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.t3 TSS g8916.t3 33794709 33794709
chr_2 g8916 g8916.t3 isoform g8916.t3 33794936 33795946
chr_2 g8916 g8916.t3 exon g8916.t3.exon1 33794936 33795064
chr_2 g8916 g8916.t3 cds g8916.t3.CDS1 33794936 33795064
chr_2 g8916 g8916.t3 exon g8916.t3.exon2 33795169 33795225
chr_2 g8916 g8916.t3 cds g8916.t3.CDS2 33795169 33795225
chr_2 g8916 g8916.t3 exon g8916.t3.exon3 33795294 33795482
chr_2 g8916 g8916.t3 cds g8916.t3.CDS3 33795294 33795482
chr_2 g8916 g8916.t3 exon g8916.t3.exon4 33795567 33795946
chr_2 g8916 g8916.t3 cds g8916.t3.CDS4 33795567 33795944
chr_2 g8916 g8916.t3 TTS g8916.t3 NA NA

Sequences

>g8916.t3 Gene=g8916 Length=755
ATGAGAACTTCTCTTATATTCCTCGCTTCTGCGGTCCTTTCGGGGGCAGTAATTGCAAAT
GCTGTGATTCAAAAGAAGCAATTTTATCCCTCTGTTGTTTATATTTCAAAAAGCAATCCT
TCAATGGCCGTGATTTACTTTCAATCGTTAATCTTGGTCTTGATGCTTGGAAAATTGATG
AGAAAAATTTTCCTTGGAACATTAAGAGCTGCAGAATTCGAGCATTTGATGGAACGATTT
TGGTACGCGCTTACAGAGACTTGTCTAGCATTTACTGTTTTTAGAGATGACTTCAATCCG
AAGTTTATTGCTCTATTTACAGTCCTTCTCTTTTTAAAGTCATTTCATTGGCTAGTTGAG
GATAGAGTTGATTATATGGAAAGAAGTCCTGTGATAAGTTGGATATTTCACGTAAGAGTA
GCTGGTCTATTGAGTGTTTTGGGAATTTTTGATTACATACTAATCATGTATGCATATCAA
TCAACTCTTGCAAAAGGCGCAACTGTGCAATTAGTTTTTGGATTTGAATATGCAATTCTT
ATAACAATGGTTGCAAATACAATGATCAAATATGTGCTTCATGCAGCAGAATTACGCTCA
GAATCACCTTGGGAGAATAAGGCTGTCTTTTTGCTCTATACTGAGCTCGTCATTGGACTT
ATTCGAGTCATTCTTTATATTGTTTTTGTATTTTTAATGGTGAAAATTTACACACTACCA
TTATTTGCATTTAGACCAATGTACTATACAATAAG

>g8916.t3 Gene=g8916 Length=251
MRTSLIFLASAVLSGAVIANAVIQKKQFYPSVVYISKSNPSMAVIYFQSLILVLMLGKLM
RKIFLGTLRAAEFEHLMERFWYALTETCLAFTVFRDDFNPKFIALFTVLLFLKSFHWLVE
DRVDYMERSPVISWIFHVRVAGLLSVLGIFDYILIMYAYQSTLAKGATVQLVFGFEYAIL
ITMVANTMIKYVLHAAELRSESPWENKAVFLLYTELVIGLIRVILYIVFVFLMVKIYTLP
LFAFRPMYYTI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
1 g8916.t3 PANTHER PTHR22765 RING FINGER AND PROTEASE ASSOCIATED DOMAIN-CONTAINING 50 251 2.6E-66
2 g8916.t3 PANTHER PTHR22765:SF213 E3 UBIQUITIN-PROTEIN LIGASE SYNOVIOLIN 50 251 2.6E-66
17 g8916.t3 Phobius SIGNAL_PEPTIDE Signal peptide region 1 19 -
18 g8916.t3 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
19 g8916.t3 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 14 -
25 g8916.t3 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 15 19 -
15 g8916.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 20 42 -
21 g8916.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 43 60 -
13 g8916.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 61 101 -
24 g8916.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 102 119 -
14 g8916.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 120 130 -
22 g8916.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 131 159 -
12 g8916.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 160 170 -
20 g8916.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 171 193 -
16 g8916.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 194 212 -
23 g8916.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 213 237 -
11 g8916.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 238 251 -
10 g8916.t3 SignalP_EUK SignalP-TM SignalP-TM 1 19 -
9 g8916.t3 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 21 -
4 g8916.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 5 23 -
6 g8916.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 43 60 -
7 g8916.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 102 119 -
5 g8916.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 134 156 -
3 g8916.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 173 195 -
8 g8916.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 210 232 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

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