Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative E3 ubiquitin-protein ligase COP1.

Parent gene

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_2 g5760 g5760.t3 isoform g5760.t3 11800521 11801468
chr_2 g5760 g5760.t3 exon g5760.t3.exon1 11800521 11801147
chr_2 g5760 g5760.t3 cds g5760.t3.CDS1 11800521 11801147
chr_2 g5760 g5760.t3 exon g5760.t3.exon2 11801265 11801468
chr_2 g5760 g5760.t3 cds g5760.t3.CDS2 11801265 11801468
chr_2 g5760 g5760.t3 TSS g5760.t3 NA NA
chr_2 g5760 g5760.t3 TTS g5760.t3 NA NA

Sequences

>g5760.t3 Gene=g5760 Length=831
ATGCCACGAAGGCAAAGTTTAGAAAGAAACCCAAGTAATTCTAGTGATTTGAATCCTCGC
AAGAAAAAGTTAAAAGATAAAATGGCAAGTAATAATGAATACTTATGTCCTATCTGTTTT
ACGACAATCAAAGAAGCTACAATTACTAAATGTGGCCACACTTATTGCGCTAAATGCATT
ACAAAATCCATTGATATCTCAAAGTCATGTCCAAAGTGTGGATCATCGTTAAATGTCGAT
CAGATTTTCCCAAATTTTTTGTTAAATGAGTTGATATCAAAACACTTGATGGAACAAAAA
GAGAAAGAACGTATGTTTGCAACAACACCAAGTATTGATGAAGACGACGATTCATTAGAA
AACTTAAAGACTTTTCTCGCGACAGAATCAAAGAAACTGTCATTATCAGAAGTTAACAAG
ATACTTGAAATATTTTCACAAAGGAAGATTCTTCTAGAAGCGGAATCACAAATCGCACAA
AACAAATTACTTTACGAGTTTCTTCAAAATTTGCTTAAACAAACTGAACAACAACAGCGT
GAGCTGGATAAAAAAATACGCTTGATAAAAGGAGATATGAAGGTTGTAGAGAACATTCTG
AAAAATGTTCAAAATTCAGTTCCAAAAATGGAAGATTTAGAGAAGCACTTTGAAAAAAGT
TCAACGAACAATATAACTGATTCAAGTACAAGTAATGCTGGTCAACAGCTGAATGCAATT
AGAGATGAAATGAAACAACTCATTACCGATATTGATTCTTCGATGCCAAATGTAACAGAA
AGTAATGAAAACAAGGAAGAAATAAATACTGAACAACAACAACCACAAAAA

>g5760.t3 Gene=g5760 Length=277
MPRRQSLERNPSNSSDLNPRKKKLKDKMASNNEYLCPICFTTIKEATITKCGHTYCAKCI
TKSIDISKSCPKCGSSLNVDQIFPNFLLNELISKHLMEQKEKERMFATTPSIDEDDDSLE
NLKTFLATESKKLSLSEVNKILEIFSQRKILLEAESQIAQNKLLYEFLQNLLKQTEQQQR
ELDKKIRLIKGDMKVVENILKNVQNSVPKMEDLEKHFEKSSTNNITDSSTSNAGQQLNAI
RDEMKQLITDIDSSMPNVTESNENKEEINTEQQQPQK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g5760.t3 CDD cd16504 RING-HC_COP1 32 77 6.16302E-20
6 g5760.t3 Coils Coil Coil 158 192 -
5 g5760.t3 Gene3D G3DSA:3.30.40.10 Zinc/RING finger domain 9 133 1.6E-18
12 g5760.t3 MobiDBLite mobidb-lite consensus disorder prediction 1 24 -
10 g5760.t3 MobiDBLite mobidb-lite consensus disorder prediction 248 277 -
11 g5760.t3 MobiDBLite mobidb-lite consensus disorder prediction 250 277 -
2 g5760.t3 PANTHER PTHR44080 E3 UBIQUITIN-PROTEIN LIGASE COP1 16 272 2.0E-42
3 g5760.t3 PANTHER PTHR44080:SF1 E3 UBIQUITIN-PROTEIN LIGASE COP1 16 272 2.0E-42
1 g5760.t3 Pfam PF13923 Zinc finger, C3HC4 type (RING finger) 36 73 4.3E-11
9 g5760.t3 ProSitePatterns PS00518 Zinc finger RING-type signature. 51 60 -
13 g5760.t3 ProSiteProfiles PS50089 Zinc finger RING-type profile. 36 73 11.87
8 g5760.t3 SMART SM00184 ring_2 36 73 7.1E-7
4 g5760.t3 SUPERFAMILY SSF57850 RING/U-box 31 99 1.25E-19

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5760/g5760.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5760.t3.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0061630 ubiquitin protein ligase activity 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. There were no conditions that were differentially expressed