Gene loci information

Transcript annotation

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

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 g12289 g12289.t5 TTS g12289.t5 22178342 22178342
chr_1 g12289 g12289.t5 isoform g12289.t5 22178859 22179787
chr_1 g12289 g12289.t5 exon g12289.t5.exon1 22178859 22179091
chr_1 g12289 g12289.t5 cds g12289.t5.CDS1 22178859 22179091
chr_1 g12289 g12289.t5 exon g12289.t5.exon2 22179151 22179428
chr_1 g12289 g12289.t5 cds g12289.t5.CDS2 22179151 22179428
chr_1 g12289 g12289.t5 exon g12289.t5.exon3 22179487 22179787
chr_1 g12289 g12289.t5 cds g12289.t5.CDS3 22179487 22179581
chr_1 g12289 g12289.t5 TSS g12289.t5 22179870 22179870

Sequences

>g12289.t5 Gene=g12289 Length=812
ATGAGTTCGGTAAGTTAGTGTATTGATAAAAATCTATAAAATCAATTAGAAATTTAAGCC
AAAAATAAGCAAACATTAGAGAAATTGTGAAATTTTAAAATTACAAACAAAAAAAAATTT
TCTCCTCCCCATTTTAATTTTCTATGTTTTTCTTTTCGAACTTGTAAAATTATCTTGAAA
TTTCTCAATTTATCTTTTCATTAAAGATGTCAAATTTAGAAAACCACAATCCTCAAGTAA
TTAGGCAAATTTCAAAAGAAGTGAAAACATTATCATCGGAGAATTTGGAGGGAATTAAAG
TAACTATAAATGAAGCAGACCTTACTGATATACAAGCTATAATAGATGGTCCAGCTGGAA
CTCCATATTCGTCAGGACAATTTCGAGTTAAATTAACACTTCCAAAAGATTTTCCTCAAA
GCCCTCCGAAAGCGTTTTTCATGACGAAAATATTTCATCCGAATGTAGCAAATAATGGAG
AAATTTGTGTAAACACACTTAAAAAAGATTGGAAACCTGACTTAGGAATTAAACATATAC
TTTTAACAATAAAATGTCTCTTGATTGTACCTAATCCAGAATCTGCACTGAACGAGGAAG
CAGGAAAAATGCTTTTAGAGCACTATGATGATTATTCACAAAGAGCAAAATTAATGACTG
AAATTCATGCGAGACCTTCCACAAGTAAAGATGTAGACGTTGATGAGGATGGATGTAGTT
CAAGTAAAAAATTGGCATCTGATAAGAAAATTCAGGATAAAAAGAAAGAAAAACTCATGA
AAGAGAAAAAGAGAATTTTAAAACGTCTCTGA

>g12289.t5 Gene=g12289 Length=201
MSNLENHNPQVIRQISKEVKTLSSENLEGIKVTINEADLTDIQAIIDGPAGTPYSSGQFR
VKLTLPKDFPQSPPKAFFMTKIFHPNVANNGEICVNTLKKDWKPDLGIKHILLTIKCLLI
VPNPESALNEEAGKMLLEHYDDYSQRAKLMTEIHARPSTSKDVDVDEDGCSSSKKLASDK
KIQDKKKEKLMKEKKRILKRL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g12289.t5 CDD cd00195 UBCc 12 151 3.52637E-47
5 g12289.t5 Gene3D G3DSA:3.10.110.10 Ubiquitin Conjugating Enzyme 1 155 6.7E-56
9 g12289.t5 MobiDBLite mobidb-lite consensus disorder prediction 155 191 -
10 g12289.t5 MobiDBLite mobidb-lite consensus disorder prediction 155 201 -
2 g12289.t5 PANTHER PTHR24068:SF328 - 8 158 2.6E-65
3 g12289.t5 PANTHER PTHR24068 UBIQUITIN-CONJUGATING ENZYME E2 8 158 2.6E-65
1 g12289.t5 Pfam PF00179 Ubiquitin-conjugating enzyme 15 149 2.8E-38
7 g12289.t5 ProSitePatterns PS00183 Ubiquitin-conjugating enzymes active site. 83 98 -
11 g12289.t5 ProSiteProfiles PS50127 Ubiquitin-conjugating enzymes family profile. 13 145 32.424
8 g12289.t5 SMART SM00212 ubc_7 13 156 1.5E-42
4 g12289.t5 SUPERFAMILY SSF54495 UBC-like 4 156 7.06E-48

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

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