General information for g5630.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5630 is located on chr_2: 10731507..10732183 (- 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_2 | g5630 | g5630.t2 | TTS | g5630.t2 | 10731482 | 10731482 |
| chr_2 | g5630 | g5630.t2 | isoform | g5630.t2 | 10731507 | 10732183 |
| chr_2 | g5630 | g5630.t2 | exon | g5630.t2.exon1 | 10731507 | 10731911 |
| chr_2 | g5630 | g5630.t2 | cds | g5630.t2.CDS1 | 10731507 | 10731911 |
| chr_2 | g5630 | g5630.t2 | exon | g5630.t2.exon2 | 10731973 | 10732089 |
| chr_2 | g5630 | g5630.t2 | cds | g5630.t2.CDS2 | 10731973 | 10732089 |
| chr_2 | g5630 | g5630.t2 | exon | g5630.t2.exon3 | 10732139 | 10732183 |
| chr_2 | g5630 | g5630.t2 | cds | g5630.t2.CDS3 | 10732139 | 10732183 |
| chr_2 | g5630 | g5630.t2 | TSS | g5630.t2 | 10732252 | 10732252 |
Sequences
>g5630.t2 Gene=g5630 Length=567
ATGGAAAAACATTTAGAGCATCAAAGAATAACTGAAGAAGATGATCAGGACAAAATGGAG
ATCAAATTGGAAGACATAAAAACAGATGTAATTATTAATGAATCAATTCAAGAAGAACAA
TGCAAAAACAATGAAAATATGCAAATAAAAGTTGAAACTATGCCAATGTCGAATTCAAAC
AACGATATAAATCATGACTCTTCAACACGAGGACTAACTGCATCTGAGAAACGTTTATAT
CATAATGCTTTAGAAAGAAAACGCCGAGAACTTATAAACCTTCAATTTCTCGATCTGCAC
AATGCAATACCATCAATTGCTGGATTAAAGGCAAGTCGAACTCAAGTTCTTATTAAAGCC
ACAGAATTTATCAACATTATGAAACGAAAAGTTAGAAAATATGAACTAGAAATTGAAAGT
TTAAAGAATCAGAACAAAAAGTTAGAAAATATACTATGTTCACTTAAGGACAATAAGAGA
AGTGATAAATCAAGAAAATTTCATGAACAAATTATATTTGAAGATGATGAAGAAGTAGTC
ATTGATGATGAAATCGAAACTGAATAA
>g5630.t2 Gene=g5630 Length=188
MEKHLEHQRITEEDDQDKMEIKLEDIKTDVIINESIQEEQCKNNENMQIKVETMPMSNSN
NDINHDSSTRGLTASEKRLYHNALERKRRELINLQFLDLHNAIPSIAGLKASRTQVLIKA
TEFINIMKRKVRKYELEIESLKNQNKKLENILCSLKDNKRSDKSRKFHEQIIFEDDEEVV
IDDEIETE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5630.t2 | Coils | Coil | Coil | 124 | 158 | - |
| 5 | g5630.t2 | Gene3D | G3DSA:4.10.280.10 | HLH | 77 | 155 | 1.3E-15 |
| 2 | g5630.t2 | PANTHER | PTHR10328 | PROTEIN MAX MYC-ASSOCIATED FACTOR X | 37 | 161 | 7.0E-22 |
| 1 | g5630.t2 | Pfam | PF00010 | Helix-loop-helix DNA-binding domain | 77 | 125 | 2.6E-8 |
| 7 | g5630.t2 | ProSiteProfiles | PS50888 | Myc-type, basic helix-loop-helix (bHLH) domain profile. | 76 | 127 | 11.109 |
| 4 | g5630.t2 | SMART | SM00353 | finulus | 82 | 133 | 2.0E-6 |
| 3 | g5630.t2 | SUPERFAMILY | SSF47459 | HLH, helix-loop-helix DNA-binding domain | 67 | 143 | 1.13E-14 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5630/g5630.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5630.t2.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0090575 | RNA polymerase II transcription regulator complex | CC |
| GO:0071339 | MLL1 complex | CC |
| GO:0046983 | protein dimerization activity | MF |
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