General information for g1589.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as CCR4-NOT transcription complex subunit 6.
Parent gene
- The parent gene g1589 is located on chr_3: 12041212..12043184 (+ 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 | g1589 | g1589.t1 | isoform | g1589.t1 | 12036052 | 12042264 |
| chr_3 | g1589 | g1589.t1 | exon | g1589.t1.exon1 | 12036052 | 12036073 |
| chr_3 | g1589 | g1589.t1 | cds | g1589.t1.CDS1 | 12036052 | 12036073 |
| chr_3 | g1589 | g1589.t1 | exon | g1589.t1.exon2 | 12040771 | 12040845 |
| chr_3 | g1589 | g1589.t1 | cds | g1589.t1.CDS2 | 12040771 | 12040845 |
| chr_3 | g1589 | g1589.t1 | exon | g1589.t1.exon3 | 12040969 | 12041075 |
| chr_3 | g1589 | g1589.t1 | cds | g1589.t1.CDS3 | 12040969 | 12041075 |
| chr_3 | g1589 | g1589.t1 | exon | g1589.t1.exon4 | 12041212 | 12041417 |
| chr_3 | g1589 | g1589.t1 | cds | g1589.t1.CDS4 | 12041212 | 12041417 |
| chr_3 | g1589 | g1589.t1 | exon | g1589.t1.exon5 | 12041484 | 12042264 |
| chr_3 | g1589 | g1589.t1 | cds | g1589.t1.CDS5 | 12041484 | 12042264 |
| chr_3 | g1589 | g1589.t1 | TTS | g1589.t1 | 12042729 | 12042729 |
| chr_3 | g1589 | g1589.t1 | TSS | g1589.t1 | NA | NA |
Sequences
>g1589.t1 Gene=g1589 Length=1191
ATGTATAATGAAAATAGTGAAATTACTGTCCCGGGCACATCACCGCCTCAAAGACCGTGG
ATACCTCTCGCAAGACCTAATAGATCGAGGCCAGCATGCATATTTACCGTAATGTGCTAC
AACGTCCTCTGCGATAAGTATGCAACAAGACAAATGTACGGCTATTGCCCGAGCTGGGCA
CTTGCATGGGAGTATCGTAAGAAGGCAATTTTAGATGAAATTCGACATTACTCAGCGGAC
ATAATATGCTTACAAGAGGTTGAAACAGATCAATTTTATAATTTCTTCAAACCTGAACTT
AAGAATGATGGATATGAAGGCATTTTTTCACCTAAATCACGAGCTAAGACAATGTCAGAA
AATGATAGAAAATATGTTGACGGTTGTGCCATCTTCTTCCGTTCAAACAAATTTACACTG
ATAAAAGAGCATTTGGTAGAATTTAATCAACTTGCAATGGCAAATGCAGAGGGATCTGAC
AATATGCTTAATCGTGTAATGCCAAAAGACAACATTGGCTTAGCCGCTGTATTAAAAGTG
AAAGAAAATGCATGGGAAGGTTTGTCGCCAGAACAAGCGGCCATTTCTCAACCAATTCTT
GTATGCACGGCTCACATACATTGGGACCCGGAATTTTGCGATGTGAAACTCATTCAGACA
ATGATGCTGTCAAATGAATTAAAAACAATCCTCGATGAGGTTTGTCACAGCTTTAAGCCA
GGTCAAAAATATGATAGCAACAATGTTCAACTGCTCTTATGTGGTGACTTCAATTCACTG
CCCGATTCTGGTGTCATCGAATTCTTAAGCACTGGCCGTGTATCCATGGATCATCAGGAC
TTTAAGGAACTCGGCTACAAATCATGCTTGCAAAAGATCTCCAATTGTGATACAGCCAAT
GAATTTACTCATTCCTTTAAGCTTGCATCAGCATACAGTGAAGACACAATGCCCTATACC
AACTTCACATTCGATTTTAAAGGTATTATCGATTACATTTTCTACTCGAAACAAGGCTTG
GTTCCATTGGGTTTGCTCGGTCCATTATCATCGGACTGGTTGCGAGAAAACAAAGTCGTT
GGCTGTCCACATCCGCGAATACCAAGTGATCATTTTCCACTTTTGGTGGAGGTCGAGCTT
GTCTTCATGAACAGCCCTCAAACTCCAAATGGGTTCATAAATCGAAGATAG
>g1589.t1 Gene=g1589 Length=396
MYNENSEITVPGTSPPQRPWIPLARPNRSRPACIFTVMCYNVLCDKYATRQMYGYCPSWA
LAWEYRKKAILDEIRHYSADIICLQEVETDQFYNFFKPELKNDGYEGIFSPKSRAKTMSE
NDRKYVDGCAIFFRSNKFTLIKEHLVEFNQLAMANAEGSDNMLNRVMPKDNIGLAAVLKV
KENAWEGLSPEQAAISQPILVCTAHIHWDPEFCDVKLIQTMMLSNELKTILDEVCHSFKP
GQKYDSNNVQLLLCGDFNSLPDSGVIEFLSTGRVSMDHQDFKELGYKSCLQKISNCDTAN
EFTHSFKLASAYSEDTMPYTNFTFDFKGIIDYIFYSKQGLVPLGLLGPLSSDWLRENKVV
GCPHPRIPSDHFPLLVEVELVFMNSPQTPNGFINRR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g1589.t1 | CDD | cd09097 | Deadenylase_CCR4 | 37 | 380 | 0 |
| 5 | g1589.t1 | Gene3D | G3DSA:3.60.10.10 | - | 6 | 388 | 0 |
| 2 | g1589.t1 | PANTHER | PTHR12121:SF33 | CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 6 | 10 | 387 | 0 |
| 3 | g1589.t1 | PANTHER | PTHR12121 | CARBON CATABOLITE REPRESSOR PROTEIN 4 | 10 | 387 | 0 |
| 1 | g1589.t1 | Pfam | PF03372 | Endonuclease/Exonuclease/phosphatase family | 40 | 371 | 0 |
| 4 | g1589.t1 | SUPERFAMILY | SSF56219 | DNase I-like | 20 | 381 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K12603 (CCR4-NOT transcription complex subunit 6)
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.
