General information for g10665.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative CCR4-NOT transcription complex subunit 3.
Parent gene
- The parent gene g10665 is located on chr_1: 11244488..11245783 (- 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_1 | g10665 | g10665.t6 | TTS | g10665.t6 | 11240846 | 11240846 |
| chr_1 | g10665 | g10665.t6 | isoform | g10665.t6 | 11241073 | 11242465 |
| chr_1 | g10665 | g10665.t6 | exon | g10665.t6.exon1 | 11241073 | 11242191 |
| chr_1 | g10665 | g10665.t6 | cds | g10665.t6.CDS1 | 11242093 | 11242191 |
| chr_1 | g10665 | g10665.t6 | exon | g10665.t6.exon2 | 11242256 | 11242465 |
| chr_1 | g10665 | g10665.t6 | cds | g10665.t6.CDS2 | 11242256 | 11242387 |
| chr_1 | g10665 | g10665.t6 | TSS | g10665.t6 | NA | NA |
Sequences
>g10665.t6 Gene=g10665 Length=1329
ACTCAACTTCCACATTCGGATACAATAGATTTCTTTCAACGTCTCGCGACCGAAACTTTA
TTCTTTGTGTTTTATTATATGGAAGGAACAAAGGCTCAATATCTTGCTGCAAAAGCTCTT
AAAAAGCAAAGTTGGAGATTTCATACAAAATATATGATGTGGTTTCAACGTCATGAAGAA
CCTAAAATTATTAATGAAGAATTTGAGCAGGGCACTTACATATACTTTGATTATGAAAAG
TGGGGTCAACGAAAAAAAGAGGGATTTACGTTTGAGTATAAGTACTTAGAAGATAAAGAC
CTGAATTGATTCAAAAATCGATGCAAATTTTTGTAGTCATAAAGTGTAAAAATATTCAAA
TTTATAAACAGTTAAAAATCGCTAAAACAACAGACGAGAGAAGAGAAGTACAGAAATCAA
CAATAGCTGAAAACAGAAAAATTTTCTGAAGAACTAAGATATATTCATGATTTTGATAAA
AGAAACAAGCAAGATAGCAAGAGAGTGAAGAAATTTCAATAGATTAAAAAAGAAGATAAT
TAGATAACAGTTTTACGAACAGAAAAAAAATGCATGCTGAAAACGTCTATATATTTCAAA
AATGCTACAACTTTCAATTACAAATGTAATTTCATTTTCTTTTGTTTATAACAAAAATTT
TGTAGAAAGAAAATCAAATCAAAAAATATAAAACTATTTTCCTTTATACTTTCATCATTA
TCATCATCATAATCACCCCTCCTCAATTTTTTCTTTTGTTCGATAGTGAAATGATATTAA
GCATTTTTGAAATCGATTATCATAAATTCTTTTTTGGAGGACGCATTTTACATTAATAAA
AAAGATTATGTGAATGAAAAATAATTAAGTGAAATATTTAATGATTTAAATAAAACAGTG
AAAAAGATAACTACATACACTCTATGGATTGATCTATTTCTACAACTACAGTTATTTAAA
CAGAATAAATTTAAATATGAAATTTGAATGAATTTTTCGCATGACTTTCACTCATACACA
TTTCTTTTTTTTTGAAAAAATATTTTATAAAACATGAAATTAAATTATAAAAAGATGAAA
ATTGTTAGATTGCTGATACTTGTTCGATTTGCTTATAGTTTTTAAATGATGACAGATTTC
AAAAGAGGAAGAGAGGGAAACGATCAGATATTCAAAAAGAAAAGATTCATTTTACTGCTC
TTTAAAAATTTTATTAAATTCCTACCTACTTTCATTGAAAAATTGAGAAACGAAATTTAC
GTAAAGTCAAAAAATTTCTTTTTAATATAATAACTGTATGGATGGAATGTATAAAGAATA
GATCAATTT
>g10665.t6 Gene=g10665 Length=76
MEGTKAQYLAAKALKKQSWRFHTKYMMWFQRHEEPKIINEEFEQGTYIYFDYEKWGQRKK
EGFTFEYKYLEDKDLN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g10665.t6 | Gene3D | G3DSA:2.30.30.1020 | - | 1 | 71 | 0 |
| 2 | g10665.t6 | PANTHER | PTHR23326 | CCR4 NOT-RELATED | 1 | 75 | 0 |
| 3 | g10665.t6 | PANTHER | PTHR23326:SF24 | CCR4-NOT TRANSCRIPTION COMPLEX, SUBUNIT 3A | 1 | 75 | 0 |
| 1 | g10665.t6 | Pfam | PF04153 | NOT2 / NOT3 / NOT5 family | 1 | 70 | 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:0006355 | regulation of transcription, DNA-templated | 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.
