General information for g5630.t1
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.t1 | TTS | g5630.t1 | 10731482 | 10731482 |
| chr_2 | g5630 | g5630.t1 | isoform | g5630.t1 | 10731507 | 10732183 |
| chr_2 | g5630 | g5630.t1 | exon | g5630.t1.exon1 | 10731507 | 10731911 |
| chr_2 | g5630 | g5630.t1 | cds | g5630.t1.CDS1 | 10731507 | 10731911 |
| chr_2 | g5630 | g5630.t1 | exon | g5630.t1.exon2 | 10731973 | 10732086 |
| chr_2 | g5630 | g5630.t1 | cds | g5630.t1.CDS2 | 10731973 | 10732086 |
| chr_2 | g5630 | g5630.t1 | exon | g5630.t1.exon3 | 10732139 | 10732183 |
| chr_2 | g5630 | g5630.t1 | cds | g5630.t1.CDS3 | 10732139 | 10732183 |
| chr_2 | g5630 | g5630.t1 | TSS | g5630.t1 | 10732252 | 10732252 |
Sequences
>g5630.t1 Gene=g5630 Length=564
ATGGAAAAACATTTAGAGCATCAAAGAATAACTGAAGAAGATGATGACAAAATGGAGATC
AAATTGGAAGACATAAAAACAGATGTAATTATTAATGAATCAATTCAAGAAGAACAATGC
AAAAACAATGAAAATATGCAAATAAAAGTTGAAACTATGCCAATGTCGAATTCAAACAAC
GATATAAATCATGACTCTTCAACACGAGGACTAACTGCATCTGAGAAACGTTTATATCAT
AATGCTTTAGAAAGAAAACGCCGAGAACTTATAAACCTTCAATTTCTCGATCTGCACAAT
GCAATACCATCAATTGCTGGATTAAAGGCAAGTCGAACTCAAGTTCTTATTAAAGCCACA
GAATTTATCAACATTATGAAACGAAAAGTTAGAAAATATGAACTAGAAATTGAAAGTTTA
AAGAATCAGAACAAAAAGTTAGAAAATATACTATGTTCACTTAAGGACAATAAGAGAAGT
GATAAATCAAGAAAATTTCATGAACAAATTATATTTGAAGATGATGAAGAAGTAGTCATT
GATGATGAAATCGAAACTGAATAA
>g5630.t1 Gene=g5630 Length=187
MEKHLEHQRITEEDDDKMEIKLEDIKTDVIINESIQEEQCKNNENMQIKVETMPMSNSNN
DINHDSSTRGLTASEKRLYHNALERKRRELINLQFLDLHNAIPSIAGLKASRTQVLIKAT
EFINIMKRKVRKYELEIESLKNQNKKLENILCSLKDNKRSDKSRKFHEQIIFEDDEEVVI
DDEIETE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5630.t1 | Coils | Coil | Coil | 123 | 157 | - |
| 5 | g5630.t1 | Gene3D | G3DSA:4.10.280.10 | HLH | 76 | 154 | 1.3E-15 |
| 2 | g5630.t1 | PANTHER | PTHR10328 | PROTEIN MAX MYC-ASSOCIATED FACTOR X | 36 | 160 | 3.5E-22 |
| 1 | g5630.t1 | Pfam | PF00010 | Helix-loop-helix DNA-binding domain | 76 | 124 | 2.6E-8 |
| 7 | g5630.t1 | ProSiteProfiles | PS50888 | Myc-type, basic helix-loop-helix (bHLH) domain profile. | 75 | 126 | 11.109 |
| 4 | g5630.t1 | SMART | SM00353 | finulus | 81 | 132 | 2.0E-6 |
| 3 | g5630.t1 | SUPERFAMILY | SSF47459 | HLH, helix-loop-helix DNA-binding domain | 66 | 142 | 1.11E-14 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5630/g5630.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5630.t1.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