General information for g10487.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t3 | TSS | g10487.t3 | 10144336 | 10144336 |
| chr_1 | g10487 | g10487.t3 | isoform | g10487.t3 | 10144405 | 10145417 |
| chr_1 | g10487 | g10487.t3 | exon | g10487.t3.exon1 | 10144405 | 10144466 |
| chr_1 | g10487 | g10487.t3 | exon | g10487.t3.exon2 | 10144530 | 10144804 |
| chr_1 | g10487 | g10487.t3 | exon | g10487.t3.exon3 | 10144854 | 10145417 |
| chr_1 | g10487 | g10487.t3 | cds | g10487.t3.CDS1 | 10144929 | 10145417 |
| chr_1 | g10487 | g10487.t3 | TTS | g10487.t3 | 10145554 | 10145554 |
Sequences
>g10487.t3 Gene=g10487 Length=901
ATGGATGCAGCACTTCTTAGAGAAAGAGAAGCGTTTAAGAAAAGAGCTTTAGCTACTCCT
ACAGTTGAAAAAAAATTACAAAAAGAATCAGCAAAATCATCATCAAGCAGCAAAAAACCA
TTACAGCCATGGGAATCAAAAGCACCGAAAGAACCAAGAGAGCCTATGAACTACAAAACT
ATGACCGGTAGTTCTAATAAAAGATTCGCAATTCTTACAAAAATAGTAAATTACATGAAA
GAAAAACATCTTAGTGGTGATGATCATCCAATTACGATAGAAGAAATTCTTGATGAAACA
AATCAATTAGATATTGGATCATCAACTAAAACAGTAATGGCTTATGACAGAAGCTCTTCC
AAACAATCCCAAACTGGAACAGCCAGAATTAGGAAGATTTCAATTTAAACCTATGTATAG
AATTAAGGATGGTAAGAGTTTAGTAAGACTACTCAAACAACATGATCTGAAAGGTCTTGG
TGGTATTTTACTTGATGACGTACAAGAATCACTGCCAAATTGTGATAAACTATTAAAAAA
TCGTGCATCGGAAATTATTTTCATTACACGACCAATTGATAAGAAAAAGATTCTATTCTA
TAATGATCGTACAGCAAATTTCCAAATCGATGAAGAATTTCAGAAGCTCTGGAGATCAGC
AACAGTTGATGCAATGGATGATAATAAAATTGAAGAGTATTTAGAAAAACAAGGCATTCG
TTCAATGCAAGACCATGGTATTAGAAAACAAATGGCACCGAAGAGAAAGAAGCAGCCACT
CAAAAAGCGTCAATTTAAGAGACCACGAGACAATGAACATCTTGCAGACATTCTTGAGAC
ATATGAAGATAACACAATCACACAGAAAGGAGATTTACATGCAAAGCAATCGGGATGTTA
A
>g10487.t3 Gene=g10487 Length=162
MYRIKDGKSLVRLLKQHDLKGLGGILLDDVQESLPNCDKLLKNRASEIIFITRPIDKKKI
LFYNDRTANFQIDEEFQKLWRSATVDAMDDNKIEEYLEKQGIRSMQDHGIRKQMAPKRKK
QPLKKRQFKRPRDNEHLADILETYEDNTITQKGDLHAKQSGC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g10487.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 105 | 136 | - |
| 4 | g10487.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 113 | 127 | - |
| 2 | g10487.t3 | PANTHER | PTHR12716:SF8 | TRANSCRIPTION INITIATION FACTOR IIE SUBUNIT BETA | 2 | 145 | 5.0E-33 |
| 3 | g10487.t3 | PANTHER | PTHR12716 | TRANSCRIPTION INITIATION FACTOR IIE, BETA SUBUNIT | 2 | 145 | 5.0E-33 |
| 1 | g10487.t3 | Pfam | PF18121 | TFA2 Winged helix domain 2 | 7 | 64 | 2.6E-7 |
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 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. There were no conditions that were differentially expressed