Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Ubiquitin conjugation factor E4 A.

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_3 g2509 g2509.t13 isoform g2509.t13 18335460 18337669
chr_3 g2509 g2509.t13 exon g2509.t13.exon1 18335460 18335816
chr_3 g2509 g2509.t13 exon g2509.t13.exon2 18335880 18336334
chr_3 g2509 g2509.t13 exon g2509.t13.exon3 18336804 18337669
chr_3 g2509 g2509.t13 cds g2509.t13.CDS1 18337323 18337526
chr_3 g2509 g2509.t13 TSS g2509.t13 NA NA
chr_3 g2509 g2509.t13 TTS g2509.t13 NA NA

Sequences

>g2509.t13 Gene=g2509 Length=1678
TTAAGATTGGCGGCGGACAACTTATTACTGACATAACAGAATTTGCTGAAAAAGTAAGAC
AAGTTGAACAACGACAAAAAGAAAATGAAGAAGCGCTTGTCAATCCACCAGATAACTTTT
TAGATCCAATATTATCGATTTTAATGCGCGATCCTGTAATTTTACCATCATCACGTGTAA
CTTGTGATAAGTCAACAATTTCAAGGCATCTTCTTAGTGATCAAAGTGATCCATTTAATC
GTTCTCCACTTTCAATGGATCAACTTATTCCCGATACTAAATTAAAAGCTCAAATCGATG
CTTGGATTAAAGAGCGATTAGAAAAGTATAAAAATGAAAATGAATAAGTTCTTTTCCTTA
ATTTTTTCTCACATATTAATGTTATTTAAAATCTTATTATGAAAGGTATATCGAGAAAAT
AATAAAATTAAATTTTTGAAACCTATAATAACATTAATGTTTCATTCAGAGTCCGAAATC
GTTTCATGAGTAACTAAAAGCAACTAAATTTACTTAAACGTAACGATTTCAAATTCTGGT
TTCAATTTCGATCCTAAATTTGCATTTGCGGTGGTGGTTGTGTAATAAGTACTAAGCATT
GTGCTGAAATTAAATTTAACATATTTGGATTTCTTTATCACAGATTAAAATATTTCGCAT
TAGTTTGTTGTAATATATCCATTTATGAATGGTAAACCAGTCTTTGTTCTTTGCTGATAT
TGAACATATTCTTGTCCAAAGAAATTGAGTAAAGTGATCTCTTCAGTATGGATTCTCTCT
TTGAAAAAAAGCCAGCTTGCAATGAGATAGAGAACAAAACAAATTGGGTTTGCCATTATT
AGCTGAAAAAAAAAGAAAGATTAATTCACTCACATAAGCAGGATGTCGAAACCAACTATA
AACTCCTATCGTTATTAATTTATGATCATCGGCTTGCTGAAATTGCACTAAATGATGGAA
ACTTTTTTTGGCTGTTAACATTGCAACCTTTCTCAAAATTTCACCACTTAAGCAAATAGT
AGAACCTATTATCCAAATTGTTTTGCACTTTTTCATTTCAGGATAATAATAAACTTCAAC
GAAATATTCTATCCAACTAATTATAGCCGCAAATTCATATTGAATTGAATGATTAAGCAT
AAAAGAATCAAGTGTCAATGATTCTGGATGACTTAACGAAATTACAAAATACTCCGAGTA
ATGAAAGAATGTTAAAAAAGCCAAATAAATTCCAAAAGACTTGTATTTATCCTCCATTGT
AATTGAAATAAAAAGAGCAATGCCAAAAAAATACCCTAAAATTCCAGCTCGAATAGCAAT
CCTGAAAGTCTGTTGATTTGAAACATATTGATAAGAATAATATCAGCACGATAAAATACA
GAACAAAAAGAGTGTAAATTGATGAAAAAAATGATTCACTAATGAATAGAGCAAGTTTTT
CTCCGAATTCTGATACACCAAACAATTGCACTAGCAAGCTTGTAATGAATGCTATGACAC
TAACTTTTCCTTCATGGCATATCATAGTAATAAATGAAACCCTTTACTTTTAGTATTCTT
TATTTAAAAAATTTGATACGCCGATAGAATTATTTCACTTGTAAATTTTAATCAGAGGGA
GACAAACTCAGTAAAAAAATTCTATTATTTTCTAACTTTTCTTTTATTCAAATTTACT

>g2509.t13 Gene=g2509 Length=67
MRDPVILPSSRVTCDKSTISRHLLSDQSDPFNRSPLSMDQLIPDTKLKAQIDAWIKERLE
KYKNENE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g2509.t13 Gene3D G3DSA:3.30.40.10 Zinc/RING finger domain 1 67 0.000
2 g2509.t13 PANTHER PTHR13931:SF2 UBIQUITIN CONJUGATION FACTOR E4 A 1 65 0.000
3 g2509.t13 PANTHER PTHR13931 UBIQUITINATION FACTOR E4 1 65 0.000
1 g2509.t13 Pfam PF04564 U-box domain 1 58 0.000
7 g2509.t13 ProSiteProfiles PS51698 U-box domain profile. 1 61 23.859
5 g2509.t13 SMART SM00504 Ubox_2 1 54 0.000
4 g2509.t13 SUPERFAMILY SSF57850 RING/U-box 1 58 0.000

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:0016567 protein ubiquitination BP
GO:0004842 ubiquitin-protein transferase activity MF

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