Gene loci information

Transcript annotation

  • This transcript has been annotated as Ubiquitin recognition factor in ER-associated degradation protein 1.

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 g11812 g11812.t5 TSS g11812.t5 18528839 18528839
chr_1 g11812 g11812.t5 isoform g11812.t5 18528948 18530084
chr_1 g11812 g11812.t5 exon g11812.t5.exon1 18528948 18528950
chr_1 g11812 g11812.t5 exon g11812.t5.exon2 18529045 18529658
chr_1 g11812 g11812.t5 cds g11812.t5.CDS1 18529236 18529658
chr_1 g11812 g11812.t5 exon g11812.t5.exon3 18529722 18530084
chr_1 g11812 g11812.t5 cds g11812.t5.CDS2 18529722 18530084
chr_1 g11812 g11812.t5 TTS g11812.t5 18530246 18530246

Sequences

>g11812.t5 Gene=g11812 Length=980
ATGTTTAATTTCGGATTTCCTGAAATGCGATGGCAACATGACATGAGGAATTTTACTCAA
AGCTATCGTTGTTTTTCTGTATCAATGCTTCCGGGAAATGAGAGAAATGATGTAGAGAAT
GGAGGAAAAAGTTAGAAACATTATTATGCTTTGTCATTATAACCAATTATAAAATTTTAT
TTATTTTAGTTATTATGCCTCCTTCTGCTTTAGATCAATTGACACGTCTTAATATAGAAT
ATCCGATGCTTTTTAAGATATCAAATACAAAAGGAGCTAGACAGACACATGTTGGTGTTT
TGGAGTTTATTGCTGATGAGGGACGAATTTATATTCCATATTGGATGATGAAAAATTTGC
TTTTAGAAGAAGGAGATTTAGTTACTGTCGAGAATGTATCGCTACCAGTAGCTTCATATT
CTAAATTCAAGCCACAAAGTGTAGATTTCTTGGACATTACAAATCCAAAAGCTGTTTTAG
AAAATTGTTTAAGAAATTTTGCGTGTTTAACATCCGGTGATGTGATTGCTATAAATTACA
ATAATAAGATATATGAACTACTTGTTCTAGAAACTAGACCTGGACAAGCAGTGACAATTA
TTGAATGCGATATGAATGTCGAATTTGATGCACCAGTAGGCTATAAAGAACCCGAGCGAG
CGCCAAAAAGTGAAGATGAAATGGATATAGAACATTCTGAAATAACTCATTTGGATGACA
ATCTATTTTATCCGTTTAGCGGAGAAGGCAATCGATTGGATGGCAAAAAAATAAAAGATT
CTGTTAAAACTGAGCTTCCTCCAGCTCACATCTTAAAAAAATATACTCGTGGAATACCAG
ACTATAATCATGATATTTTCGAATTGAAGTTTGACAGAAGTATGAAATCAAAAAATAATT
CAACGCAAAGCGATAAAGATGAAAATCTATTCAAAACTTTTCAGGGCGAAGGAAAAAGCT
TACGTCCACGAAAACAATAG

>g11812.t5 Gene=g11812 Length=261
MPPSALDQLTRLNIEYPMLFKISNTKGARQTHVGVLEFIADEGRIYIPYWMMKNLLLEEG
DLVTVENVSLPVASYSKFKPQSVDFLDITNPKAVLENCLRNFACLTSGDVIAINYNNKIY
ELLVLETRPGQAVTIIECDMNVEFDAPVGYKEPERAPKSEDEMDIEHSEITHLDDNLFYP
FSGEGNRLDGKKIKDSVKTELPPAHILKKYTRGIPDYNHDIFELKFDRSMKSKNNSTQSD
KDENLFKTFQGEGKSLRPRKQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g11812.t5 Gene3D G3DSA:2.40.40.50 - 1 71 3.2E-32
5 g11812.t5 Gene3D G3DSA:3.10.330.10 - 72 146 6.5E-35
4 g11812.t5 MobiDBLite mobidb-lite consensus disorder prediction 229 261 -
2 g11812.t5 PANTHER PTHR12555 UBIQUITIN FUSION DEGRADATON PROTEIN 1 1 258 4.6E-94
3 g11812.t5 PANTHER PTHR12555:SF20 UBIQUITIN RECOGNITION FACTOR IN ER-ASSOCIATED DEGRADATION PROTEIN 1 1 258 4.6E-94
1 g11812.t5 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.

Raw TPM values