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.t6 TSS g11812.t6 18528839 18528839
chr_1 g11812 g11812.t6 isoform g11812.t6 18528948 18530084
chr_1 g11812 g11812.t6 exon g11812.t6.exon1 18528948 18529171
chr_1 g11812 g11812.t6 cds g11812.t6.CDS1 18529066 18529171
chr_1 g11812 g11812.t6 exon g11812.t6.exon2 18529231 18529658
chr_1 g11812 g11812.t6 cds g11812.t6.CDS2 18529231 18529658
chr_1 g11812 g11812.t6 exon g11812.t6.exon3 18529722 18530084
chr_1 g11812 g11812.t6 cds g11812.t6.CDS3 18529722 18530084
chr_1 g11812 g11812.t6 TTS g11812.t6 18530246 18530246

Sequences

>g11812.t6 Gene=g11812 Length=1015
ATGGTTTGTTATAGTCATTCAACTAATCATTTATCTGGAAAATTTATTTATGAATATTGA
AATTCATTTCTTTTGTTTTTATTTTTTATTAAATCAGTTTAATTTCGGATTTCCTGAAAT
GCGATGGCAACATGACATGAGGAATTTTACTCAAAGCTATCGTTGTTTTTCTGTATCAAT
GCTTCCGGGAAATGAGAGAAATGATGTAGAGAATGGAGGAAAAATTATTATGCCTCCTTC
TGCTTTAGATCAATTGACACGTCTTAATATAGAATATCCGATGCTTTTTAAGATATCAAA
TACAAAAGGAGCTAGACAGACACATGTTGGTGTTTTGGAGTTTATTGCTGATGAGGGACG
AATTTATATTCCATATTGGATGATGAAAAATTTGCTTTTAGAAGAAGGAGATTTAGTTAC
TGTCGAGAATGTATCGCTACCAGTAGCTTCATATTCTAAATTCAAGCCACAAAGTGTAGA
TTTCTTGGACATTACAAATCCAAAAGCTGTTTTAGAAAATTGTTTAAGAAATTTTGCGTG
TTTAACATCCGGTGATGTGATTGCTATAAATTACAATAATAAGATATATGAACTACTTGT
TCTAGAAACTAGACCTGGACAAGCAGTGACAATTATTGAATGCGATATGAATGTCGAATT
TGATGCACCAGTAGGCTATAAAGAACCCGAGCGAGCGCCAAAAAGTGAAGATGAAATGGA
TATAGAACATTCTGAAATAACTCATTTGGATGACAATCTATTTTATCCGTTTAGCGGAGA
AGGCAATCGATTGGATGGCAAAAAAATAAAAGATTCTGTTAAAACTGAGCTTCCTCCAGC
TCACATCTTAAAAAAATATACTCGTGGAATACCAGACTATAATCATGATATTTTCGAATT
GAAGTTTGACAGAAGTATGAAATCAAAAAATAATTCAACGCAAAGCGATAAAGATGAAAA
TCTATTCAAAACTTTTCAGGGCGAAGGAAAAAGCTTACGTCCACGAAAACAATAG

>g11812.t6 Gene=g11812 Length=298
MRWQHDMRNFTQSYRCFSVSMLPGNERNDVENGGKIIMPPSALDQLTRLNIEYPMLFKIS
NTKGARQTHVGVLEFIADEGRIYIPYWMMKNLLLEEGDLVTVENVSLPVASYSKFKPQSV
DFLDITNPKAVLENCLRNFACLTSGDVIAINYNNKIYELLVLETRPGQAVTIIECDMNVE
FDAPVGYKEPERAPKSEDEMDIEHSEITHLDDNLFYPFSGEGNRLDGKKIKDSVKTELPP
AHILKKYTRGIPDYNHDIFELKFDRSMKSKNNSTQSDKDENLFKTFQGEGKSLRPRKQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g11812.t6 Gene3D G3DSA:2.40.40.50 - 2 108 2.3E-46
5 g11812.t6 Gene3D G3DSA:3.10.330.10 - 109 183 8.3E-35
4 g11812.t6 MobiDBLite mobidb-lite consensus disorder prediction 265 298 -
2 g11812.t6 PANTHER PTHR12555 UBIQUITIN FUSION DEGRADATON PROTEIN 1 9 295 8.5E-109
3 g11812.t6 PANTHER PTHR12555:SF20 UBIQUITIN RECOGNITION FACTOR IN ER-ASSOCIATED DEGRADATION PROTEIN 1 9 295 8.5E-109
1 g11812.t6 Pfam PF03152 Ubiquitin fusion degradation protein UFD1 10 184 3.5E-78

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

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.

Raw TPM values