General information for g1589.t3
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.t3 | isoform | g1589.t3 | 12041212 | 12043184 |
| chr_3 | g1589 | g1589.t3 | exon | g1589.t3.exon1 | 12041212 | 12041417 |
| chr_3 | g1589 | g1589.t3 | cds | g1589.t3.CDS1 | 12041359 | 12041417 |
| chr_3 | g1589 | g1589.t3 | exon | g1589.t3.exon2 | 12041484 | 12043184 |
| chr_3 | g1589 | g1589.t3 | cds | g1589.t3.CDS2 | 12041484 | 12042264 |
| chr_3 | g1589 | g1589.t3 | TTS | g1589.t3 | 12043317 | 12043317 |
| chr_3 | g1589 | g1589.t3 | TSS | g1589.t3 | NA | NA |
Sequences
>g1589.t3 Gene=g1589 Length=1907
GCAATTTTAGATGAAATTCGACATTACTCAGCGGACATAATATGCTTACAAGAGGTTGAA
ACAGATCAATTTTATAATTTCTTCAAACCTGAACTTAAGAATGATGGATATGAAGGCATT
TTTTCACCTAAATCACGAGCTAAGACAATGTCAGAAAATGATAGAAAATATGTTGACGGT
TGTGCCATCTTCTTCCGTTCAAACAAATTTACACTGATAAAAGAGCATTTGGTAGAATTT
AATCAACTTGCAATGGCAAATGCAGAGGGATCTGACAATATGCTTAATCGTGTAATGCCA
AAAGACAACATTGGCTTAGCCGCTGTATTAAAAGTGAAAGAAAATGCATGGGAAGGTTTG
TCGCCAGAACAAGCGGCCATTTCTCAACCAATTCTTGTATGCACGGCTCACATACATTGG
GACCCGGAATTTTGCGATGTGAAACTCATTCAGACAATGATGCTGTCAAATGAATTAAAA
ACAATCCTCGATGAGGTTTGTCACAGCTTTAAGCCAGGTCAAAAATATGATAGCAACAAT
GTTCAACTGCTCTTATGTGGTGACTTCAATTCACTGCCCGATTCTGGTGTCATCGAATTC
TTAAGCACTGGCCGTGTATCCATGGATCATCAGGACTTTAAGGAACTCGGCTACAAATCA
TGCTTGCAAAAGATCTCCAATTGTGATACAGCCAATGAATTTACTCATTCCTTTAAGCTT
GCATCAGCATACAGTGAAGACACAATGCCCTATACCAACTTCACATTCGATTTTAAAGGT
ATTATCGATTACATTTTCTACTCGAAACAAGGCTTGGTTCCATTGGGTTTGCTCGGTCCA
TTATCATCGGACTGGTTGCGAGAAAACAAAGTCGTTGGCTGTCCACATCCGCGAATACCA
AGTGATCATTTTCCACTTTTGGTGGAGGTCGAGCTTGTCTTCATGAACAGCCCTCAAACT
CCAAATGGGTTCATAAATCGAAGATAGTCAACTTTGTAGTCATCATCGCTGCCGGCAATA
GAATGAAAGTTTTTAATCATCATCAAAATCTCCTTTCCCTGCCACCCATAAAATCATCAG
TTTACACTCTCATCCATCCTATAAACTATCACATTGGACATTCTTTTTGACATTAATTTC
TCTTTTCTTGGACAAATTTTTTTAATTTAAAAATGCATGGAGAAGAAGAAAAAAATCTAG
AACATAATACGTAGATATATAAATAAGATCAACGATAAAATTGTTTAAAGTTCTACAATT
AAATTAAATCCGATTTTAAAAGTCCTTTTTTACTCTCAATTTTTTTTTGTCACAACATTT
CTTACATGTGTGGTCCTTTCATTTTATCAGGAGCTTTTTTTCTTAGTCTTAATTATTATT
GTACAATTTTTTTGTGTTTCATTTATGATTTTTTTTGTAACTATTAAAAAACAAGAAAGA
AGAAATTGCAGAAAAAAAACTTGACGGAAGCTACTTGATGACTTTTTATTATTTGAAAGA
AATGCAAAACACACTCATGCACTCAATTTCTTTGTCCATGTGATTTAATCACGAGCATCT
ACAGTAAAAAATGAACAAGGTAGTTTGCACGTGTGTCTTCAGTAAAACTTTTAGTGAAAA
ATGATGAAAATTTTTTTAAAATGTCTGCATTTACAACACATGGAAGTAAAGAATAGTGAT
TTTTGATAAAGAAAAAATTCCATTCATCTTGAATAGCAGAAAGAAAAAACTTTTGATTTA
AAATACAGAACCGTAAACTGATTGTGATTTATAATATAAAAAAATTTGAATGAAAGTATT
CAAGTAAAATTGAGAAATTTTAGCACATTTTTTAACAATTTATAGAAAAATTTGGCTGTA
AAAGTGAATTTTTAAAAGCATGTTTTATATATTTTAACCAAAAATGC
>g1589.t3 Gene=g1589 Length=279
MSENDRKYVDGCAIFFRSNKFTLIKEHLVEFNQLAMANAEGSDNMLNRVMPKDNIGLAAV
LKVKENAWEGLSPEQAAISQPILVCTAHIHWDPEFCDVKLIQTMMLSNELKTILDEVCHS
FKPGQKYDSNNVQLLLCGDFNSLPDSGVIEFLSTGRVSMDHQDFKELGYKSCLQKISNCD
TANEFTHSFKLASAYSEDTMPYTNFTFDFKGIIDYIFYSKQGLVPLGLLGPLSSDWLREN
KVVGCPHPRIPSDHFPLLVEVELVFMNSPQTPNGFINRR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g1589.t3 | Gene3D | G3DSA:3.60.10.10 | - | 1 | 271 | 0 |
| 2 | g1589.t3 | PANTHER | PTHR12121:SF35 | CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 6-LIKE | 2 | 268 | 0 |
| 3 | g1589.t3 | PANTHER | PTHR12121 | CARBON CATABOLITE REPRESSOR PROTEIN 4 | 2 | 268 | 0 |
| 1 | g1589.t3 | Pfam | PF03372 | Endonuclease/Exonuclease/phosphatase family | 7 | 254 | 0 |
| 4 | g1589.t3 | SUPERFAMILY | SSF56219 | DNase I-like | 9 | 264 | 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 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.
