Gene loci information

Transcript annotation

  • This transcript has been annotated as Ubiquitin-conjugating enzyme E2-18 kDa.

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 g3123 g3123.t9 TSS g3123.t9 23070356 23070356
chr_3 g3123 g3123.t9 isoform g3123.t9 23070357 23071621
chr_3 g3123 g3123.t9 exon g3123.t9.exon1 23070357 23070447
chr_3 g3123 g3123.t9 cds g3123.t9.CDS1 23070412 23070447
chr_3 g3123 g3123.t9 exon g3123.t9.exon2 23070561 23070747
chr_3 g3123 g3123.t9 cds g3123.t9.CDS2 23070561 23070747
chr_3 g3123 g3123.t9 exon g3123.t9.exon3 23070809 23071621
chr_3 g3123 g3123.t9 cds g3123.t9.CDS3 23070809 23070960
chr_3 g3123 g3123.t9 TTS g3123.t9 23071631 23071631

Sequences

>g3123.t9 Gene=g3123 Length=1091
GAATTGGCCGATATCAAAGCAAGTGGCCTCAAATCATTTCGTGACATAGAGGTTGATGAT
CGCAATATTTTATTATGGTCAGGATCAGTTTGATAATCCTCCTTACAATAAAGGTGCATT
TCGAATTGAAATCACATTCCCAGCTGAATATCCCTTTAAACCACCAAAAATATGCTTCAA
AACAAAAATCTACCATCCAAATATCGATGAAAAAGGACAAGTTTGTTTACCAATAATATC
TGCAGAAAATTGGAAACCAGCTACAAAAACAGATCAAGTAATTCAAGCTTTAGTCGCATT
AGTAAATGATCCAGAACCCGAACATCCTTTGCGTGCAGAATTGGCTGAAGAGTTTCTAAA
AGATCGCAAAAAGTTTATGAAAAATGCTGAAGAATTTACTCGAAAACATAGTGAGAAGCG
ACATGACTAAAAAAGAATAACAGCAAATTTCAATGTTGTATTTTGTCTACATTTATCTAC
GAATTAAACAAAAAAGCAGAATTCTGTCATCTTCTTCATTAAAATATGCTCTTTTAATGA
GCCTCATTCTATCAGTTTTTAATTTTTCTCCTCCCTCTTTCTCATCTTACATTTATATTT
TTAATTTTAGAAGCAAATGAGTGTGAGATAAAGATGTAGAGAAAAACTAAAAGAGTTGTG
AAATAAGAAGTTGAATGTGTGATGTAATGCTAAAAAAATTATTTAATAGTGAAACTCTGT
ATACCTTCATCTCTATCTATATCTATATAACTGCTCTATTCAATTAAATTAATATAAAAA
CATCTATTTGAGTACTAGATAAATTGCAGCTAAGACTTTGTTCCTTTTTATTTCATTAAT
TTCATTGCAATCAAAAAAAAGAGAAATTAAAATGAGGATGAGATTGAGACGAAAAATGTG
ATTTTACTTATTATTACTCTTTTATAATCATCTCGTGCTGCAAAAAATTTTAGAGAAATG
AAATTTGAAAATACTTTAATCATCATCAAACCAAACTTCCTTATAGCCTTTTTATCCTTG
AAAATATCTTGTCGATCAAAAAGCATTGTTTTCCTTTATAGAGAATAAAAAAAAGTATAA
TAATGATTAAA

>g3123.t9 Gene=g3123 Length=124
MIAIFYYGQDQFDNPPYNKGAFRIEITFPAEYPFKPPKICFKTKIYHPNIDEKGQVCLPI
ISAENWKPATKTDQVIQALVALVNDPEPEHPLRAELAEEFLKDRKKFMKNAEEFTRKHSE
KRHD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g3123.t9 CDD cd00195 UBCc 13 115 9.50933E-48
5 g3123.t9 Gene3D G3DSA:3.10.110.10 Ubiquitin Conjugating Enzyme 5 123 2.5E-44
2 g3123.t9 PANTHER PTHR24068:SF170 UBIQUITIN-CONJUGATING ENZYME E2 L5 12 120 5.2E-60
3 g3123.t9 PANTHER PTHR24068 UBIQUITIN-CONJUGATING ENZYME E2 12 120 5.2E-60
1 g3123.t9 Pfam PF00179 Ubiquitin-conjugating enzyme 13 114 6.1E-37
7 g3123.t9 ProSitePatterns PS00183 Ubiquitin-conjugating enzymes active site. 46 61 -
9 g3123.t9 ProSiteProfiles PS50127 Ubiquitin-conjugating enzymes family profile. 1 109 30.77
8 g3123.t9 SMART SM00212 ubc_7 1 120 2.1E-34
4 g3123.t9 SUPERFAMILY SSF54495 UBC-like 12 120 1.57E-37

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