General information for g10665.t4
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.t4 | isoform | g10665.t4 | 11236753 | 11244937 |
| chr_1 | g10665 | g10665.t4 | exon | g10665.t4.exon1 | 11236753 | 11236763 |
| chr_1 | g10665 | g10665.t4 | exon | g10665.t4.exon2 | 11237197 | 11237917 |
| chr_1 | g10665 | g10665.t4 | exon | g10665.t4.exon3 | 11238186 | 11238566 |
| chr_1 | g10665 | g10665.t4 | cds | g10665.t4.CDS1 | 11238508 | 11238566 |
| chr_1 | g10665 | g10665.t4 | exon | g10665.t4.exon4 | 11244481 | 11244937 |
| chr_1 | g10665 | g10665.t4 | cds | g10665.t4.CDS2 | 11244481 | 11244934 |
| chr_1 | g10665 | g10665.t4 | TSS | g10665.t4 | NA | NA |
| chr_1 | g10665 | g10665.t4 | TTS | g10665.t4 | NA | NA |
Sequences
>g10665.t4 Gene=g10665 Length=1570
CAAATGGAGAGATTTAAAGTAGTGGAAAGAGAGACGAAAACGAAAGCATACTCAAAAGAA
GGACTTGGAGCTGCACAAAAGCTTGATCCAGCACAGCGAGAAAAAGAGTCTGTTAGTTGT
TGGCTTCAAAATTCCATTAGTTCCCTACAAATACAAACTGATCAGTACGAGAGCGAAATT
GAATCGCTGCTGGCGAATAAAAAAAAGCGTCTCGATAAAGAGAAACAAGACAAAATGGAC
GATCTTAAGTCAAAACTTGAACGTCACAAGTTTCATATAACAAAACTCGAAACTCTATTA
AGGATGCTTGACAATGATAGTGTCGATGTAGAGCAGATAAGAAAGATTCATGACGATGTG
GAGTACTATATTGAATCATCACAAGAACCTGATTTCGAAGAGAACGAATTCATATATGAC
GATATTGAAGGTCTTGATGAAGTGGAATTGAGTGGCGCGCATATATTGATAATTGTTTCA
ACCTTGCTTCTTCCTTTTATTGATGTTAACAAATGAAGATATATGTGTTTGTTATCATTA
CAGGATACTTATTTTGGATGTTAAAAATTAAAACAGTTCATATCGTTTTAATATTACGAT
AAAAAGTGCATTATGCTCGCAAGGTATTTCATATAAAACGCATTGTCGTTTATGCTTCAG
ATTCAGCTTCGATTCTGGCGAGAATGTCAGCTTTTCTTTGTGCAACGCCAGCTTTGCGTT
GCTCAAGTGTGAGCTTAGCTTTGTTCCATCTCTTCTTGGTCACCTTCTTCTCTGGTTTCT
TGGTGTGCGATGGATCAGCACGAATGTTGGCATGTGCTTTTTTATAAATTGATTCAATGT
CATCAGCACGGATTCCGAGTTTGATGTAGCGAGAGAATTGACGTTTGTATGCTTCTTCAT
CTTCGCCCTCTAATTCTTTCATGTATTTTGCAACGTGCTGACCAAAGATATGCTCACGAT
GAACTTCAGCATTAAGACTCTTATCTTCAGCACTGTAGCCTGGGAAACGTTTGACTGAGT
GTGGAATATTGAGTCCGCCATCAACAGCTCCTTTCATTGCTCCAAAGACACGGGCACCAG
TTGTTGTTCTAGATAAACCGACATCTAAATAGCAACGGAATGAACCTGGACCATCTTCGA
CTGATTCAACCAAGTATTCGTCACCATTAACATCAGTACAACCGCTATATATACTGTCGA
GTCCTAATTTTTGAAGAATACGACGAGCAACCAATAATCCAGTGCAATATGCTGCAGCAT
AGTTTGTCAAACCGACCTTAACACCATAGCGTGGTAATTCATGAGCATAAGCTGCACAGA
CGATACGATCTCCCTCAATGCGAGCATAAGCAATTTGACAAGTGATATCGCGGTTGCTCA
AACGAACAATCAGACGATACTTGGGTGTATTATATTTATTCTTGTCTTGAAAGATCAGGC
GTTTACGAGCCTGATAGTCAGTTTTACATTCTCGGCGCCTCTTGAATTTGACTTGATAGC
GCTTAAAATATTGTTTATTCTTGACCACTTTAACGAATCCCATGATTATTCGTTTTCAGT
TCGTCGATGA
>g10665.t4 Gene=g10665 Length=170
MERFKVVERETKTKAYSKEGLGAAQKLDPAQREKESVSCWLQNSISSLQIQTDQYESEIE
SLLANKKKRLDKEKQDKMDDLKSKLERHKFHITKLETLLRMLDNDSVDVEQIRKIHDDVE
YYIESSQEPDFEENEFIYDDIEGLDEVELSGAHILIIVSTLLLPFIDVNK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g10665.t4 | Coils | Coil | Coil | 45 | 65 | - |
| 4 | g10665.t4 | Coils | Coil | Coil | 67 | 87 | - |
| 2 | g10665.t4 | PANTHER | PTHR23326 | CCR4 NOT-RELATED | 1 | 152 | 2.5E-69 |
| 3 | g10665.t4 | PANTHER | PTHR23326:SF24 | CCR4-NOT TRANSCRIPTION COMPLEX, SUBUNIT 3A | 1 | 152 | 2.5E-69 |
| 1 | g10665.t4 | Pfam | PF04065 | Not1 N-terminal domain, CCR4-Not complex component | 1 | 142 | 5.1E-46 |
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:0005634 | nucleus | CC |
| 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.
