General information for g4799.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative CCR4-NOT transcription complex subunit 1.
Parent gene
- The parent gene g4799 is located on chr_2: 5016681..5021304 (+ 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 | g4799 | g4799.t6 | isoform | g4799.t6 | 5016681 | 5021304 |
| chr_2 | g4799 | g4799.t6 | exon | g4799.t6.exon1 | 5016681 | 5017164 |
| chr_2 | g4799 | g4799.t6 | cds | g4799.t6.CDS1 | 5016780 | 5016986 |
| chr_2 | g4799 | g4799.t6 | exon | g4799.t6.exon2 | 5021148 | 5021304 |
| chr_2 | g4799 | g4799.t6 | TTS | g4799.t6 | 5021978 | 5021978 |
| chr_2 | g4799 | g4799.t6 | TSS | g4799.t6 | NA | NA |
Sequences
>g4799.t6 Gene=g4799 Length=641
TATTTGTTTTATCATAAAAACTTTTTATTAATCAATCTTTTTAATTATAGTCAGAAGAAT
CAAAATCCAACTATTACAAATATCATTCACAATGCGCATATGGATATTCTTCAAAACTTA
GCTGTCGATTTGGATAATGAAGGACGTTACTTATTCTTGAATGCTATCGCAAATCAGTTA
CGTTATCCAAACATTCACACACATTACTTTAGCTGTGCATTGCTTTATCTATTTGATGAG
GCCAATTCGGAAGCCATTCAAGTAAGCATTCATTTTATAGCATGTTTGACAATTAAAAAT
CTGTGATTAATTAACTATTGTTTTCTTCTTTTCCTGTCCATGTATTGATTTTTATTTATA
GGAGCAAATAACGCGTGTATTGTTGGAGCGATTGATTGTGAACCGACCACATCCATGGGG
CTTGCTAATTACATTTATTGAGCTGATAAAAAATCCATCATACAAGTTTTGGGATCACGA
TTTTCAAAACTCGCTTACCTACATTTTAGTCGATTTGTGGCACAAGTTTTGTATTACAAG
TTGAGTTAATATACTGAATGTATAAAATTCAACAATGAATTAGCATTCAGCAAACTCACT
TACTCACTTACTTCATTCTATTCCATATAAAAATGATATCT
>g4799.t6 Gene=g4799 Length=68
MDILQNLAVDLDNEGRYLFLNAIANQLRYPNIHTHYFSCALLYLFDEANSEAIQVSIHFI
ACLTIKNL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g4799.t6 | Gene3D | G3DSA:1.25.40.800 | - | 1 | 63 | 0 |
| 2 | g4799.t6 | PANTHER | PTHR13162:SF8 | CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1 | 1 | 55 | 0 |
| 3 | g4799.t6 | PANTHER | PTHR13162 | CCR4-NOT TRANSCRIPTION COMPLEX | 1 | 55 | 0 |
| 1 | g4799.t6 | Pfam | PF04054 | CCR4-Not complex component, Not1 | 1 | 56 | 0 |
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:0006417 | regulation of translation | BP |
| GO:0030015 | CCR4-NOT core complex | CC |
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.
