General information for g11812.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Ubiquitin recognition factor in ER-associated degradation protein 1.
Parent gene
- The parent gene g11812 is located on chr_1: 18529983..18530269 (+ 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_1 | g11812 | g11812.t4 | TSS | g11812.t4 | 18528839 | 18528839 |
| chr_1 | g11812 | g11812.t4 | isoform | g11812.t4 | 18528948 | 18530084 |
| chr_1 | g11812 | g11812.t4 | exon | g11812.t4.exon1 | 18528948 | 18528950 |
| chr_1 | g11812 | g11812.t4 | exon | g11812.t4.exon2 | 18529045 | 18529167 |
| chr_1 | g11812 | g11812.t4 | exon | g11812.t4.exon3 | 18529231 | 18529658 |
| chr_1 | g11812 | g11812.t4 | cds | g11812.t4.CDS1 | 18529236 | 18529658 |
| chr_1 | g11812 | g11812.t4 | exon | g11812.t4.exon4 | 18529722 | 18530084 |
| chr_1 | g11812 | g11812.t4 | cds | g11812.t4.CDS2 | 18529722 | 18530084 |
| chr_1 | g11812 | g11812.t4 | TTS | g11812.t4 | 18530246 | 18530246 |
Sequences
>g11812.t4 Gene=g11812 Length=917
ATGTTTAATTTCGGATTTCCTGAAATGCGATGGCAACATGACATGAGGAATTTTACTCAA
AGCTATCGTTGTTTTTCTGTATCAATGCTTCCGGGAAATGAGAGAAATGATGTAGAGAAT
GGAGGATTATTATGCCTCCTTCTGCTTTAGATCAATTGACACGTCTTAATATAGAATATC
CGATGCTTTTTAAGATATCAAATACAAAAGGAGCTAGACAGACACATGTTGGTGTTTTGG
AGTTTATTGCTGATGAGGGACGAATTTATATTCCATATTGGATGATGAAAAATTTGCTTT
TAGAAGAAGGAGATTTAGTTACTGTCGAGAATGTATCGCTACCAGTAGCTTCATATTCTA
AATTCAAGCCACAAAGTGTAGATTTCTTGGACATTACAAATCCAAAAGCTGTTTTAGAAA
ATTGTTTAAGAAATTTTGCGTGTTTAACATCCGGTGATGTGATTGCTATAAATTACAATA
ATAAGATATATGAACTACTTGTTCTAGAAACTAGACCTGGACAAGCAGTGACAATTATTG
AATGCGATATGAATGTCGAATTTGATGCACCAGTAGGCTATAAAGAACCCGAGCGAGCGC
CAAAAAGTGAAGATGAAATGGATATAGAACATTCTGAAATAACTCATTTGGATGACAATC
TATTTTATCCGTTTAGCGGAGAAGGCAATCGATTGGATGGCAAAAAAATAAAAGATTCTG
TTAAAACTGAGCTTCCTCCAGCTCACATCTTAAAAAAATATACTCGTGGAATACCAGACT
ATAATCATGATATTTTCGAATTGAAGTTTGACAGAAGTATGAAATCAAAAAATAATTCAA
CGCAAAGCGATAAAGATGAAAATCTATTCAAAACTTTTCAGGGCGAAGGAAAAAGCTTAC
GTCCACGAAAACAATAG
>g11812.t4 Gene=g11812 Length=261
MPPSALDQLTRLNIEYPMLFKISNTKGARQTHVGVLEFIADEGRIYIPYWMMKNLLLEEG
DLVTVENVSLPVASYSKFKPQSVDFLDITNPKAVLENCLRNFACLTSGDVIAINYNNKIY
ELLVLETRPGQAVTIIECDMNVEFDAPVGYKEPERAPKSEDEMDIEHSEITHLDDNLFYP
FSGEGNRLDGKKIKDSVKTELPPAHILKKYTRGIPDYNHDIFELKFDRSMKSKNNSTQSD
KDENLFKTFQGEGKSLRPRKQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g11812.t4 | Gene3D | G3DSA:2.40.40.50 | - | 1 | 71 | 3.2E-32 |
| 5 | g11812.t4 | Gene3D | G3DSA:3.10.330.10 | - | 72 | 146 | 6.5E-35 |
| 4 | g11812.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 229 | 261 | - |
| 2 | g11812.t4 | PANTHER | PTHR12555 | UBIQUITIN FUSION DEGRADATON PROTEIN 1 | 1 | 258 | 4.6E-94 |
| 3 | g11812.t4 | PANTHER | PTHR12555:SF20 | UBIQUITIN RECOGNITION FACTOR IN ER-ASSOCIATED DEGRADATION PROTEIN 1 | 1 | 258 | 4.6E-94 |
| 1 | g11812.t4 | Pfam | PF03152 | Ubiquitin fusion degradation protein UFD1 | 1 | 147 | 1.1E-67 |
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:0006511 | ubiquitin-dependent protein catabolic process | 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. There were no conditions that were differentially expressed