General information for g176.t4
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.t4 | isoform | g176.t4 | 1493137 | 1495383 |
| chr_3 | g176 | g176.t4 | exon | g176.t4.exon1 | 1493137 | 1493698 |
| chr_3 | g176 | g176.t4 | exon | g176.t4.exon2 | 1493860 | 1494069 |
| chr_3 | g176 | g176.t4 | cds | g176.t4.CDS1 | 1493892 | 1494069 |
| chr_3 | g176 | g176.t4 | exon | g176.t4.exon3 | 1494122 | 1494299 |
| chr_3 | g176 | g176.t4 | cds | g176.t4.CDS2 | 1494122 | 1494299 |
| chr_3 | g176 | g176.t4 | exon | g176.t4.exon4 | 1494375 | 1494682 |
| chr_3 | g176 | g176.t4 | cds | g176.t4.CDS3 | 1494375 | 1494682 |
| chr_3 | g176 | g176.t4 | exon | g176.t4.exon5 | 1494745 | 1494859 |
| chr_3 | g176 | g176.t4 | cds | g176.t4.CDS4 | 1494745 | 1494859 |
| chr_3 | g176 | g176.t4 | exon | g176.t4.exon6 | 1494914 | 1495383 |
| chr_3 | g176 | g176.t4 | cds | g176.t4.CDS5 | 1494914 | 1494914 |
| chr_3 | g176 | g176.t4 | TTS | g176.t4 | 1495441 | 1495441 |
| chr_3 | g176 | g176.t4 | TSS | g176.t4 | NA | NA |
Sequences
>g176.t4 Gene=g176 Length=1843
ATGGTAACACATTTATTAATTATTCAAACACTCTTTTTTAATTTAATCTCGCCCGATCTT
ATTTAATTTTAAAATTTTATTCACTGATTATGACTTATCGCTCACGAAAATTTTCTGCAT
CTTTTTCTTTTTGAAAATGTATTTATGTTTATAGTCAATATTACCAAATGGATAAAATTA
CCCAATGAGTATAATCATAAAACTATGAGATAGATTGAAATTTTTCATAATTTTTAGAAA
AGAATTCTGGTAATTATGATCTACAAATTTTAACACAAAAGATTATGAGCACAAAAAATG
CAAACACTGAGCATTTTAATAATATTTCAATGATGAGCACAAAACACTCAACGACACAAA
AAAATAATTTAAAATTTCTCGGGTTAGCTTTTTCTATTGTAACATTTACTCGCATCTTTC
ATAAAAATAAGAAATATTTTTAAAAAATAATTTTAAGCTCATTTCTGCTCTTTTAATCAT
CCAATAACTTTTTAGTTATTGTTTTTTAAAATTGTCTCAAGTGTGGCTGAAGAAAAAGAG
GAGAAAAATTTCAATGAGCAAGCTACTGATCGGATAGACGATAAAATATTAACAATGCCA
TCAGCAATCGTTGCCGCTCAGCAATCCAACCAATTACAACATCAAGGTGATGATATTAAT
CAAGAATGTGGAATACGCGATGTTTGGCGACATAATCTTGAAGAAGAGTTTGTTCTAATT
CGTAAAATTGTCACAAAATATTGCTATGTTGCAATGGACACTGAATTTCCAGGCGTCGTT
GCTCGGCCAATTGGTGAATTCAGATCAACCTCTGATTATCAGTATCAACTATTAAGATGC
AATGTAGATCTTTTGAAAATCATTCAACTTGGATTAACTTTCATGGATGAAGATGGCAAC
ACAGCTCCTGAATTTTCTACTTTTCAATTCAATTTCAAATTCAGTCTTACTGATGATATG
TATGCTCAAGATTCTATTGATTTACTTCAAAATTCTGGCATACAATTTAAAAAGCACGAA
GAAGATGGCATTGATCCAATTGAATTTGCTGAACTGCTCATGACAAGTGGCATTGTTCTT
ATGGATAACATAAAATGGCTCAGTTTCCATTCAGGATATGATTTCGGTTATCTCTTAAAA
GTTCTAACCGATCAGAACTTGCCTAGCGATGAAAGTGAATTCTTTGAACTTTTGCGAATC
TACTTTCCTACTATTTATGATGTCAAGTATCTAATGAAGTCTTGCAAAAATTTAAAAGGT
GGATTGCAAGAAGTTGCAGAACAATTAGATATCAGAAGAATTGGACCTCAACATCAAGCT
GGTTCCGATTCACTTCTAACTGGAATGGCCTTTTTCAAAATGAGAGAAGTATGATGTTTT
TTGAAGATAATATCGATAACGACAAGTACTCAGGTCATTTATTTGGTTTGTCTTTCAATC
AGAATGATCGTGTAGTGTCGGCTGAATAAACGAAAATATGAATTAAATTACACAAGCATA
TATACACACACTCAATTTATGAATTCGACAAATATAAATATTTAAAATATATTTGGTGAA
AACAATATGCAGTGCGACATTCACTTAAAAAAGAGATAAATTAAATGCTTTTGTGCACAC
AATAGATATTTCAAACAAATATAAAAAAATTTATTATTGCTTTGAAATGTTCTTTGAAAT
ATACTAATCTAATATAAAGTAAAAGAGAAATTATTCAAAAAAATTGAAGCAAACTGATGC
ATATTAAAAAGTTAAATAATCAGCATAAATACACATACAACTCAAACAATTTAAAGCATT
ACAAAAATTAATGATTTATCCTTATTCTTTATGTTATAACAAA
>g176.t4 Gene=g176 Length=259
MPSAIVAAQQSNQLQHQGDDINQECGIRDVWRHNLEEEFVLIRKIVTKYCYVAMDTEFPG
VVARPIGEFRSTSDYQYQLLRCNVDLLKIIQLGLTFMDEDGNTAPEFSTFQFNFKFSLTD
DMYAQDSIDLLQNSGIQFKKHEEDGIDPIEFAELLMTSGIVLMDNIKWLSFHSGYDFGYL
LKVLTDQNLPSDESEFFELLRIYFPTIYDVKYLMKSCKNLKGGLQEVAEQLDIRRIGPQH
QAGSDSLLTGMAFFKMREV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g176.t4 | Gene3D | G3DSA:3.30.420.10 | - | 14 | 259 | 0 |
| 3 | g176.t4 | PANTHER | PTHR10797 | CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT | 23 | 258 | 0 |
| 4 | g176.t4 | PANTHER | PTHR10797:SF1 | CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 8 | 23 | 258 | 0 |
| 1 | g176.t4 | Pfam | PF04857 | CAF1 family ribonuclease | 30 | 146 | 0 |
| 2 | g176.t4 | Pfam | PF04857 | CAF1 family ribonuclease | 162 | 253 | 0 |
| 5 | g176.t4 | SUPERFAMILY | SSF53098 | Ribonuclease H-like | 27 | 258 | 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:0006351 | transcription, DNA-templated | BP |
| GO:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K12581 (CCR4-NOT transcription complex subunit 7/8)
Pathway
- This transcript belongs to the following pathways
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.
