General information for g4799.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t2 | isoform | g4799.t2 | 5013015 | 5013598 |
| chr_2 | g4799 | g4799.t2 | exon | g4799.t2.exon1 | 5013015 | 5013598 |
| chr_2 | g4799 | g4799.t2 | cds | g4799.t2.CDS1 | 5013053 | 5013598 |
| chr_2 | g4799 | g4799.t2 | TSS | g4799.t2 | NA | NA |
| chr_2 | g4799 | g4799.t2 | TTS | g4799.t2 | NA | NA |
Sequences
>g4799.t2 Gene=g4799 Length=584
AAATTAAAGAGATATTACAGAAAGAATATTATCCTTGGATGTCACAATATTTAGTTCTTA
AGCGTGCAAGTATTGAAATTAATTTCCATACGCTTTATTCAAATTTCTTAGACGCATTAA
AAATATCCGAGCTATTGATACTCACAACAAACGAGACATTTAGAAATATCAAGGTGCTTT
TAAGAAGTGATAAGAGCATTGCTAACTTTTCTGATCGAAGTTTACTCAAGAATTTAGGGC
ATTGGTTGGGTATGTTAACATTAGGAAGAAATCGTCCAATTTTACACAATGATATAGATT
TGAAGTCATTAGTGCTCGAAGCATATTCAAAGGGACAGCAAGAATTACTATATGTAGTTC
CATTTGTAGCAAAAGTTTTGGAATCAACAGCAAAAAGTAGAATTTTCAAACCACCAAATC
CCTGGACAATGGCAATTATGAATGTTTTAGCTGAACTTCATCAAGAACCTGAGCTCAAAT
TGAATTTAAAATTTGAAATTGAAGTTCTCTGTAAGAGTCTTAATTTAGAAGTTTCAGAAT
TGAAGCCTGCGTATTATCTTAAAGATCCAGAACGACCATCAAAA
>g4799.t2 Gene=g4799 Length=182
MSQYLVLKRASIEINFHTLYSNFLDALKISELLILTTNETFRNIKVLLRSDKSIANFSDR
SLLKNLGHWLGMLTLGRNRPILHNDIDLKSLVLEAYSKGQQELLYVVPFVAKVLESTAKS
RIFKPPNPWTMAIMNVLAELHQEPELKLNLKFEIEVLCKSLNLEVSELKPAYYLKDPERP
SK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g4799.t2 | Gene3D | G3DSA:1.25.40.180 | - | 1 | 182 | 0 |
| 2 | g4799.t2 | PANTHER | PTHR13162:SF8 | CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1 | 2 | 180 | 0 |
| 3 | g4799.t2 | PANTHER | PTHR13162 | CCR4-NOT TRANSCRIPTION COMPLEX | 2 | 180 | 0 |
| 1 | g4799.t2 | Pfam | PF16415 | CCR4-NOT transcription complex subunit 1 CAF1-binding domain | 1 | 180 | 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.
