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.t12 TSS g14285.t12 36305915 36305915
chr_1 g14285 g14285.t12 isoform g14285.t12 36305946 36307460
chr_1 g14285 g14285.t12 exon g14285.t12.exon1 36305946 36306476
chr_1 g14285 g14285.t12 exon g14285.t12.exon2 36306531 36307160
chr_1 g14285 g14285.t12 cds g14285.t12.CDS1 36306672 36307160
chr_1 g14285 g14285.t12 exon g14285.t12.exon3 36307228 36307460
chr_1 g14285 g14285.t12 cds g14285.t12.CDS2 36307228 36307458
chr_1 g14285 g14285.t12 TTS g14285.t12 36307699 36307699

Sequences

>g14285.t12 Gene=g14285 Length=1394
ATGCTAGAGCTTTTTAGTTTTGGACGCAAAAAGATATCAAATAAGCTCCTTATCTTTATT
AAAACTAATACGGGACAGAGTTTAAGCTTAAATTTGGATCCAGAATGGAATATTTCTAAT
GTAAAGAAATTGGTTGCGCCACAATTAGGACTAAAAAGCGAAGAAGTAAGTTGATGCATT
TAATAAAGTACCTGTTTTATTATTTGATCACAATTTGAGGTGAAAATTATATTTGCTGGA
AAAGAATTAGAAGACAACACAAGAATTAGTGAATGTGATTTAGGACAACAAAGTGTGCTT
CATGCAGTAAAAACGAAATCACGAGTGAATATCGAATCGAAAACGAAGAGATGTTTAGAT
GTAGTTTATGACGATGACAATGGAAATAATGTAATTGATGTGGCATCAAAACCTTTATCA
TCAACTCTAGTCGATTTACAATTGTGTGGAGAAGAGAGAAGACATGTATCAGAAAAGCAA
AGTGATAAAGTAAAAGCAAATTTCTTTGTACACTGTCCTGAGTGTAAAAAGCTGTGTAAA
GGAAAATTAAGAGTTCGTTGCAATATATGTAAAGAAAGCTGTTTCACTGTTCATAGAGAT
CCTGAATGTTGGGATGACGTTTTAATTCCAAAAAAAATTCAAGGACATTGTGAAAGTTTT
GAAATTGCATGCATGTCTGATGAAGAAAATGGACTTCCATTTGCTGAATTCTATTTTAAA
TGTGCAGAACATGTTTCTGGAGGTGAAAAAGACTATGCGGCGCCACTAAATCTAATAAAA
ATGAACCTTAAAGAAATTGGTTGTCTATCGTGTGGAGATATATCTGAAATAGTATTAGTT
TTTCCATGTGATGCAGGTCATGTCACTTGTCTTGAATGCTTCAAACTCTATTGTACATCA
AGATTACAAGAACGACAATTTATTTCACATGAAAACTATGGCTATACACTTTCGTGTCCT
GTCGGCTGTGAAAATTCTTTCATACAAGAGATTCATCATTTTAAATTGCTTGATAAAGAA
CTATATGATAGATACCAATCATTTGGCGCAGAAGAATTCGTTATTCAATCTGGTGGTGTC
TTGTGTCCTTTTCCTAATTGTGGAATGGGCATCATAGTTGATGAAGATTGTAATCGAGTG
CATTGCCTTAATGGGTGTGGATTTGTATTTTGTAAAATTTGCAAACAAGGCTATCATATT
GGGGAGTGTTTACCAGAAACATCAGCACAAAATAATTCAACATTAACTGAATATTCAGTT
AATCCAAATAAGGTTGCTGATTCGAGGTGGGAACAAGAAAGAATAGCTACAAAAATTGCA
ATACAAGTAACAACAAAACCATGTCCGAAATGCAGAGTTGCAACTGAAAGAGCAGGCGGT
TGTATGCATATGGT

>g14285.t12 Gene=g14285 Length=240
MSDEENGLPFAEFYFKCAEHVSGGEKDYAAPLNLIKMNLKEIGCLSCGDISEIVLVFPCD
AGHVTCLECFKLYCTSRLQERQFISHENYGYTLSCPVGCENSFIQEIHHFKLLDKELYDR
YQSFGAEEFVIQSGGVLCPFPNCGMGIIVDEDCNRVHCLNGCGFVFCKICKQGYHIGECL
PETSAQNNSTLTEYSVNPNKVADSRWEQERIATKIAIQVTTKPCPKCRVATERAGGCMHM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g14285.t12 CDD cd16627 RING-HC_RBR_parkin 42 100 0.000e+00
12 g14285.t12 Gene3D G3DSA:3.30.40.10 Zinc/RING finger domain 40 130 3.200e-06
10 g14285.t12 Gene3D G3DSA:2.20.25.20 - 131 201 0.000e+00
11 g14285.t12 Gene3D G3DSA:1.20.120.1750 - 202 240 1.600e-06
2 g14285.t12 PANTHER PTHR11685 RBR FAMILY RING FINGER AND IBR DOMAIN-CONTAINING 43 240 0.000e+00
3 g14285.t12 PANTHER PTHR11685:SF212 E3 UBIQUITIN-PROTEIN LIGASE PARKIN 43 240 0.000e+00
8 g14285.t12 PRINTS PR01475 Parkin signature 10 20 0.000e+00
7 g14285.t12 PRINTS PR01475 Parkin signature 27 47 0.000e+00
4 g14285.t12 PRINTS PR01475 Parkin signature 55 71 0.000e+00
5 g14285.t12 PRINTS PR01475 Parkin signature 106 127 0.000e+00
6 g14285.t12 PRINTS PR01475 Parkin signature 135 151 0.000e+00
1 g14285.t12 Pfam PF17978 RING/Ubox like zinc-binding domain 34 124 0.000e+00
15 g14285.t12 ProSiteProfiles PS51873 TRIAD supradomain profile. 40 240 2.703e+01
14 g14285.t12 SMART SM00647 ibrneu5 119 179 0.000e+00
9 g14285.t12 SUPERFAMILY SSF57850 RING/U-box 129 176 0.000e+00

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