General information for g5763.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Regulator of gene activity.
Parent gene
- The parent gene g5763 is located on chr_2: 11808354..11809722 (+ 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 | g5763 | g5763.t6 | TSS | g5763.t6 | 11808285 | 11808285 |
| chr_2 | g5763 | g5763.t6 | isoform | g5763.t6 | 11808354 | 11809298 |
| chr_2 | g5763 | g5763.t6 | exon | g5763.t6.exon1 | 11808354 | 11809029 |
| chr_2 | g5763 | g5763.t6 | cds | g5763.t6.CDS1 | 11808479 | 11809029 |
| chr_2 | g5763 | g5763.t6 | exon | g5763.t6.exon2 | 11809097 | 11809298 |
| chr_2 | g5763 | g5763.t6 | cds | g5763.t6.CDS2 | 11809097 | 11809298 |
| chr_2 | g5763 | g5763.t6 | TTS | g5763.t6 | 11809740 | 11809740 |
Sequences
>g5763.t6 Gene=g5763 Length=878
CGCTACCGGGAACATCTGAAAATGTGGCGGGAGCTGTAGGTAGTGGAGTTGTGAGTCAAC
ATCAATCGTCAGTGTCTGTGTCATCGGTCATTGGTTCAGCGGGTGGAAGTCATCATCATC
ATCAGATGGGAATGATGGATTCGAATTCATTAATGAGTGGTGACAGTAAAAACTCAATTG
GATCAAATCTTTGTATGGATATGATGCAAAGTGAAACGGTCACGGGAGGTCATCAAATGG
GTAGCGGTCATATGTCGAGTAATGTTAGTGAAAAGGCGAAAAGAGGTGTGCAAACGTCAC
CAAATGGTCTAGTGACGAATATCCCACCAACGATGGTCAATAATCAATTTGGCATGATTG
GTTTGCTCACATTCATTCGCGCAGCAGAATCAGATCCAAATCTCGTTTCTTTGGCAATGG
GACAAGATTTAACGGCTCTAGGATTAAATCTTAATTCAATGGAGAATCTTTATCAAAGCT
TTGGCGGACCGTTCTCAGATTCGCCAGCGAGACCACAGGACATTGATTTTCCCGTTCCAT
CTGAGTATTTAATTAACGTAGCAATTCGTGACAAACTTGCACAGATGAAAATGAAACAGT
ACAAGGATGATTTGCTCTTTTTTCTCTTTTATACCAATTGTGGTGATGTGATGCAATTAG
CTGCGGCAAATGAACTTTACAATCGAGATTGGCGATATCATATCGAAGAGAAGATTTGGC
TTATGCGAGTACCAGGCCATACGAATTATGACAAAAGTGGAACGATTGAACGAGGCACTT
ATTATTATTTCGATGCTACAAATTGGCGTCGTGTGCCCAAAGAATTTCAAATTGACACTA
AAAAATTGGACACGAATCCTCCTATAGCTATGTCGTAA
>g5763.t6 Gene=g5763 Length=250
MGMMDSNSLMSGDSKNSIGSNLCMDMMQSETVTGGHQMGSGHMSSNVSEKAKRGVQTSPN
GLVTNIPPTMVNNQFGMIGLLTFIRAAESDPNLVSLAMGQDLTALGLNLNSMENLYQSFG
GPFSDSPARPQDIDFPVPSEYLINVAIRDKLAQMKMKQYKDDLLFFLFYTNCGDVMQLAA
ANELYNRDWRYHIEEKIWLMRVPGHTNYDKSGTIERGTYYYFDATNWRRVPKEFQIDTKK
LDTNPPIAMS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g5763.t6 | Gene3D | G3DSA:2.30.30.1020 | - | 66 | 250 | 0 |
| 2 | g5763.t6 | PANTHER | PTHR23326:SF3 | CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2 | 41 | 245 | 0 |
| 3 | g5763.t6 | PANTHER | PTHR23326 | CCR4 NOT-RELATED | 41 | 245 | 0 |
| 1 | g5763.t6 | Pfam | PF04153 | NOT2 / NOT3 / NOT5 family | 118 | 241 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5763/g5763.t6; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5763.t6.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0006355 | regulation of transcription, DNA-templated | BP |
| GO:0030015 | CCR4-NOT core complex | CC |
KEGG
Orthology
- This transcript has been annotated with K12605 (CCR4-NOT transcription complex subunit 2)
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.
