General information for g3788.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as CCR4-NOT transcription complex subunit 9.
Parent gene
- The parent gene g3788 is located on chr_3: 27963870..27966374 (- 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 | g3788 | g3788.t4 | isoform | g3788.t4 | 27963484 | 27965006 |
| chr_3 | g3788 | g3788.t4 | exon | g3788.t4.exon1 | 27963484 | 27964124 |
| chr_3 | g3788 | g3788.t4 | cds | g3788.t4.CDS1 | 27963870 | 27964124 |
| chr_3 | g3788 | g3788.t4 | exon | g3788.t4.exon2 | 27964188 | 27964633 |
| chr_3 | g3788 | g3788.t4 | cds | g3788.t4.CDS2 | 27964188 | 27964633 |
| chr_3 | g3788 | g3788.t4 | exon | g3788.t4.exon3 | 27964695 | 27965006 |
| chr_3 | g3788 | g3788.t4 | cds | g3788.t4.CDS3 | 27964695 | 27964725 |
| chr_3 | g3788 | g3788.t4 | TSS | g3788.t4 | 27965046 | 27965046 |
| chr_3 | g3788 | g3788.t4 | TTS | g3788.t4 | NA | NA |
Sequences
>g3788.t4 Gene=g3788 Length=1399
ATGGATCAAGTAAATATTATTTTTAGTGTGAAATTAGTTTGAAATAATCTCAAATATATA
GTTATTTAACTTTTTTGTGCATTACTCAATTTAAATAAGTAAAAATGCAAACCCTAAATA
CAAATTTGAATTAGAAATCATTTTGCAGAAATATTGATGTTTCTTATTTTTTTCTTCAGG
ATGTTTACACATATATTAATCAATTAAGTAATCCTGATACGCGTGAAAATGCATTATTAG
AGTTGAGTAAAAAGAGAGAATCAGTCTCTGATTTAGCTGTTATGCTATGGAACTCGTTTG
GAACAATTGGAGCATTATTACAGGAAATCGTAAACATCTATCCTTCGATAACACCACCAA
CATTGACTGCTCAACAATCAAATCGAGTTTGTAATGCTTTAGCACTTTTGCAAAACGTTG
CTTCTCATCCAGATACCCGCTCTGCCTTTCTTCAAGCTCATATTCCATTGTTTTTATATC
CATTTTTACACACCTCATCTAAAACCAGACCATTTGAGTATTTGCGCTTGACAAGTCTTG
GTGTTATTGGAGCACTAGTCAAAACTGATGAACAAGAGGTCATAACGTTTTTGCTTACCA
CTGAAATTATTCCATTATGCTTACGCATCATGGAAAGTGGATCCGAATTATCGAAAACTG
TAGCAACCTTCATTTTACAAAAGATTCTTCTTGATGACAGTGGATTATCATACATTTGTC
AAACTTATGATCGTTTTTCACATGTTGCCATCATTTTGGGAAAAATGGTAATATCGTTGG
CAAAAGAACCATCATCACGTCTCTTGAAACATGTTGTTCGTTGTTATTTACGTTTATCCG
ACAATTCTAGAGCTCGTGAGGCTCTCCGTAGATGTTTACCTGATCAATTAAGAGATGCCA
CATTCAATCAGTGTTTGCAAGAAGATCGATCAACAAAACATTGGCTTACAATGTTGATTA
AAAACTTAGAATCTGGAAATGATTCAATGCAAATACCAGCCACAATGGAGTAGTATGTCA
GCATTAATTTAATTATATAAATATTTTATGTGGCAGTAGAAAACATTTTTCTTACAATTC
AAACAACTCAATCTGATAGATTAAAGCTTTGAAAAAAAAATTGTCACAAGCATGCACACA
CACGCTCTTGAGAATAGATCGAAGAATAAATTTTATTTTTCGATATTTATACAATACTTT
TAATCTCGATGAAATTTTCTGTAGATAAGTATAATTTTAATAAACAATCTCAAGAGTATT
TGTGTTATAATCTAATTTTTATATTTTAAACATAATAATCATAATATACTTAACGAAATA
ATTTTAAATAGTTTTTTATTATAAAAATGAATCACTCACTGATTAACAAAAAATATATTA
TTGAAGTTAGCTAAAAAAT
>g3788.t4 Gene=g3788 Length=243
MLWNSFGTIGALLQEIVNIYPSITPPTLTAQQSNRVCNALALLQNVASHPDTRSAFLQAH
IPLFLYPFLHTSSKTRPFEYLRLTSLGVIGALVKTDEQEVITFLLTTEIIPLCLRIMESG
SELSKTVATFILQKILLDDSGLSYICQTYDRFSHVAIILGKMVISLAKEPSSRLLKHVVR
CYLRLSDNSRAREALRRCLPDQLRDATFNQCLQEDRSTKHWLTMLIKNLESGNDSMQIPA
TME
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g3788.t4 | Gene3D | G3DSA:1.25.10.10 | - | 1 | 231 | 0 |
| 2 | g3788.t4 | PANTHER | PTHR12262:SF0 | CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 9 | 1 | 231 | 0 |
| 3 | g3788.t4 | PANTHER | PTHR12262 | UNCHARACTERIZED | 1 | 231 | 0 |
| 1 | g3788.t4 | Pfam | PF04078 | Cell differentiation family, Rcd1-like | 1 | 229 | 0 |
| 4 | g3788.t4 | SUPERFAMILY | SSF48371 | ARM repeat | 31 | 229 | 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:0030014 | CCR4-NOT complex | CC |
| GO:0006402 | mRNA catabolic process | BP |
KEGG
Orthology
- This transcript has been annotated with K12606 (CCR4-NOT transcription complex subunit 9)
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.
