Gene loci information

Transcript annotation

  • This transcript has been annotated as Ubiquitin-conjugating enzyme E2 R2.

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 g13409 g13409.t5 TTS g13409.t5 29885566 29885566
chr_1 g13409 g13409.t5 isoform g13409.t5 29886521 29888805
chr_1 g13409 g13409.t5 exon g13409.t5.exon1 29886521 29886625
chr_1 g13409 g13409.t5 cds g13409.t5.CDS1 29886521 29886625
chr_1 g13409 g13409.t5 exon g13409.t5.exon2 29886688 29886802
chr_1 g13409 g13409.t5 cds g13409.t5.CDS2 29886688 29886802
chr_1 g13409 g13409.t5 exon g13409.t5.exon3 29886953 29887132
chr_1 g13409 g13409.t5 cds g13409.t5.CDS3 29886953 29887132
chr_1 g13409 g13409.t5 exon g13409.t5.exon4 29887227 29887366
chr_1 g13409 g13409.t5 cds g13409.t5.CDS4 29887227 29887366
chr_1 g13409 g13409.t5 exon g13409.t5.exon5 29888653 29888805
chr_1 g13409 g13409.t5 cds g13409.t5.CDS5 29888653 29888805
chr_1 g13409 g13409.t5 TSS g13409.t5 29889048 29889048

Sequences

>g13409.t5 Gene=g13409 Length=693
ATGAATTCGTCTTCGCTAAGAGCACTTGCATTAGAATACAAAAGTCTACAAGAAGAGCCA
GTTGAAGGCTTTAAAGTGAAATTATTAAATGATGATAACTTTTACGAATGGAGTGTAAGT
TTCCAAATACATATATCTGCATATATTAATAAGGCTACTATGAAATTTCCGCAAGATTAC
CCTTATTCACCACCATCAATTCGTTTCATAACAAAAGTCTGGCATCCGAATGTTTATGAA
AATGGGGACTTGTGTATTTCAATTTTACATCCGCCAGTTGATGATCCTCAGAGTGGTGAG
TTGCCGTGCGAACGATGGAATCCAACTCAAAATGTCCGCACCATTCTCCTCTCTGTAATC
TCATTGCTCAATGAACCCAACACATTTTCACCAGCTAATGTAGACGCAAGTGTTATGTAC
AGAAGATGGCGTGAATCAAATGGTCGCGATAACGAATATCCAAACATAATCAGGAAACAA
GCGTTACAAGCTAAGTTAGAAGCTGAAAAAGAAGGAATTGTTGTTCCATTAACATTAGAG
GAATATTGCCTGAAACCTAAAACGAACCCAAATAATCAGGAACCTCAACTCGATATGACA
GACTTTTATGACGATTTCGATGATGATGAGTGTAGCGAATCTGAAACAGAATCACAAAAT
GGTGATGGAGAAGATTCGGGGAACGCTGAATAA

>g13409.t5 Gene=g13409 Length=230
MNSSSLRALALEYKSLQEEPVEGFKVKLLNDDNFYEWSVSFQIHISAYINKATMKFPQDY
PYSPPSIRFITKVWHPNVYENGDLCISILHPPVDDPQSGELPCERWNPTQNVRTILLSVI
SLLNEPNTFSPANVDASVMYRRWRESNGRDNEYPNIIRKQALQAKLEAEKEGIVVPLTLE
EYCLKPKTNPNNQEPQLDMTDFYDDFDDDECSESETESQNGDGEDSGNAE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g13409.t5 CDD cd00195 UBCc 7 146 5.26174E-48
5 g13409.t5 Gene3D G3DSA:3.10.110.10 Ubiquitin Conjugating Enzyme 1 176 2.0E-65
9 g13409.t5 MobiDBLite mobidb-lite consensus disorder prediction 186 230 -
10 g13409.t5 MobiDBLite mobidb-lite consensus disorder prediction 200 220 -
2 g13409.t5 PANTHER PTHR24067 UBIQUITIN-CONJUGATING ENZYME E2 2 211 1.3E-87
3 g13409.t5 PANTHER PTHR24067:SF157 FI11905P 2 211 1.3E-87
1 g13409.t5 Pfam PF00179 Ubiquitin-conjugating enzyme 9 144 1.9E-34
7 g13409.t5 ProSitePatterns PS00183 Ubiquitin-conjugating enzymes active site. 74 89 -
11 g13409.t5 ProSiteProfiles PS50127 Ubiquitin-conjugating enzymes family profile. 7 149 31.247
8 g13409.t5 SMART SM00212 ubc_7 7 166 1.7E-44
4 g13409.t5 SUPERFAMILY SSF54495 UBC-like 4 145 3.41E-41

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

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