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.t1 TSS g14285.t1 36305915 36305915
chr_1 g14285 g14285.t1 isoform g14285.t1 36305946 36307607
chr_1 g14285 g14285.t1 exon g14285.t1.exon1 36305946 36306110
chr_1 g14285 g14285.t1 cds g14285.t1.CDS1 36305946 36306110
chr_1 g14285 g14285.t1 exon g14285.t1.exon2 36306165 36306476
chr_1 g14285 g14285.t1 cds g14285.t1.CDS2 36306165 36306476
chr_1 g14285 g14285.t1 exon g14285.t1.exon3 36306531 36307160
chr_1 g14285 g14285.t1 cds g14285.t1.CDS3 36306531 36307160
chr_1 g14285 g14285.t1 exon g14285.t1.exon4 36307228 36307458
chr_1 g14285 g14285.t1 cds g14285.t1.CDS4 36307228 36307458
chr_1 g14285 g14285.t1 exon g14285.t1.exon5 36307515 36307607
chr_1 g14285 g14285.t1 cds g14285.t1.CDS5 36307515 36307607
chr_1 g14285 g14285.t1 TTS g14285.t1 36307699 36307699

Sequences

>g14285.t1 Gene=g14285 Length=1431
ATGCTAGAGCTTTTTAGTTTTGGACGCAAAAAGATATCAAATAAGCTCCTTATCTTTATT
AAAACTAATACGGGACAGAGTTTAAGCTTAAATTTGGATCCAGAATGGAATATTTCTAAT
GTAAAGAAATTGGTTGCGCCACAATTAGGACTAAAAAGCGAAGAAGTGAAAATTATATTT
GCTGGAAAAGAATTAGAAGACAACACAAGAATTAGTGAATGTGATTTAGGACAACAAAGT
GTGCTTCATGCAGTAAAAACGAAATCACGAGTGAATATCGAATCGAAAACGAAGAGATGT
TTAGATGTAGTTTATGACGATGACAATGGAAATAATGTAATTGATGTGGCATCAAAACCT
TTATCATCAACTCTAGTCGATTTACAATTGTGTGGAGAAGAGAGAAGACATGTATCAGAA
AAGCAAAGTGATAAAGTAAAAGCAAATTTCTTTGTACACTGTCCTGAGTGTAAAAAGCTG
TGTAAAGGAAAATTAAGAGTTCGTTGCAATATATGTAAAGAAAGCTGTTTCACTGTTCAT
AGAGATCCTGAATGTTGGGATGACGTTTTAATTCCAAAAAAAATTCAAGGACATTGTGAA
AGTTTTGAAATTGCATGCATGTCTGATGAAGAAAATGGACTTCCATTTGCTGAATTCTAT
TTTAAATGTGCAGAACATGTTTCTGGAGGTGAAAAAGACTATGCGGCGCCACTAAATCTA
ATAAAAATGAACCTTAAAGAAATTGGTTGTCTATCGTGTGGAGATATATCTGAAATAGTA
TTAGTTTTTCCATGTGATGCAGGTCATGTCACTTGTCTTGAATGCTTCAAACTCTATTGT
ACATCAAGATTACAAGAACGACAATTTATTTCACATGAAAACTATGGCTATACACTTTCG
TGTCCTGTCGGCTGTGAAAATTCTTTCATACAAGAGATTCATCATTTTAAATTGCTTGAT
AAAGAACTATATGATAGATACCAATCATTTGGCGCAGAAGAATTCGTTATTCAATCTGGT
GGTGTCTTGTGTCCTTTTCCTAATTGTGGAATGGGCATCATAGTTGATGAAGATTGTAAT
CGAGTGCATTGCCTTAATGGGTGTGGATTTGTATTTTGTAAAATTTGCAAACAAGGCTAT
CATATTGGGGAGTGTTTACCAGAAACATCAGCACAAAATAATTCAACATTAACTGAATAT
TCAGTTAATCCAAATAAGGTTGCTGATTCGAGGTGGGAACAAGAAAGAATAGCTACAAAA
ATTGCAATACAAGTAACAACAAAACCATGTCCGAAATGCAGAGTTGCAACTGAAAGAGCA
GGCGGTTGTATGCATATGGTGTGCACTAGAGCTGGTTGTAATTTCGATTGGTGTTGGGTT
TGTCAAACAGAGTGGACTCGTGATTGTATGGGTTCACATTGGTTTGGATAG

>g14285.t1 Gene=g14285 Length=476
MLELFSFGRKKISNKLLIFIKTNTGQSLSLNLDPEWNISNVKKLVAPQLGLKSEEVKIIF
AGKELEDNTRISECDLGQQSVLHAVKTKSRVNIESKTKRCLDVVYDDDNGNNVIDVASKP
LSSTLVDLQLCGEERRHVSEKQSDKVKANFFVHCPECKKLCKGKLRVRCNICKESCFTVH
RDPECWDDVLIPKKIQGHCESFEIACMSDEENGLPFAEFYFKCAEHVSGGEKDYAAPLNL
IKMNLKEIGCLSCGDISEIVLVFPCDAGHVTCLECFKLYCTSRLQERQFISHENYGYTLS
CPVGCENSFIQEIHHFKLLDKELYDRYQSFGAEEFVIQSGGVLCPFPNCGMGIIVDEDCN
RVHCLNGCGFVFCKICKQGYHIGECLPETSAQNNSTLTEYSVNPNKVADSRWEQERIATK
IAIQVTTKPCPKCRVATERAGGCMHMVCTRAGCNFDWCWVCQTEWTRDCMGSHWFG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
23 g14285.t1 CDD cd16627 RING-HC_RBR_parkin 248 306 0.0000000
19 g14285.t1 Gene3D G3DSA:3.10.20.90 - 9 97 0.0000000
20 g14285.t1 Gene3D G3DSA:2.20.25.20 - 333 407 0.0000000
21 g14285.t1 Gene3D G3DSA:1.20.120.1750 - 408 475 0.0000000
5 g14285.t1 PANTHER PTHR10677 UBIQUILIN 17 301 0.0000000
6 g14285.t1 PANTHER PTHR10677:SF40 E3 UBIQUITIN-PROTEIN LIGASE PARKIN 17 301 0.0000000
22 g14285.t1 PIRSF PIRSF037880 Parkin 9 476 0.0000000
12 g14285.t1 PRINTS PR01475 Parkin signature 45 65 0.0000000
8 g14285.t1 PRINTS PR01475 Parkin signature 157 172 0.0000000
14 g14285.t1 PRINTS PR01475 Parkin signature 178 201 0.0000000
10 g14285.t1 PRINTS PR01475 Parkin signature 216 226 0.0000000
11 g14285.t1 PRINTS PR01475 Parkin signature 233 253 0.0000000
15 g14285.t1 PRINTS PR01475 Parkin signature 261 277 0.0000000
9 g14285.t1 PRINTS PR01475 Parkin signature 312 333 0.0000000
13 g14285.t1 PRINTS PR01475 Parkin signature 341 357 0.0000000
7 g14285.t1 PRINTS PR01475 Parkin signature 453 475 0.0000000
1 g14285.t1 Pfam PF00240 Ubiquitin family 18 87 0.0000000
4 g14285.t1 Pfam PF17976 RING/Ubox like zinc-binding domain 149 228 0.0000000
2 g14285.t1 Pfam PF17978 RING/Ubox like zinc-binding domain 240 330 0.0000000
3 g14285.t1 Pfam PF01485 IBR domain, a half RING-finger domain 411 467 0.0000071
27 g14285.t1 ProSiteProfiles PS50053 Ubiquitin domain profile. 16 85 16.2760000
28 g14285.t1 ProSiteProfiles PS51873 TRIAD supradomain profile. 246 476 33.3340000
24 g14285.t1 SMART SM00213 ubq_7 16 87 0.0000000
25 g14285.t1 SMART SM00647 ibrneu5 325 385 0.0000000
26 g14285.t1 SMART SM00647 ibrneu5 410 469 0.0380000
18 g14285.t1 SUPERFAMILY SSF54236 Ubiquitin-like 12 89 0.0000000
17 g14285.t1 SUPERFAMILY SSF57850 RING/U-box 335 382 0.0000000
16 g14285.t1 SUPERFAMILY SSF57850 RING/U-box 424 467 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

Pathway

  • This transcript belongs to the following pathways

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