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.t6 TTS g12289.t6 22178342 22178342
chr_1 g12289 g12289.t6 isoform g12289.t6 22178859 22180273
chr_1 g12289 g12289.t6 exon g12289.t6.exon1 22178859 22179091
chr_1 g12289 g12289.t6 cds g12289.t6.CDS1 22178859 22179091
chr_1 g12289 g12289.t6 exon g12289.t6.exon2 22179151 22179428
chr_1 g12289 g12289.t6 cds g12289.t6.CDS2 22179151 22179428
chr_1 g12289 g12289.t6 exon g12289.t6.exon3 22179487 22179581
chr_1 g12289 g12289.t6 cds g12289.t6.CDS3 22179487 22179581
chr_1 g12289 g12289.t6 exon g12289.t6.exon4 22179779 22179814
chr_1 g12289 g12289.t6 cds g12289.t6.CDS4 22179779 22179814
chr_1 g12289 g12289.t6 exon g12289.t6.exon5 22180069 22180273
chr_1 g12289 g12289.t6 cds g12289.t6.CDS5 22180069 22180137
chr_1 g12289 g12289.t6 TSS g12289.t6 NA NA

Sequences

>g12289.t6 Gene=g12289 Length=847
TTTCGTATTTACTTTTTTCAATTCTTTATTTTGTCGTGTTTTCACGTTGCACAATATATC
AAATCACACGAACACTTTATATATGTGAAGCTTGTAAATTCTTTTTTGGATAATTGAAAG
ATATTTATAGAAAACTATGTGTAATCTTGCAAAGTTTCCAAATTTCAGTGTTTTCTTTTT
CCCATTTGTTTGCTACAAGATTAAACAGCTAGATTCTGCTCTAATTTCAAAAATGAGTTC
GATGTCAAATTTAGAAAACCACAATCCTCAAGTAATTAGGCAAATTTCAAAAGAAGTGAA
AACATTATCATCGGAGAATTTGGAGGGAATTAAAGTAACTATAAATGAAGCAGACCTTAC
TGATATACAAGCTATAATAGATGGTCCAGCTGGAACTCCATATTCGTCAGGACAATTTCG
AGTTAAATTAACACTTCCAAAAGATTTTCCTCAAAGCCCTCCGAAAGCGTTTTTCATGAC
GAAAATATTTCATCCGAATGTAGCAAATAATGGAGAAATTTGTGTAAACACACTTAAAAA
AGATTGGAAACCTGACTTAGGAATTAAACATATACTTTTAACAATAAAATGTCTCTTGAT
TGTACCTAATCCAGAATCTGCACTGAACGAGGAAGCAGGAAAAATGCTTTTAGAGCACTA
TGATGATTATTCACAAAGAGCAAAATTAATGACTGAAATTCATGCGAGACCTTCCACAAG
TAAAGATGTAGACGTTGATGAGGATGGATGTAGTTCAAGTAAAAAATTGGCATCTGATAA
GAAAATTCAGGATAAAAAGAAAGAAAAACTCATGAAAGAGAAAAAGAGAATTTTAAAACG
TCTCTGA

>g12289.t6 Gene=g12289 Length=236
MCNLAKFPNFSVFFFPFVCYKIKQLDSALISKMSSMSNLENHNPQVIRQISKEVKTLSSE
NLEGIKVTINEADLTDIQAIIDGPAGTPYSSGQFRVKLTLPKDFPQSPPKAFFMTKIFHP
NVANNGEICVNTLKKDWKPDLGIKHILLTIKCLLIVPNPESALNEEAGKMLLEHYDDYSQ
RAKLMTEIHARPSTSKDVDVDEDGCSSSKKLASDKKIQDKKKEKLMKEKKRILKRL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g12289.t6 CDD cd00195 UBCc 47 186 1.55762E-46
6 g12289.t6 Coils Coil Coil 222 236 -
5 g12289.t6 Gene3D G3DSA:3.10.110.10 Ubiquitin Conjugating Enzyme 33 190 7.6E-56
10 g12289.t6 MobiDBLite mobidb-lite consensus disorder prediction 190 226 -
11 g12289.t6 MobiDBLite mobidb-lite consensus disorder prediction 190 236 -
2 g12289.t6 PANTHER PTHR24068:SF328 - 36 193 1.6E-65
3 g12289.t6 PANTHER PTHR24068 UBIQUITIN-CONJUGATING ENZYME E2 36 193 1.6E-65
1 g12289.t6 Pfam PF00179 Ubiquitin-conjugating enzyme 50 184 4.5E-38
9 g12289.t6 ProSitePatterns PS00183 Ubiquitin-conjugating enzymes active site. 118 133 -
12 g12289.t6 ProSiteProfiles PS50127 Ubiquitin-conjugating enzymes family profile. 48 180 32.424
8 g12289.t6 SMART SM00212 ubc_7 48 191 1.5E-42
4 g12289.t6 SUPERFAMILY SSF54495 UBC-like 35 191 4.41E-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