDAEQDAESMLEKVAQSAVQAS
SWQTPAPAITTTSKNKKETEENIMSVLLAHEKQTTKANNDAVRNLNNQDDSSGGGDSSGD
DDDEIDRTEIPNIELEIMNEDEESDEEDVPKVMIGNKSYPVTEVMDNTELIAKMTPHEKA
QYIQIYQEYFEHLY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g12007.t1 | Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain | 114 | 175 | 1.8E-25 |
| 9 | g12007.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 297 | 318 | - |
| 10 | g12007.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 297 | 313 | - |
| 7 | g12007.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 340 | 366 | - |
| 8 | g12007.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 340 | 354 | - |
| 4 | g12007.t1 | PANTHER | PTHR13097 | TRANSCRIPTION INITIATION FACTOR IIE, ALPHA SUBUNIT | 1 | 385 | 9.2E-73 |
| 2 | g12007.t1 | Pfam | PF02002 | TFIIE alpha subunit | 18 | 122 | 2.1E-21 |
| 3 | g12007.t1 | Pfam | PF08271 | TFIIB zinc-binding | 128 | 165 | 2.6E-7 |
| 1 | g12007.t1 | Pfam | PF11521 | C-terminal general transcription factor TFIIE alpha | 357 | 434 | 3.8E-15 |
| 12 | g12007.t1 | ProSiteProfiles | PS51344 | TFE/IIEalpha-type HTH domain profile. | 15 | 105 | 28.387 |
| 6 | g12007.t1 | SMART | SM00531 | tfiie3 | 29 | 176 | 1.2E-55 |
| 5 | g12007.t1 | SUPERFAMILY | SSF57783 | Zinc beta-ribbon | 114 | 174 | 2.42E-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 transcript has been annotated with K03136 (transcription initiation factor TFIIE 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.
