Gene loci information

Transcript annotation

  • This transcript has been annotated as E3 ubiquitin-protein ligase HRD1.

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_2 g8916 g8916.t4 TSS g8916.t4 33794709 33794709
chr_2 g8916 g8916.t4 isoform g8916.t4 33794936 33796126
chr_2 g8916 g8916.t4 exon g8916.t4.exon1 33794936 33795064
chr_2 g8916 g8916.t4 cds g8916.t4.CDS1 33794936 33795064
chr_2 g8916 g8916.t4 exon g8916.t4.exon2 33795169 33795225
chr_2 g8916 g8916.t4 cds g8916.t4.CDS2 33795169 33795225
chr_2 g8916 g8916.t4 exon g8916.t4.exon3 33795294 33795482
chr_2 g8916 g8916.t4 cds g8916.t4.CDS3 33795294 33795482
chr_2 g8916 g8916.t4 exon g8916.t4.exon4 33795567 33795946
chr_2 g8916 g8916.t4 cds g8916.t4.CDS4 33795567 33795946
chr_2 g8916 g8916.t4 exon g8916.t4.exon5 33796009 33796126
chr_2 g8916 g8916.t4 cds g8916.t4.CDS5 33796009 33796126
chr_2 g8916 g8916.t4 TTS g8916.t4 NA NA

Sequences

>g8916.t4 Gene=g8916 Length=873
ATGAGAACTTCTCTTATATTCCTCGCTTCTGCGGTCCTTTCGGGGGCAGTAATTGCAAAT
GCTGTGATTCAAAAGAAGCAATTTTATCCCTCTGTTGTTTATATTTCAAAAAGCAATCCT
TCAATGGCCGTGATTTACTTTCAATCGTTAATCTTGGTCTTGATGCTTGGAAAATTGATG
AGAAAAATTTTCCTTGGAACATTAAGAGCTGCAGAATTCGAGCATTTGATGGAACGATTT
TGGTACGCGCTTACAGAGACTTGTCTAGCATTTACTGTTTTTAGAGATGACTTCAATCCG
AAGTTTATTGCTCTATTTACAGTCCTTCTCTTTTTAAAGTCATTTCATTGGCTAGTTGAG
GATAGAGTTGATTATATGGAAAGAAGTCCTGTGATAAGTTGGATATTTCACGTAAGAGTA
GCTGGTCTATTGAGTGTTTTGGGAATTTTTGATTACATACTAATCATGTATGCATATCAA
TCAACTCTTGCAAAAGGCGCAACTGTGCAATTAGTTTTTGGATTTGAATATGCAATTCTT
ATAACAATGGTTGCAAATACAATGATCAAATATGTGCTTCATGCAGCAGAATTACGCTCA
GAATCACCTTGGGAGAATAAGGCTGTCTTTTTGCTCTATACTGAGCTCGTCATTGGACTT
ATTCGAGTCATTCTTTATATTGTTTTTGTATTTTTAATGGTGAAAATTTACACACTACCA
TTATTTGCATTTAGACCAATGTACTATACAATAAGGAACTTTAAAAAAGCACTCAACGAT
GTCATTTTATCTCGTCGAGCTATTCACAATATGAATACGCTTTATCCAGATGCAACTCCC
GAAGAGCTCGCAATGTCTGATAATATTTGTATC

>g8916.t4 Gene=g8916 Length=291
MRTSLIFLASAVLSGAVIANAVIQKKQFYPSVVYISKSNPSMAVIYFQSLILVLMLGKLM
RKIFLGTLRAAEFEHLMERFWYALTETCLAFTVFRDDFNPKFIALFTVLLFLKSFHWLVE
DRVDYMERSPVISWIFHVRVAGLLSVLGIFDYILIMYAYQSTLAKGATVQLVFGFEYAIL
ITMVANTMIKYVLHAAELRSESPWENKAVFLLYTELVIGLIRVILYIVFVFLMVKIYTLP
LFAFRPMYYTIRNFKKALNDVILSRRAIHNMNTLYPDATPEELAMSDNICI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
1 g8916.t4 PANTHER PTHR22763:SF169 E3 UBIQUITIN-PROTEIN LIGASE SYNOVIOLIN 9 291 5.1E-75
2 g8916.t4 PANTHER PTHR22763 RING ZINC FINGER PROTEIN 9 291 5.1E-75
17 g8916.t4 Phobius SIGNAL_PEPTIDE Signal peptide region 1 19 -
18 g8916.t4 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
19 g8916.t4 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 14 -
25 g8916.t4 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 15 19 -
15 g8916.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 20 42 -
21 g8916.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 43 60 -
12 g8916.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 61 101 -
24 g8916.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 102 119 -
14 g8916.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 120 130 -
22 g8916.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 131 159 -
11 g8916.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 160 170 -
20 g8916.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 171 193 -
16 g8916.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 194 212 -
23 g8916.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 213 237 -
13 g8916.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 238 291 -
10 g8916.t4 SignalP_EUK SignalP-TM SignalP-TM 1 19 -
9 g8916.t4 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 21 -
3 g8916.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 5 23 -
5 g8916.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 43 60 -
7 g8916.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 102 119 -
4 g8916.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 134 156 -
8 g8916.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 163 185 -
6 g8916.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 220 242 -

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:0061630 ubiquitin protein ligase activity MF
GO:0000836 Hrd1p ubiquitin ligase complex CC
GO:0030433 ubiquitin-dependent ERAD pathway BP
GO:0016567 protein ubiquitination BP

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