General information for g8916.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as E3 ubiquitin-protein ligase HRD1.
Parent gene
- The parent gene g8916 is located on chr_2: 33796442..33797434 (+ strand)
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.t1 | TSS | g8916.t1 | 33794709 | 33794709 |
| chr_2 | g8916 | g8916.t1 | isoform | g8916.t1 | 33794936 | 33797258 |
| chr_2 | g8916 | g8916.t1 | exon | g8916.t1.exon1 | 33794936 | 33795064 |
| chr_2 | g8916 | g8916.t1 | cds | g8916.t1.CDS1 | 33794936 | 33795064 |
| chr_2 | g8916 | g8916.t1 | exon | g8916.t1.exon2 | 33795169 | 33795225 |
| chr_2 | g8916 | g8916.t1 | cds | g8916.t1.CDS2 | 33795169 | 33795225 |
| chr_2 | g8916 | g8916.t1 | exon | g8916.t1.exon3 | 33795294 | 33795482 |
| chr_2 | g8916 | g8916.t1 | cds | g8916.t1.CDS3 | 33795294 | 33795482 |
| chr_2 | g8916 | g8916.t1 | exon | g8916.t1.exon4 | 33795567 | 33795946 |
| chr_2 | g8916 | g8916.t1 | cds | g8916.t1.CDS4 | 33795567 | 33795946 |
| chr_2 | g8916 | g8916.t1 | exon | g8916.t1.exon5 | 33796009 | 33796134 |
| chr_2 | g8916 | g8916.t1 | cds | g8916.t1.CDS5 | 33796009 | 33796134 |
| chr_2 | g8916 | g8916.t1 | exon | g8916.t1.exon6 | 33796196 | 33796261 |
| chr_2 | g8916 | g8916.t1 | cds | g8916.t1.CDS6 | 33796196 | 33796261 |
| chr_2 | g8916 | g8916.t1 | exon | g8916.t1.exon7 | 33796337 | 33797258 |
| chr_2 | g8916 | g8916.t1 | cds | g8916.t1.CDS7 | 33796337 | 33797258 |
| chr_2 | g8916 | g8916.t1 | TTS | g8916.t1 | 33797431 | 33797431 |
Sequences
>g8916.t1 Gene=g8916 Length=1869
ATGAGAACTTCTCTTATATTCCTCGCTTCTGCGGTCCTTTCGGGGGCAGTAATTGCAAAT
GCTGTGATTCAAAAGAAGCAATTTTATCCCTCTGTTGTTTATATTTCAAAAAGCAATCCT
TCAATGGCCGTGATTTACTTTCAATCGTTAATCTTGGTCTTGATGCTTGGAAAATTGATG
AGAAAAATTTTCCTTGGAACATTAAGAGCTGCAGAATTCGAGCATTTGATGGAACGATTT
TGGTACGCGCTTACAGAGACTTGTCTAGCATTTACTGTTTTTAGAGATGACTTCAATCCG
AAGTTTATTGCTCTATTTACAGTCCTTCTCTTTTTAAAGTCATTTCATTGGCTAGTTGAG
GATAGAGTTGATTATATGGAAAGAAGTCCTGTGATAAGTTGGATATTTCACGTAAGAGTA
GCTGGTCTATTGAGTGTTTTGGGAATTTTTGATTACATACTAATCATGTATGCATATCAA
TCAACTCTTGCAAAAGGCGCAACTGTGCAATTAGTTTTTGGATTTGAATATGCAATTCTT
ATAACAATGGTTGCAAATACAATGATCAAATATGTGCTTCATGCAGCAGAATTACGCTCA
GAATCACCTTGGGAGAATAAGGCTGTCTTTTTGCTCTATACTGAGCTCGTCATTGGACTT
ATTCGAGTCATTCTTTATATTGTTTTTGTATTTTTAATGGTGAAAATTTACACACTACCA
TTATTTGCATTTAGACCAATGTACTATACAATAAGGAACTTTAAAAAAGCACTCAACGAT
GTCATTTTATCTCGTCGAGCTATTCACAATATGAATACGCTTTATCCAGATGCAACTCCC
GAAGAGCTCGCAATGTCTGATAATATTTGTATCATTTGTCGTGAAGATATGGTCAACAGT
TCCAAAAAATTGCCCTGCAATCATATTTTTCATAGTGCTTGCTTAAGATCATGGTTTCAA
AGACAACAAACTTGTCCAACATGTAGATTAAACATTCTAAGAACTCCAATTACCTCAAAT
TCAACTCCTCCTCAGCAAGCAGCAGCAGCAGCAAATAACAATAATGCAAATGCTAATCAA
AATGTTAGGCCGAATGCTGCCGAACAACAAAATCCATTCCTTAATTTATTAAATCATGCT
GCAGCGATGGGCAATCAACAACAACAATCGTCATCAGCAACTTCTTCAACCACATCACCA
ACGCCCAATATAACTCCGCCTTTTAACATTCAAAATTTACCATCAACTGGTCCACTTCCT
CCATTATTTTTTCCTTCATTGCCAACACCATTTATGACACCATTCTCAATTCCTCCTCCA
CCAATGCCTCAAAATTTGGAACAATTGTCAGTAGAAGAATTGCGTGCAATGGAAGGAAAT
GAAAGAAAACACATTGAAGAAAGACTTAAATTACTTAAAAATATAAACACAATGATAAAT
GCATCAGTTGTATTAATGAATCAATATAATATGGTAGTAGCAAATCTTCCATCAATTCCG
CAACAACAGTCTAATCAACAACAACCATCAACATCTGCATCATCTTCATTTAGTGATATT
ATAAAGAAAAATGAAGAAAAATCTTCATCGTCAGTTTCTTCTACAAGCGAAGTTAAATTT
GATACAAGTAAAGTAAAATTAGAAGATATAGGAATGGAAGATGATCATTTAGATCAACCA
ACAACATCAACTAACAAATCAATGCCCAGTTCAAGCAAAATAAAAACGGCAGAGACATCA
TCTTCATTAGATAGTCCATCGTCATCATCATCAGCTTCATTTATTGCAAACGAAAGTGGT
GAATGTGAATCAAACGAGGCAAACGAAATAAGAAAACGTAGATTACAAAAATTTTTGCCT
ACTAATTGA
>g8916.t1 Gene=g8916 Length=622
MRTSLIFLASAVLSGAVIANAVIQKKQFYPSVVYISKSNPSMAVIYFQSLILVLMLGKLM
RKIFLGTLRAAEFEHLMERFWYALTETCLAFTVFRDDFNPKFIALFTVLLFLKSFHWLVE
DRVDYMERSPVISWIFHVRVAGLLSVLGIFDYILIMYAYQSTLAKGATVQLVFGFEYAIL
ITMVANTMIKYVLHAAELRSESPWENKAVFLLYTELVIGLIRVILYIVFVFLMVKIYTLP
LFAFRPMYYTIRNFKKALNDVILSRRAIHNMNTLYPDATPEELAMSDNICIICREDMVNS
SKKLPCNHIFHSACLRSWFQRQQTCPTCRLNILRTPITSNSTPPQQAAAAANNNNANANQ
NVRPNAAEQQNPFLNLLNHAAAMGNQQQQSSSATSSTTSPTPNITPPFNIQNLPSTGPLP
PLFFPSLPTPFMTPFSIPPPPMPQNLEQLSVEELRAMEGNERKHIEERLKLLKNINTMIN
ASVVLMNQYNMVVANLPSIPQQQSNQQQPSTSASSSFSDIIKKNEEKSSSSVSSTSEVKF
DTSKVKLEDIGMEDDHLDQPTTSTNKSMPSSSKIKTAETSSSLDSPSSSSSASFIANESG
ECESNEANEIRKRRLQKFLPTN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 23 | g8916.t1 | CDD | cd16479 | RING-H2_synoviolin | 287 | 329 | 7.37336E-31 |
| 7 | g8916.t1 | Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain | 263 | 336 | 1.5E-19 |
| 30 | g8916.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 500 | 519 | - |
| 31 | g8916.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 500 | 622 | - |
| 32 | g8916.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 541 | 560 | - |
| 33 | g8916.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 561 | 603 | - |
| 2 | g8916.t1 | PANTHER | PTHR22763:SF169 | E3 UBIQUITIN-PROTEIN LIGASE SYNOVIOLIN | 9 | 360 | 4.9E-107 |
| 3 | g8916.t1 | PANTHER | PTHR22763 | RING ZINC FINGER PROTEIN | 9 | 360 | 4.9E-107 |
| 1 | g8916.t1 | Pfam | PF13639 | Ring finger domain | 289 | 329 | 7.0E-10 |
| 14 | g8916.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 19 | - |
| 15 | g8916.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 16 | g8916.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 14 | - |
| 22 | g8916.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 19 | - |
| 12 | g8916.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 20 | 42 | - |
| 18 | g8916.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 43 | 60 | - |
| 9 | g8916.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 61 | 101 | - |
| 21 | g8916.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 102 | 119 | - |
| 11 | g8916.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 120 | 130 | - |
| 19 | g8916.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 131 | 159 | - |
| 8 | g8916.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 160 | 170 | - |
| 17 | g8916.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 171 | 193 | - |
| 13 | g8916.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 194 | 212 | - |
| 20 | g8916.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 213 | 237 | - |
| 10 | g8916.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 238 | 622 | - |
| 34 | g8916.t1 | ProSiteProfiles | PS50089 | Zinc finger RING-type profile. | 290 | 329 | 12.784 |
| 29 | g8916.t1 | SMART | SM00184 | ring_2 | 290 | 328 | 1.2E-6 |
| 4 | g8916.t1 | SUPERFAMILY | SSF57850 | RING/U-box | 270 | 335 | 3.31E-20 |
| 6 | g8916.t1 | SignalP_EUK | SignalP-TM | SignalP-TM | 1 | 19 | - |
| 5 | g8916.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 21 | - |
| 25 | g8916.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 5 | 23 | - |
| 26 | g8916.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 43 | 60 | - |
| 28 | g8916.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 135 | 157 | - |
| 24 | g8916.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 167 | 189 | - |
| 27 | g8916.t1 | 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
| 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 transcript has been annotated with K10601 (E3 ubiquitin-protein ligase synoviolin)
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.
