General information for g5760.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as E3 ubiquitin-protein ligase COP1.
Parent gene
- The parent gene g5760 is located on chr_2: 11801468..11802885 (- 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_2 | g5760 | g5760.t1 | isoform | g5760.t1 | 11799006 | 11801468 |
| chr_2 | g5760 | g5760.t1 | exon | g5760.t1.exon1 | 11799006 | 11799209 |
| chr_2 | g5760 | g5760.t1 | cds | g5760.t1.CDS1 | 11799006 | 11799209 |
| chr_2 | g5760 | g5760.t1 | exon | g5760.t1.exon2 | 11799346 | 11799570 |
| chr_2 | g5760 | g5760.t1 | cds | g5760.t1.CDS2 | 11799346 | 11799570 |
| chr_2 | g5760 | g5760.t1 | exon | g5760.t1.exon3 | 11799633 | 11801147 |
| chr_2 | g5760 | g5760.t1 | cds | g5760.t1.CDS3 | 11799633 | 11801147 |
| chr_2 | g5760 | g5760.t1 | exon | g5760.t1.exon4 | 11801265 | 11801468 |
| chr_2 | g5760 | g5760.t1 | cds | g5760.t1.CDS4 | 11801265 | 11801468 |
| chr_2 | g5760 | g5760.t1 | TSS | g5760.t1 | NA | NA |
| chr_2 | g5760 | g5760.t1 | TTS | g5760.t1 | NA | NA |
Sequences
>g5760.t1 Gene=g5760 Length=2148
ATGCCACGAAGGCAAAGTTTAGAAAGAAACCCAAGTAATTCTAGTGATTTGAATCCTCGC
AAGAAAAAGTTAAAAGATAAAATGGCAAGTAATAATGAATACTTATGTCCTATCTGTTTT
ACGACAATCAAAGAAGCTACAATTACTAAATGTGGCCACACTTATTGCGCTAAATGCATT
ACAAAATCCATTGATATCTCAAAGTCATGTCCAAAGTGTGGATCATCGTTAAATGTCGAT
CAGATTTTCCCAAATTTTTTGTTAAATGAGTTGATATCAAAACACTTGATGGAACAAAAA
GAGAAAGAACGTATGTTTGCAACAACACCAAGTATTGATGAAGACGACGATTCATTAGAA
AACTTAAAGACTTTTCTCGCGACAGAATCAAAGAAACTGTCATTATCAGAAGTTAACAAG
ATACTTGAAATATTTTCACAAAGGAAGATTCTTCTAGAAGCGGAATCACAAATCGCACAA
AACAAATTACTTTACGAGTTTCTTCAAAATTTGCTTAAACAAACTGAACAACAACAGCGT
GAGCTGGATAAAAAAATACGCTTGATAAAAGGAGATATGAAGGTTGTAGAGAACATTCTG
AAAAATGTTCAAAATTCAGTTCCAAAAATGGAAGATTTAGAGAAGCACTTTGAAAAAAGT
TCAACGAACAATATAACTGATTCAAGTACAAGTAATGCTGGTCAACAGCTGAATGCAATT
AGAGATGAAATGAAACAACTCATTACCGATATTGATTCTTCGATGCCAAATGTAACAGAA
AGTAATGAAAACAAGGAAGAAATAAATACTGAACAACAACAACCACAAAAAGATGAAGCT
CAAACAGCAGCAGCAACTTCTTCTCAGTCGACTGCACAAATATCTTTATCACAATCATCC
ACATATAAAGTTAGAAAACAACGAATGTTTCAGCATTTTGATGACTTTGTTAAATGTTAT
TTTACAAATAGAGCTGACGATTTACATTTTCAACAAAATGACGATGAAGTCATGATTACT
GACACAAATGAATCAACTCAAACACCAGCAACTTCCAATCCAGAATTGCCAAAAGTTAGC
AAATCATTAGATATTTTTCGAGAGAATCTGATTAAATTTAGTAAATTTAATCAATTGCGA
ACGCTATCAACACTAAATTATTCAAATGAAAATACTGTCATGCCATCAACAATCGTGAGT
TCAATCGAATTTGACAAGGATTCTGAGTTCTTTGCTATTGCGGGCGTTACTAAACGTATT
AAGATTTTCGACTACTATGCTAGCATTAGAGACGCTGTTGTTGATATTAAACATCCGATC
AATGAAATTGTGTGTACATCAAAAATCTCATGTGTAGTATGGAATTCTTACTTTAAAGAG
CTTCTTGCTTCATCTGATTATGAAGGAATCGTTACAGTGTATGATGTTGAAACGCGAGTT
CGTAAACGAACTTTTCAAGAACATGATAAACGTTGTTGGTCAGTAGATTTCAATGAGATT
GATACAAAATTGCTGGCTAGTGGAAGCGATGATGCTCGTGTCAAATTATGGTCAATTGAT
TGTGAAAATTCAGTTGCAACGCTTGAAGTCAAAACAGCTAATGTATGTTGTGTAAAATTC
AATCCTAAGAGTTCTTGTCATTTAGCATTCGGTTCAGCTGATCATTGTGTTCATTATTAT
GACCTGCGAAATCTAAAATCTCCATTGTTGATACTTAAAGGTCATAAGAAAGCTGTCTCG
TATGTCAAATTTCTTAATACAAATGAAATAATTTCTGCGGGTACTGATGGTCAGCTTAAG
CTTTGGGATATAAATAAACATCCTTATTGTGTTCGTTCATTCGTTGGAGGGCATATTAAT
GAGAAAAATTTCGTTGGATTAGCTACGAATGGTGACTATATAGCATGCGGAAGCGAAGAT
AATTCATTATGTATCTACTATAAGGGACTATCGAAGCAACTATTCAATTTGAGATTTGAT
TTACAACAACGATATAGTGGCTATGATGTCGACACAAAGAGCGGTTCATCAGATAATGAA
TTTGTGTCTGCAGTTTGTTGGAAAAAATCACTTTCATCCAATCAGCAATCGAATACAATA
ATTGCGGGTAATAGTAAGGGCATTATAAAAATACTAGAGCTTGTTTAA
>g5760.t1 Gene=g5760 Length=715
MPRRQSLERNPSNSSDLNPRKKKLKDKMASNNEYLCPICFTTIKEATITKCGHTYCAKCI
TKSIDISKSCPKCGSSLNVDQIFPNFLLNELISKHLMEQKEKERMFATTPSIDEDDDSLE
NLKTFLATESKKLSLSEVNKILEIFSQRKILLEAESQIAQNKLLYEFLQNLLKQTEQQQR
ELDKKIRLIKGDMKVVENILKNVQNSVPKMEDLEKHFEKSSTNNITDSSTSNAGQQLNAI
RDEMKQLITDIDSSMPNVTESNENKEEINTEQQQPQKDEAQTAAATSSQSTAQISLSQSS
TYKVRKQRMFQHFDDFVKCYFTNRADDLHFQQNDDEVMITDTNESTQTPATSNPELPKVS
KSLDIFRENLIKFSKFNQLRTLSTLNYSNENTVMPSTIVSSIEFDKDSEFFAIAGVTKRI
KIFDYYASIRDAVVDIKHPINEIVCTSKISCVVWNSYFKELLASSDYEGIVTVYDVETRV
RKRTFQEHDKRCWSVDFNEIDTKLLASGSDDARVKLWSIDCENSVATLEVKTANVCCVKF
NPKSSCHLAFGSADHCVHYYDLRNLKSPLLILKGHKKAVSYVKFLNTNEIISAGTDGQLK
LWDINKHPYCVRSFVGGHINEKNFVGLATNGDYIACGSEDNSLCIYYKGLSKQLFNLRFD
LQQRYSGYDVDTKSGSSDNEFVSAVCWKKSLSSNQQSNTIIAGNSKGIIKILELV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g5760.t1 | CDD | cd16504 | RING-HC_COP1 | 32 | 77 | 5.8613E-19 |
| 11 | g5760.t1 | Coils | Coil | Coil | 158 | 192 | - |
| 10 | g5760.t1 | Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain | 9 | 128 | 7.2E-18 |
| 9 | g5760.t1 | Gene3D | G3DSA:2.130.10.10 | - | 365 | 715 | 1.6E-116 |
| 25 | g5760.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 24 | - |
| 23 | g5760.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 255 | 297 | - |
| 24 | g5760.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 274 | 297 | - |
| 5 | g5760.t1 | PANTHER | PTHR44080 | E3 UBIQUITIN-PROTEIN LIGASE COP1 | 18 | 713 | 2.2E-213 |
| 6 | g5760.t1 | PANTHER | PTHR44080:SF1 | E3 UBIQUITIN-PROTEIN LIGASE COP1 | 18 | 713 | 2.2E-213 |
| 1 | g5760.t1 | Pfam | PF13923 | Zinc finger, C3HC4 type (RING finger) | 36 | 73 | 1.5E-10 |
| 4 | g5760.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 483 | 518 | 0.041 |
| 2 | g5760.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 567 | 603 | 0.0011 |
| 3 | g5760.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 610 | 646 | 0.23 |
| 22 | g5760.t1 | ProSitePatterns | PS00518 | Zinc finger RING-type signature. | 51 | 60 | - |
| 21 | g5760.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 590 | 604 | - |
| 27 | g5760.t1 | ProSiteProfiles | PS50089 | Zinc finger RING-type profile. | 36 | 73 | 11.87 |
| 26 | g5760.t1 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 442 | 656 | 25.655 |
| 29 | g5760.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 485 | 527 | 10.876 |
| 28 | g5760.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 572 | 605 | 11.879 |
| 20 | g5760.t1 | SMART | SM00184 | ring_2 | 36 | 73 | 7.1E-7 |
| 19 | g5760.t1 | SMART | SM00320 | WD40_4 | 386 | 424 | 4.0 |
| 15 | g5760.t1 | SMART | SM00320 | WD40_4 | 436 | 475 | 3.9 |
| 14 | g5760.t1 | SMART | SM00320 | WD40_4 | 478 | 518 | 1.2E-6 |
| 18 | g5760.t1 | SMART | SM00320 | WD40_4 | 521 | 561 | 0.0055 |
| 13 | g5760.t1 | SMART | SM00320 | WD40_4 | 565 | 603 | 1.1E-5 |
| 16 | g5760.t1 | SMART | SM00320 | WD40_4 | 607 | 647 | 1.6 |
| 17 | g5760.t1 | SMART | SM00320 | WD40_4 | 666 | 713 | 400.0 |
| 7 | g5760.t1 | SUPERFAMILY | SSF57850 | RING/U-box | 32 | 99 | 5.42E-19 |
| 8 | g5760.t1 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 397 | 711 | 1.55E-50 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5760/g5760.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5760.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0061630 | ubiquitin protein ligase activity | MF |
| GO:0005515 | protein binding | MF |
KEGG
Orthology
- This transcript has been annotated with K10143 (E3 ubiquitin-protein ligase RFWD2)
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.
