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.t14 TSS g14285.t14 36305915 36305915
chr_1 g14285 g14285.t14 isoform g14285.t14 36305946 36307607
chr_1 g14285 g14285.t14 exon g14285.t14.exon1 36305946 36306476
chr_1 g14285 g14285.t14 exon g14285.t14.exon2 36306531 36307160
chr_1 g14285 g14285.t14 cds g14285.t14.CDS1 36306672 36307160
chr_1 g14285 g14285.t14 exon g14285.t14.exon3 36307228 36307458
chr_1 g14285 g14285.t14 cds g14285.t14.CDS2 36307228 36307458
chr_1 g14285 g14285.t14 exon g14285.t14.exon4 36307515 36307607
chr_1 g14285 g14285.t14 cds g14285.t14.CDS3 36307515 36307607
chr_1 g14285 g14285.t14 TTS g14285.t14 36307699 36307699

Sequences

>g14285.t14 Gene=g14285 Length=1485
ATGCTAGAGCTTTTTAGTTTTGGACGCAAAAAGATATCAAATAAGCTCCTTATCTTTATT
AAAACTAATACGGGACAGAGTTTAAGCTTAAATTTGGATCCAGAATGGAATATTTCTAAT
GTAAAGAAATTGGTTGCGCCACAATTAGGACTAAAAAGCGAAGAAGTAAGTTGATGCATT
TAATAAAGTACCTGTTTTATTATTTGATCACAATTTGAGGTGAAAATTATATTTGCTGGA
AAAGAATTAGAAGACAACACAAGAATTAGTGAATGTGATTTAGGACAACAAAGTGTGCTT
CATGCAGTAAAAACGAAATCACGAGTGAATATCGAATCGAAAACGAAGAGATGTTTAGAT
GTAGTTTATGACGATGACAATGGAAATAATGTAATTGATGTGGCATCAAAACCTTTATCA
TCAACTCTAGTCGATTTACAATTGTGTGGAGAAGAGAGAAGACATGTATCAGAAAAGCAA
AGTGATAAAGTAAAAGCAAATTTCTTTGTACACTGTCCTGAGTGTAAAAAGCTGTGTAAA
GGAAAATTAAGAGTTCGTTGCAATATATGTAAAGAAAGCTGTTTCACTGTTCATAGAGAT
CCTGAATGTTGGGATGACGTTTTAATTCCAAAAAAAATTCAAGGACATTGTGAAAGTTTT
GAAATTGCATGCATGTCTGATGAAGAAAATGGACTTCCATTTGCTGAATTCTATTTTAAA
TGTGCAGAACATGTTTCTGGAGGTGAAAAAGACTATGCGGCGCCACTAAATCTAATAAAA
ATGAACCTTAAAGAAATTGGTTGTCTATCGTGTGGAGATATATCTGAAATAGTATTAGTT
TTTCCATGTGATGCAGGTCATGTCACTTGTCTTGAATGCTTCAAACTCTATTGTACATCA
AGATTACAAGAACGACAATTTATTTCACATGAAAACTATGGCTATACACTTTCGTGTCCT
GTCGGCTGTGAAAATTCTTTCATACAAGAGATTCATCATTTTAAATTGCTTGATAAAGAA
CTATATGATAGATACCAATCATTTGGCGCAGAAGAATTCGTTATTCAATCTGGTGGTGTC
TTGTGTCCTTTTCCTAATTGTGGAATGGGCATCATAGTTGATGAAGATTGTAATCGAGTG
CATTGCCTTAATGGGTGTGGATTTGTATTTTGTAAAATTTGCAAACAAGGCTATCATATT
GGGGAGTGTTTACCAGAAACATCAGCACAAAATAATTCAACATTAACTGAATATTCAGTT
AATCCAAATAAGGTTGCTGATTCGAGGTGGGAACAAGAAAGAATAGCTACAAAAATTGCA
ATACAAGTAACAACAAAACCATGTCCGAAATGCAGAGTTGCAACTGAAAGAGCAGGCGGT
TGTATGCATATGGTGTGCACTAGAGCTGGTTGTAATTTCGATTGGTGTTGGGTTTGTCAA
ACAGAGTGGACTCGTGATTGTATGGGTTCACATTGGTTTGGATAG

>g14285.t14 Gene=g14285 Length=270
MSDEENGLPFAEFYFKCAEHVSGGEKDYAAPLNLIKMNLKEIGCLSCGDISEIVLVFPCD
AGHVTCLECFKLYCTSRLQERQFISHENYGYTLSCPVGCENSFIQEIHHFKLLDKELYDR
YQSFGAEEFVIQSGGVLCPFPNCGMGIIVDEDCNRVHCLNGCGFVFCKICKQGYHIGECL
PETSAQNNSTLTEYSVNPNKVADSRWEQERIATKIAIQVTTKPCPKCRVATERAGGCMHM
VCTRAGCNFDWCWVCQTEWTRDCMGSHWFG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g14285.t14 CDD cd16627 RING-HC_RBR_parkin 42 100 0.0000000
15 g14285.t14 Gene3D G3DSA:3.30.40.10 Zinc/RING finger domain 40 130 0.0000045
13 g14285.t14 Gene3D G3DSA:2.20.25.20 - 131 202 0.0000000
14 g14285.t14 Gene3D G3DSA:1.20.120.1750 - 203 270 0.0000000
3 g14285.t14 PANTHER PTHR11685 RBR FAMILY RING FINGER AND IBR DOMAIN-CONTAINING 43 264 0.0000000
4 g14285.t14 PANTHER PTHR11685:SF212 E3 UBIQUITIN-PROTEIN LIGASE PARKIN 43 264 0.0000000
10 g14285.t14 PRINTS PR01475 Parkin signature 10 20 0.0000000
9 g14285.t14 PRINTS PR01475 Parkin signature 27 47 0.0000000
5 g14285.t14 PRINTS PR01475 Parkin signature 55 71 0.0000000
6 g14285.t14 PRINTS PR01475 Parkin signature 106 127 0.0000000
7 g14285.t14 PRINTS PR01475 Parkin signature 135 151 0.0000000
8 g14285.t14 PRINTS PR01475 Parkin signature 247 269 0.0000000
1 g14285.t14 Pfam PF17978 RING/Ubox like zinc-binding domain 34 124 0.0000000
2 g14285.t14 Pfam PF01485 IBR domain, a half RING-finger domain 205 261 0.0000030
19 g14285.t14 ProSiteProfiles PS51873 TRIAD supradomain profile. 40 270 33.3340000
17 g14285.t14 SMART SM00647 ibrneu5 119 179 0.0000000
18 g14285.t14 SMART SM00647 ibrneu5 204 263 0.0380000
11 g14285.t14 SUPERFAMILY SSF57850 RING/U-box 129 176 0.0000000
12 g14285.t14 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