General information for g10487.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as General transcription factor IIE subunit 2.
Parent gene
- The parent gene g10487 is located on chr_1: 10144405..10145417 (+ 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 | g10487 | g10487.t1 | TSS | g10487.t1 | 10144336 | 10144336 |
| chr_1 | g10487 | g10487.t1 | isoform | g10487.t1 | 10144405 | 10145417 |
| chr_1 | g10487 | g10487.t1 | exon | g10487.t1.exon1 | 10144405 | 10144466 |
| chr_1 | g10487 | g10487.t1 | cds | g10487.t1.CDS1 | 10144405 | 10144466 |
| chr_1 | g10487 | g10487.t1 | exon | g10487.t1.exon2 | 10144530 | 10144800 |
| chr_1 | g10487 | g10487.t1 | cds | g10487.t1.CDS2 | 10144530 | 10144800 |
| chr_1 | g10487 | g10487.t1 | exon | g10487.t1.exon3 | 10144854 | 10145417 |
| chr_1 | g10487 | g10487.t1 | cds | g10487.t1.CDS3 | 10144854 | 10145417 |
| chr_1 | g10487 | g10487.t1 | TTS | g10487.t1 | 10145554 | 10145554 |
Sequences
>g10487.t1 Gene=g10487 Length=897
ATGGATGCAGCACTTCTTAGAGAAAGAGAAGCGTTTAAGAAAAGAGCTTTAGCTACTCCT
ACAGTTGAAAAAAAATTACAAAAAGAATCAGCAAAATCATCATCAAGCAGCAAAAAACCA
TTACAGCCATGGGAATCAAAAGCACCGAAAGAACCAAGAGAGCCTATGAACTACAAAACT
ATGACCGGTAGTTCTAATAAAAGATTCGCAATTCTTACAAAAATAGTAAATTACATGAAA
GAAAAACATCTTAGTGGTGATGATCATCCAATTACGATAGAAGAAATTCTTGATGAAACA
AATCAATTAGATATTGGATCATCAACTAAAACATGGCTTATGACAGAAGCTCTTCCAAAC
AATCCCAAACTGGAACAGCCAGAATTAGGAAGATTTCAATTTAAACCTATGTATAGAATT
AAGGATGGTAAGAGTTTAGTAAGACTACTCAAACAACATGATCTGAAAGGTCTTGGTGGT
ATTTTACTTGATGACGTACAAGAATCACTGCCAAATTGTGATAAACTATTAAAAAATCGT
GCATCGGAAATTATTTTCATTACACGACCAATTGATAAGAAAAAGATTCTATTCTATAAT
GATCGTACAGCAAATTTCCAAATCGATGAAGAATTTCAGAAGCTCTGGAGATCAGCAACA
GTTGATGCAATGGATGATAATAAAATTGAAGAGTATTTAGAAAAACAAGGCATTCGTTCA
ATGCAAGACCATGGTATTAGAAAACAAATGGCACCGAAGAGAAAGAAGCAGCCACTCAAA
AAGCGTCAATTTAAGAGACCACGAGACAATGAACATCTTGCAGACATTCTTGAGACATAT
GAAGATAACACAATCACACAGAAAGGAGATTTACATGCAAAGCAATCGGGATGTTAA
>g10487.t1 Gene=g10487 Length=298
MDAALLREREAFKKRALATPTVEKKLQKESAKSSSSSKKPLQPWESKAPKEPREPMNYKT
MTGSSNKRFAILTKIVNYMKEKHLSGDDHPITIEEILDETNQLDIGSSTKTWLMTEALPN
NPKLEQPELGRFQFKPMYRIKDGKSLVRLLKQHDLKGLGGILLDDVQESLPNCDKLLKNR
ASEIIFITRPIDKKKILFYNDRTANFQIDEEFQKLWRSATVDAMDDNKIEEYLEKQGIRS
MQDHGIRKQMAPKRKKQPLKKRQFKRPRDNEHLADILETYEDNTITQKGDLHAKQSGC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g10487.t1 | CDD | cd07977 | TFIIE_beta_winged_helix | 62 | 141 | 1.18432E-24 |
| 6 | g10487.t1 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 60 | 141 | 4.1E-32 |
| 11 | g10487.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 62 | - |
| 12 | g10487.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 32 | - |
| 9 | g10487.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 241 | 272 | - |
| 10 | g10487.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 249 | 263 | - |
| 3 | g10487.t1 | PANTHER | PTHR12716:SF8 | TRANSCRIPTION INITIATION FACTOR IIE SUBUNIT BETA | 1 | 281 | 3.8E-60 |
| 4 | g10487.t1 | PANTHER | PTHR12716 | TRANSCRIPTION INITIATION FACTOR IIE, BETA SUBUNIT | 1 | 281 | 3.8E-60 |
| 7 | g10487.t1 | PIRSF | PIRSF016398 | TFIIE-beta | 1 | 285 | 2.3E-106 |
| 1 | g10487.t1 | Pfam | PF02186 | TFIIE beta subunit core domain | 69 | 140 | 2.5E-17 |
| 2 | g10487.t1 | Pfam | PF18121 | TFA2 Winged helix domain 2 | 143 | 200 | 8.2E-7 |
| 13 | g10487.t1 | ProSiteProfiles | PS51351 | TFIIE beta central core DNA-binding domain profile. | 60 | 141 | 14.393 |
| 5 | g10487.t1 | SUPERFAMILY | SSF46785 | Winged helix DNA-binding domain | 61 | 141 | 2.72E-28 |
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:0005673 | transcription factor TFIIE complex | CC |
| GO:0006367 | transcription initiation from RNA polymerase II promoter | BP |
KEGG
Orthology
- This transcript has been annotated with K03137 (transcription initiation factor TFIIE subunit beta)
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.
