General information for g1589.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as CCR4-NOT transcription complex subunit 6-like.
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.t2 | isoform | g1589.t2 | 12040771 | 12042264 |
| chr_3 | g1589 | g1589.t2 | exon | g1589.t2.exon1 | 12040771 | 12040845 |
| chr_3 | g1589 | g1589.t2 | exon | g1589.t2.exon2 | 12040969 | 12041075 |
| chr_3 | g1589 | g1589.t2 | cds | g1589.t2.CDS1 | 12040983 | 12041075 |
| chr_3 | g1589 | g1589.t2 | exon | g1589.t2.exon3 | 12041212 | 12041417 |
| chr_3 | g1589 | g1589.t2 | cds | g1589.t2.CDS2 | 12041212 | 12041417 |
| chr_3 | g1589 | g1589.t2 | exon | g1589.t2.exon4 | 12041484 | 12042264 |
| chr_3 | g1589 | g1589.t2 | cds | g1589.t2.CDS3 | 12041484 | 12042264 |
| chr_3 | g1589 | g1589.t2 | TTS | g1589.t2 | 12042729 | 12042729 |
| chr_3 | g1589 | g1589.t2 | TSS | g1589.t2 | NA | NA |
Sequences
>g1589.t2 Gene=g1589 Length=1169
TTACTGTCCCGGGCACATCACCGCCTCAAAGACCGTGGATACCTCTCGCAAGACCTAATA
GATCGAGGCCAGCATGCATATTTACCGTAATGTGCTACAACGTCCTCTGCGATAAGTATG
CAACAAGACAAATGTACGGCTATTGCCCGAGCTGGGCACTTGCATGGGAGTATCGTAAGA
AGGCAATTTTAGATGAAATTCGACATTACTCAGCGGACATAATATGCTTACAAGAGGTTG
AAACAGATCAATTTTATAATTTCTTCAAACCTGAACTTAAGAATGATGGATATGAAGGCA
TTTTTTCACCTAAATCACGAGCTAAGACAATGTCAGAAAATGATAGAAAATATGTTGACG
GTTGTGCCATCTTCTTCCGTTCAAACAAATTTACACTGATAAAAGAGCATTTGGTAGAAT
TTAATCAACTTGCAATGGCAAATGCAGAGGGATCTGACAATATGCTTAATCGTGTAATGC
CAAAAGACAACATTGGCTTAGCCGCTGTATTAAAAGTGAAAGAAAATGCATGGGAAGGTT
TGTCGCCAGAACAAGCGGCCATTTCTCAACCAATTCTTGTATGCACGGCTCACATACATT
GGGACCCGGAATTTTGCGATGTGAAACTCATTCAGACAATGATGCTGTCAAATGAATTAA
AAACAATCCTCGATGAGGTTTGTCACAGCTTTAAGCCAGGTCAAAAATATGATAGCAACA
ATGTTCAACTGCTCTTATGTGGTGACTTCAATTCACTGCCCGATTCTGGTGTCATCGAAT
TCTTAAGCACTGGCCGTGTATCCATGGATCATCAGGACTTTAAGGAACTCGGCTACAAAT
CATGCTTGCAAAAGATCTCCAATTGTGATACAGCCAATGAATTTACTCATTCCTTTAAGC
TTGCATCAGCATACAGTGAAGACACAATGCCCTATACCAACTTCACATTCGATTTTAAAG
GTATTATCGATTACATTTTCTACTCGAAACAAGGCTTGGTTCCATTGGGTTTGCTCGGTC
CATTATCATCGGACTGGTTGCGAGAAAACAAAGTCGTTGGCTGTCCACATCCGCGAATAC
CAAGTGATCATTTTCCACTTTTGGTGGAGGTCGAGCTTGTCTTCATGAACAGCCCTCAAA
CTCCAAATGGGTTCATAAATCGAAGATAG
>g1589.t2 Gene=g1589 Length=359
MCYNVLCDKYATRQMYGYCPSWALAWEYRKKAILDEIRHYSADIICLQEVETDQFYNFFK
PELKNDGYEGIFSPKSRAKTMSENDRKYVDGCAIFFRSNKFTLIKEHLVEFNQLAMANAE
GSDNMLNRVMPKDNIGLAAVLKVKENAWEGLSPEQAAISQPILVCTAHIHWDPEFCDVKL
IQTMMLSNELKTILDEVCHSFKPGQKYDSNNVQLLLCGDFNSLPDSGVIEFLSTGRVSMD
HQDFKELGYKSCLQKISNCDTANEFTHSFKLASAYSEDTMPYTNFTFDFKGIIDYIFYSK
QGLVPLGLLGPLSSDWLRENKVVGCPHPRIPSDHFPLLVEVELVFMNSPQTPNGFINRR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g1589.t2 | CDD | cd09097 | Deadenylase_CCR4 | 1 | 343 | 0 |
| 5 | g1589.t2 | Gene3D | G3DSA:3.60.10.10 | - | 1 | 351 | 0 |
| 2 | g1589.t2 | PANTHER | PTHR12121:SF33 | CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 6 | 1 | 350 | 0 |
| 3 | g1589.t2 | PANTHER | PTHR12121 | CARBON CATABOLITE REPRESSOR PROTEIN 4 | 1 | 350 | 0 |
| 1 | g1589.t2 | Pfam | PF03372 | Endonuclease/Exonuclease/phosphatase family | 3 | 334 | 0 |
| 4 | g1589.t2 | SUPERFAMILY | SSF56219 | DNase I-like | 1 | 343 | 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.
