General information for g1587.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative CCR4-NOT transcription complex subunit 6-like.
Parent gene
- The parent gene g1587 is located on chr_3: 12023343..12023972 (+ 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 | g1587 | g1587.t1 | isoform | g1587.t1 | 12023343 | 12023972 |
| chr_3 | g1587 | g1587.t1 | exon | g1587.t1.exon1 | 12023343 | 12023454 |
| chr_3 | g1587 | g1587.t1 | cds | g1587.t1.CDS1 | 12023343 | 12023454 |
| chr_3 | g1587 | g1587.t1 | exon | g1587.t1.exon2 | 12023520 | 12023706 |
| chr_3 | g1587 | g1587.t1 | cds | g1587.t1.CDS2 | 12023520 | 12023706 |
| chr_3 | g1587 | g1587.t1 | exon | g1587.t1.exon3 | 12023765 | 12023972 |
| chr_3 | g1587 | g1587.t1 | cds | g1587.t1.CDS3 | 12023765 | 12023972 |
| chr_3 | g1587 | g1587.t1 | TSS | g1587.t1 | NA | NA |
| chr_3 | g1587 | g1587.t1 | TTS | g1587.t1 | NA | NA |
Sequences
>g1587.t1 Gene=g1587 Length=507
ATGTCTCGAAAAGACAAATATGAGACAAACAATAGGAGACAACAAACTTTTATGTCAGCC
GAAGACGTCGCTGCAGGCCGAAAATCATCATGGCAAGGCGTTGAAATAACAGGCCTTGTT
CGCAACATTAGTCCTCAATTATGGCATTTTGAGCACTTGACTGCATTATATCTTAATGAC
AACTGTTTAATTCGTCTGCCATCCGACATTGGACTTCTTGTTAATCTACGAACGTTAGAC
TTATCGAATAACAAATTAAGAAGCTTGCCTGCTGAACTAGGAGAATTGATTCAATTGAGA
GAACTACATCTTAATCACAACTTGCTCCGCAGTTTGCCTTACGAACTCGGGAAATTATTT
CATCTTGTGTTATTAGGACTGCATGGAAATCCATTGACAAAAGACATATTATCAATTTAC
AATGACATAAACGGAACCAACAAACTATTGACGCACATGTTGGACAATTATAGTCGTGAG
TACTTCTTCAAACTTATTCTTTTTTGA
>g1587.t1 Gene=g1587 Length=168
MSRKDKYETNNRRQQTFMSAEDVAAGRKSSWQGVEITGLVRNISPQLWHFEHLTALYLND
NCLIRLPSDIGLLVNLRTLDLSNNKLRSLPAELGELIQLRELHLNHNLLRSLPYELGKLF
HLVLLGLHGNPLTKDILSIYNDINGTNKLLTHMLDNYSREYFFKLILF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g1587.t1 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 2 | 156 | 0.000000 |
| 2 | g1587.t1 | PANTHER | PTHR12121:SF35 | CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 6-LIKE | 18 | 159 | 0.000000 |
| 3 | g1587.t1 | PANTHER | PTHR12121 | CARBON CATABOLITE REPRESSOR PROTEIN 4 | 18 | 159 | 0.000000 |
| 5 | g1587.t1 | PRINTS | PR00019 | Leucine-rich repeat signature | 76 | 89 | 0.000017 |
| 4 | g1587.t1 | PRINTS | PR00019 | Leucine-rich repeat signature | 96 | 109 | 0.000017 |
| 1 | g1587.t1 | Pfam | PF12799 | Leucine Rich repeats (2 copies) | 75 | 112 | 0.000000 |
| 11 | g1587.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 52 | 73 | 7.065000 |
| 12 | g1587.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 75 | 96 | 8.898000 |
| 13 | g1587.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 98 | 120 | 7.158000 |
| 8 | g1587.t1 | SMART | SM00369 | LRR_typ_2 | 50 | 72 | 80.000000 |
| 7 | g1587.t1 | SMART | SM00369 | LRR_typ_2 | 73 | 94 | 0.022000 |
| 9 | g1587.t1 | SMART | SM00369 | LRR_typ_2 | 96 | 119 | 0.075000 |
| 6 | g1587.t1 | SUPERFAMILY | SSF52058 | L domain-like | 41 | 149 | 0.000000 |
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:0005515 | protein binding | MF |
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.
