General information for g176.t11
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as CCR4-NOT transcription complex subunit 7.
Parent gene
- The parent gene g176 is located on chr_3: 1494654..1495383 (+ 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_3 | g176 | g176.t11 | TSS | g176.t11 | 1493551 | 1493551 |
| chr_3 | g176 | g176.t11 | isoform | g176.t11 | 1493924 | 1495383 |
| chr_3 | g176 | g176.t11 | exon | g176.t11.exon1 | 1493924 | 1494170 |
| chr_3 | g176 | g176.t11 | exon | g176.t11.exon2 | 1494484 | 1494682 |
| chr_3 | g176 | g176.t11 | cds | g176.t11.CDS1 | 1494484 | 1494682 |
| chr_3 | g176 | g176.t11 | exon | g176.t11.exon3 | 1494745 | 1494854 |
| chr_3 | g176 | g176.t11 | cds | g176.t11.CDS2 | 1494745 | 1494854 |
| chr_3 | g176 | g176.t11 | exon | g176.t11.exon4 | 1494914 | 1495383 |
| chr_3 | g176 | g176.t11 | cds | g176.t11.CDS3 | 1494914 | 1495009 |
| chr_3 | g176 | g176.t11 | TTS | g176.t11 | 1495441 | 1495441 |
Sequences
>g176.t11 Gene=g176 Length=1026
CAACCAATTACAACATCAAGGTGATGATATTAATCAAGAATGTGGAATACGCGATGTTTG
GCGACATAATCTTGAAGAAGAGTTTGTTCTAATTCGTAAAATTGTCACAAAATATTGCTA
TGTTGCAATGGACACTGAATTTCCAGGTAAATTTAAACATCCAGAAAAATCTATACGACA
TTAATTTTTAAATTTTAGGCGTCGTTGCTCGGCCAATTGGTGAATTCAGATCAACCTCTG
ATTATCAATGACAAGTGGCATTGTTCTTATGGATAACATAAAATGGCTCAGTTTCCATTC
AGGATATGATTTCGGTTATCTCTTAAAAGTTCTAACCGATCAGAACTTGCCTAGCGATGA
AAGTGAATTCTTTGAACTTTTGCGAATCTACTTTCCTACTATTTATGATGTCAAGTATCT
AATGAAGTCTTGCAAAAATTTAAAAGGTGGATTGCAAGAAGTTGCAGAACAATTAGATAT
CAGAAGAATTGGACCTCAACATCAAGCTGGTTCCGATTCACTTCTAACTGGAATGGCCTT
TTTCAAAATGAGAGAAATGTTTTTTGAAGATAATATCGATAACGACAAGTACTCAGGTCA
TTTATTTGGTTTGTCTTTCAATCAGAATGATCGTGTAGTGTCGGCTGAATAAACGAAAAT
ATGAATTAAATTACACAAGCATATATACACACACTCAATTTATGAATTCGACAAATATAA
ATATTTAAAATATATTTGGTGAAAACAATATGCAGTGCGACATTCACTTAAAAAAGAGAT
AAATTAAATGCTTTTGTGCACACAATAGATATTTCAAACAAATATAAAAAAATTTATTAT
TGCTTTGAAATGTTCTTTGAAATATACTAATCTAATATAAAGTAAAAGAGAAATTATTCA
AAAAAATTGAAGCAAACTGATGCATATTAAAAAGTTAAATAATCAGCATAAATACACATA
CAACTCAAACAATTTAAAGCATTACAAAAATTAATGATTTATCCTTATTCTTTATGTTAT
AACAAA
>g176.t11 Gene=g176 Length=134
MTSGIVLMDNIKWLSFHSGYDFGYLLKVLTDQNLPSDESEFFELLRIYFPTIYDVKYLMK
SCKNLKGGLQEVAEQLDIRRIGPQHQAGSDSLLTGMAFFKMREMFFEDNIDNDKYSGHLF
GLSFNQNDRVVSAE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g176.t11 | Gene3D | G3DSA:3.30.420.10 | - | 1 | 122 | 0 |
| 2 | g176.t11 | PANTHER | PTHR10797:SF2 | CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 7 | 1 | 124 | 0 |
| 3 | g176.t11 | PANTHER | PTHR10797 | CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT | 1 | 124 | 0 |
| 1 | g176.t11 | Pfam | PF04857 | CAF1 family ribonuclease | 7 | 98 | 0 |
| 4 | g176.t11 | SUPERFAMILY | SSF53098 | Ribonuclease H-like | 1 | 122 | 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:0004535 | poly(A)-specific ribonuclease activity | MF |
| GO:0030014 | CCR4-NOT complex | CC |
| GO:0000175 | 3’-5’-exoribonuclease activity | MF |
| GO:0003676 | nucleic acid binding | MF |
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.
