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.t13 TSS g14285.t13 36305915 36305915
chr_1 g14285 g14285.t13 isoform g14285.t13 36305946 36307607
chr_1 g14285 g14285.t13 exon g14285.t13.exon1 36305946 36306110
chr_1 g14285 g14285.t13 cds g14285.t13.CDS1 36305946 36306110
chr_1 g14285 g14285.t13 exon g14285.t13.exon2 36306165 36306476
chr_1 g14285 g14285.t13 cds g14285.t13.CDS2 36306165 36306476
chr_1 g14285 g14285.t13 exon g14285.t13.exon3 36306531 36307153
chr_1 g14285 g14285.t13 cds g14285.t13.CDS3 36306531 36307153
chr_1 g14285 g14285.t13 exon g14285.t13.exon4 36307228 36307458
chr_1 g14285 g14285.t13 cds g14285.t13.CDS4 36307228 36307312
chr_1 g14285 g14285.t13 exon g14285.t13.exon5 36307515 36307607
chr_1 g14285 g14285.t13 TTS g14285.t13 36307699 36307699

Sequences

>g14285.t13 Gene=g14285 Length=1424
ATGCTAGAGCTTTTTAGTTTTGGACGCAAAAAGATATCAAATAAGCTCCTTATCTTTATT
AAAACTAATACGGGACAGAGTTTAAGCTTAAATTTGGATCCAGAATGGAATATTTCTAAT
GTAAAGAAATTGGTTGCGCCACAATTAGGACTAAAAAGCGAAGAAGTGAAAATTATATTT
GCTGGAAAAGAATTAGAAGACAACACAAGAATTAGTGAATGTGATTTAGGACAACAAAGT
GTGCTTCATGCAGTAAAAACGAAATCACGAGTGAATATCGAATCGAAAACGAAGAGATGT
TTAGATGTAGTTTATGACGATGACAATGGAAATAATGTAATTGATGTGGCATCAAAACCT
TTATCATCAACTCTAGTCGATTTACAATTGTGTGGAGAAGAGAGAAGACATGTATCAGAA
AAGCAAAGTGATAAAGTAAAAGCAAATTTCTTTGTACACTGTCCTGAGTGTAAAAAGCTG
TGTAAAGGAAAATTAAGAGTTCGTTGCAATATATGTAAAGAAAGCTGTTTCACTGTTCAT
AGAGATCCTGAATGTTGGGATGACGTTTTAATTCCAAAAAAAATTCAAGGACATTGTGAA
AGTTTTGAAATTGCATGCATGTCTGATGAAGAAAATGGACTTCCATTTGCTGAATTCTAT
TTTAAATGTGCAGAACATGTTTCTGGAGGTGAAAAAGACTATGCGGCGCCACTAAATCTA
ATAAAAATGAACCTTAAAGAAATTGGTTGTCTATCGTGTGGAGATATATCTGAAATAGTA
TTAGTTTTTCCATGTGATGCAGGTCATGTCACTTGTCTTGAATGCTTCAAACTCTATTGT
ACATCAAGATTACAAGAACGACAATTTATTTCACATGAAAACTATGGCTATACACTTTCG
TGTCCTGTCGGCTGTGAAAATTCTTTCATACAAGAGATTCATCATTTTAAATTGCTTGAT
AAAGAACTATATGATAGATACCAATCATTTGGCGCAGAAGAATTCGTTATTCAATCTGGT
GGTGTCTTGTGTCCTTTTCCTAATTGTGGAATGGGCATCATAGTTGATGAAGATTGTAAT
CGAGTGCATTGCCTTAATGGTTTGTATTTTGTAAAATTTGCAAACAAGGCTATCATATTG
GGGAGTGTTTACCAGAAACATCAGCACAAAATAATTCAACATTAACTGAATATTCAGTTA
ATCCAAATAAGGTTGCTGATTCGAGGTGGGAACAAGAAAGAATAGCTACAAAAATTGCAA
TACAAGTAACAACAAAACCATGTCCGAAATGCAGAGTTGCAACTGAAAGAGCAGGCGGTT
GTATGCATATGGTGTGCACTAGAGCTGGTTGTAATTTCGATTGGTGTTGGGTTTGTCAAA
CAGAGTGGACTCGTGATTGTATGGGTTCACATTGGTTTGGATAG

>g14285.t13 Gene=g14285 Length=394
MLELFSFGRKKISNKLLIFIKTNTGQSLSLNLDPEWNISNVKKLVAPQLGLKSEEVKIIF
AGKELEDNTRISECDLGQQSVLHAVKTKSRVNIESKTKRCLDVVYDDDNGNNVIDVASKP
LSSTLVDLQLCGEERRHVSEKQSDKVKANFFVHCPECKKLCKGKLRVRCNICKESCFTVH
RDPECWDDVLIPKKIQGHCESFEIACMSDEENGLPFAEFYFKCAEHVSGGEKDYAAPLNL
IKMNLKEIGCLSCGDISEIVLVFPCDAGHVTCLECFKLYCTSRLQERQFISHENYGYTLS
CPVGCENSFIQEIHHFKLLDKELYDRYQSFGAEEFVIQSGGVLCPFPNCGMGIIVDEDCN
RVHCLNGLYFVKFANKAIILGSVYQKHQHKIIQH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g14285.t13 CDD cd16627 RING-HC_RBR_parkin 248 306 0.0000000
15 g14285.t13 Gene3D G3DSA:3.10.20.90 - 9 97 0.0000000
17 g14285.t13 Gene3D G3DSA:3.30.40.10 Zinc/RING finger domain 246 334 0.0000095
16 g14285.t13 Gene3D G3DSA:2.20.25.20 - 335 393 0.0000000
4 g14285.t13 PANTHER PTHR10677 UBIQUILIN 17 301 0.0000000
5 g14285.t13 PANTHER PTHR10677:SF40 E3 UBIQUITIN-PROTEIN LIGASE PARKIN 17 301 0.0000000
18 g14285.t13 PIRSF PIRSF037880 Parkin 9 379 0.0000000
10 g14285.t13 PRINTS PR01475 Parkin signature 45 65 0.0000000
6 g14285.t13 PRINTS PR01475 Parkin signature 157 172 0.0000000
12 g14285.t13 PRINTS PR01475 Parkin signature 178 201 0.0000000
8 g14285.t13 PRINTS PR01475 Parkin signature 216 226 0.0000000
9 g14285.t13 PRINTS PR01475 Parkin signature 233 253 0.0000000
13 g14285.t13 PRINTS PR01475 Parkin signature 261 277 0.0000000
7 g14285.t13 PRINTS PR01475 Parkin signature 312 333 0.0000000
11 g14285.t13 PRINTS PR01475 Parkin signature 341 357 0.0000000
1 g14285.t13 Pfam PF00240 Ubiquitin family 18 87 0.0000000
3 g14285.t13 Pfam PF17976 RING/Ubox like zinc-binding domain 149 228 0.0000000
2 g14285.t13 Pfam PF17978 RING/Ubox like zinc-binding domain 240 330 0.0000000
21 g14285.t13 ProSiteProfiles PS50053 Ubiquitin domain profile. 16 85 16.2760000
22 g14285.t13 ProSiteProfiles PS51873 TRIAD supradomain profile. 246 394 15.1170000
20 g14285.t13 SMART SM00213 ubq_7 16 87 0.0000000
14 g14285.t13 SUPERFAMILY SSF54236 Ubiquitin-like 12 89 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:0005515 protein binding MF
GO:0005829 cytosol CC
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