Gene loci information

Transcript annotation

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

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_1 g14285 g14285.t16 TSS g14285.t16 36305915 36305915
chr_1 g14285 g14285.t16 isoform g14285.t16 36306543 36307607
chr_1 g14285 g14285.t16 exon g14285.t16.exon1 36306543 36307160
chr_1 g14285 g14285.t16 cds g14285.t16.CDS1 36306672 36307160
chr_1 g14285 g14285.t16 exon g14285.t16.exon2 36307228 36307458
chr_1 g14285 g14285.t16 cds g14285.t16.CDS2 36307228 36307458
chr_1 g14285 g14285.t16 exon g14285.t16.exon3 36307515 36307607
chr_1 g14285 g14285.t16 cds g14285.t16.CDS3 36307515 36307607
chr_1 g14285 g14285.t16 TTS g14285.t16 36307699 36307699

Sequences

>g14285.t16 Gene=g14285 Length=942
AAATTAAGAGTTCGTTGCAATATATGTAAAGAAAGCTGTTTCACTGTTCATAGAGATCCT
GAATGTTGGGATGACGTTTTAATTCCAAAAAAAATTCAAGGACATTGTGAAAGTTTTGAA
ATTGCATGCATGTCTGATGAAGAAAATGGACTTCCATTTGCTGAATTCTATTTTAAATGT
GCAGAACATGTTTCTGGAGGTGAAAAAGACTATGCGGCGCCACTAAATCTAATAAAAATG
AACCTTAAAGAAATTGGTTGTCTATCGTGTGGAGATATATCTGAAATAGTATTAGTTTTT
CCATGTGATGCAGGTCATGTCACTTGTCTTGAATGCTTCAAACTCTATTGTACATCAAGA
TTACAAGAACGACAATTTATTTCACATGAAAACTATGGCTATACACTTTCGTGTCCTGTC
GGCTGTGAAAATTCTTTCATACAAGAGATTCATCATTTTAAATTGCTTGATAAAGAACTA
TATGATAGATACCAATCATTTGGCGCAGAAGAATTCGTTATTCAATCTGGTGGTGTCTTG
TGTCCTTTTCCTAATTGTGGAATGGGCATCATAGTTGATGAAGATTGTAATCGAGTGCAT
TGCCTTAATGGGTGTGGATTTGTATTTTGTAAAATTTGCAAACAAGGCTATCATATTGGG
GAGTGTTTACCAGAAACATCAGCACAAAATAATTCAACATTAACTGAATATTCAGTTAAT
CCAAATAAGGTTGCTGATTCGAGGTGGGAACAAGAAAGAATAGCTACAAAAATTGCAATA
CAAGTAACAACAAAACCATGTCCGAAATGCAGAGTTGCAACTGAAAGAGCAGGCGGTTGT
ATGCATATGGTGTGCACTAGAGCTGGTTGTAATTTCGATTGGTGTTGGGTTTGTCAAACA
GAGTGGACTCGTGATTGTATGGGTTCACATTGGTTTGGATAG

>g14285.t16 Gene=g14285 Length=270
MSDEENGLPFAEFYFKCAEHVSGGEKDYAAPLNLIKMNLKEIGCLSCGDISEIVLVFPCD
AGHVTCLECFKLYCTSRLQERQFISHENYGYTLSCPVGCENSFIQEIHHFKLLDKELYDR
YQSFGAEEFVIQSGGVLCPFPNCGMGIIVDEDCNRVHCLNGCGFVFCKICKQGYHIGECL
PETSAQNNSTLTEYSVNPNKVADSRWEQERIATKIAIQVTTKPCPKCRVATERAGGCMHM
VCTRAGCNFDWCWVCQTEWTRDCMGSHWFG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g14285.t16 CDD cd16627 RING-HC_RBR_parkin 42 100 0.0000000
15 g14285.t16 Gene3D G3DSA:3.30.40.10 Zinc/RING finger domain 40 130 0.0000045
13 g14285.t16 Gene3D G3DSA:2.20.25.20 - 131 202 0.0000000
14 g14285.t16 Gene3D G3DSA:1.20.120.1750 - 203 270 0.0000000
3 g14285.t16 PANTHER PTHR11685 RBR FAMILY RING FINGER AND IBR DOMAIN-CONTAINING 43 264 0.0000000
4 g14285.t16 PANTHER PTHR11685:SF212 E3 UBIQUITIN-PROTEIN LIGASE PARKIN 43 264 0.0000000
10 g14285.t16 PRINTS PR01475 Parkin signature 10 20 0.0000000
9 g14285.t16 PRINTS PR01475 Parkin signature 27 47 0.0000000
5 g14285.t16 PRINTS PR01475 Parkin signature 55 71 0.0000000
6 g14285.t16 PRINTS PR01475 Parkin signature 106 127 0.0000000
7 g14285.t16 PRINTS PR01475 Parkin signature 135 151 0.0000000
8 g14285.t16 PRINTS PR01475 Parkin signature 247 269 0.0000000
1 g14285.t16 Pfam PF17978 RING/Ubox like zinc-binding domain 34 124 0.0000000
2 g14285.t16 Pfam PF01485 IBR domain, a half RING-finger domain 205 261 0.0000030
19 g14285.t16 ProSiteProfiles PS51873 TRIAD supradomain profile. 40 270 33.3340000
17 g14285.t16 SMART SM00647 ibrneu5 119 179 0.0000000
18 g14285.t16 SMART SM00647 ibrneu5 204 263 0.0380000
11 g14285.t16 SUPERFAMILY SSF57850 RING/U-box 129 176 0.0000000
12 g14285.t16 SUPERFAMILY SSF57850 RING/U-box 218 261 0.0000000

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:0005829 cytosol CC
GO:0016567 protein ubiquitination BP
GO:0005739 mitochondrion CC
GO:0004842 ubiquitin-protein transferase 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.

Raw TPM values