Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t11 TSS g14285.t11 36305915 36305915
chr_1 g14285 g14285.t11 isoform g14285.t11 36305946 36306747
chr_1 g14285 g14285.t11 exon g14285.t11.exon1 36305946 36306110
chr_1 g14285 g14285.t11 cds g14285.t11.CDS1 36305946 36306110
chr_1 g14285 g14285.t11 exon g14285.t11.exon2 36306165 36306476
chr_1 g14285 g14285.t11 cds g14285.t11.CDS2 36306165 36306476
chr_1 g14285 g14285.t11 exon g14285.t11.exon3 36306531 36306747
chr_1 g14285 g14285.t11 cds g14285.t11.CDS3 36306531 36306746
chr_1 g14285 g14285.t11 TTS g14285.t11 36307699 36307699

Sequences

>g14285.t11 Gene=g14285 Length=694
ATGCTAGAGCTTTTTAGTTTTGGACGCAAAAAGATATCAAATAAGCTCCTTATCTTTATT
AAAACTAATACGGGACAGAGTTTAAGCTTAAATTTGGATCCAGAATGGAATATTTCTAAT
GTAAAGAAATTGGTTGCGCCACAATTAGGACTAAAAAGCGAAGAAGTGAAAATTATATTT
GCTGGAAAAGAATTAGAAGACAACACAAGAATTAGTGAATGTGATTTAGGACAACAAAGT
GTGCTTCATGCAGTAAAAACGAAATCACGAGTGAATATCGAATCGAAAACGAAGAGATGT
TTAGATGTAGTTTATGACGATGACAATGGAAATAATGTAATTGATGTGGCATCAAAACCT
TTATCATCAACTCTAGTCGATTTACAATTGTGTGGAGAAGAGAGAAGACATGTATCAGAA
AAGCAAAGTGATAAAGTAAAAGCAAATTTCTTTGTACACTGTCCTGAGTGTAAAAAGCTG
TGTAAAGGAAAATTAAGAGTTCGTTGCAATATATGTAAAGAAAGCTGTTTCACTGTTCAT
AGAGATCCTGAATGTTGGGATGACGTTTTAATTCCAAAAAAAATTCAAGGACATTGTGAA
AGTTTTGAAATTGCATGCATGTCTGATGAAGAAAATGGACTTCCATTTGCTGAATTCTAT
TTTAAATGTGCAGAACATGTTTCTGGAGGTGAAA

>g14285.t11 Gene=g14285 Length=231
MLELFSFGRKKISNKLLIFIKTNTGQSLSLNLDPEWNISNVKKLVAPQLGLKSEEVKIIF
AGKELEDNTRISECDLGQQSVLHAVKTKSRVNIESKTKRCLDVVYDDDNGNNVIDVASKP
LSSTLVDLQLCGEERRHVSEKQSDKVKANFFVHCPECKKLCKGKLRVRCNICKESCFTVH
RDPECWDDVLIPKKIQGHCESFEIACMSDEENGLPFAEFYFKCAEHVSGGE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g14285.t11 Gene3D G3DSA:3.10.20.90 - 9 97 0.000
3 g14285.t11 PANTHER PTHR10677 UBIQUILIN 17 227 0.000
4 g14285.t11 PANTHER PTHR10677:SF40 E3 UBIQUITIN-PROTEIN LIGASE PARKIN 17 227 0.000
7 g14285.t11 PRINTS PR01475 Parkin signature 45 65 0.000
6 g14285.t11 PRINTS PR01475 Parkin signature 157 172 0.000
8 g14285.t11 PRINTS PR01475 Parkin signature 178 201 0.000
5 g14285.t11 PRINTS PR01475 Parkin signature 216 226 0.000
1 g14285.t11 Pfam PF00240 Ubiquitin family 18 87 0.000
2 g14285.t11 Pfam PF17976 RING/Ubox like zinc-binding domain 149 228 0.000
12 g14285.t11 ProSiteProfiles PS50053 Ubiquitin domain profile. 16 85 16.276
10 g14285.t11 SMART SM00213 ubq_7 16 87 0.000
9 g14285.t11 SUPERFAMILY SSF54236 Ubiquitin-like 12 89 0.000

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. There were no conditions that were differentially expressed