Gene loci information

Transcript annotation

  • This transcript has been annotated as (E3-independent) E2 ubiquitin-conjugating enzyme.

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_4 g15001 g15001.t1 TSS g15001.t1 3478271 3478271
chr_4 g15001 g15001.t1 isoform g15001.t1 3478393 3482530
chr_4 g15001 g15001.t1 exon g15001.t1.exon1 3478393 3478476
chr_4 g15001 g15001.t1 cds g15001.t1.CDS1 3478393 3478476
chr_4 g15001 g15001.t1 exon g15001.t1.exon2 3478608 3478673
chr_4 g15001 g15001.t1 cds g15001.t1.CDS2 3478608 3478673
chr_4 g15001 g15001.t1 exon g15001.t1.exon3 3478745 3478792
chr_4 g15001 g15001.t1 cds g15001.t1.CDS3 3478745 3478792
chr_4 g15001 g15001.t1 exon g15001.t1.exon4 3478854 3479107
chr_4 g15001 g15001.t1 cds g15001.t1.CDS4 3478854 3479107
chr_4 g15001 g15001.t1 exon g15001.t1.exon5 3479164 3479615
chr_4 g15001 g15001.t1 cds g15001.t1.CDS5 3479164 3479615
chr_4 g15001 g15001.t1 exon g15001.t1.exon6 3479673 3482096
chr_4 g15001 g15001.t1 cds g15001.t1.CDS6 3479673 3482096
chr_4 g15001 g15001.t1 exon g15001.t1.exon7 3482153 3482353
chr_4 g15001 g15001.t1 cds g15001.t1.CDS7 3482153 3482353
chr_4 g15001 g15001.t1 exon g15001.t1.exon8 3482409 3482530
chr_4 g15001 g15001.t1 cds g15001.t1.CDS8 3482409 3482530
chr_4 g15001 g15001.t1 TTS g15001.t1 3482711 3482711

Sequences

>g15001.t1 Gene=g15001 Length=3651
ATGAATCAATACTTTTATGAAGATCAAGTTTTCACTGTTGATAAGAAAGGAAACATAAAA
TTCGGTTTAGTTGTTGAAAATGAAGTTCCAAGTGATGGTGAAGAAAATCAAACAGAAACG
GAAAAGTTTCTTAGAAAAGGCGAGCTTAGGGTTGTATGGTATCCAGAAGGAAAAGATGAA
GTTGTTTTGGAGAAAAATGTCGGATTGGCTGATAGAACTTTAATGCCAGGCGATGTAGTG
AGACGAATGACTGACACTGACACACAAAGAGGCTATTGTCGTGAAATTCATGTGAAAGCT
GATTTAAAAATTATTGGCAATTCTCGTTATGTTGTTAAAGATGTTGCCTCAGAGCGACTT
GTTCCTATTGTGTCAATGCCAAGAGATAATGCCGTTTGCTTAGACTCATGGGTTGGAAGT
ACTAAAAATATTGATGAAAAGTTAACACTGAGATCAACATGTGGTTCAATTTTAGAATTA
CGACCCGACATTGATTATTTTCCATTCAAAGATAAAAATAATCGTTCAGTTTTTTCAAAT
AATTTATTTTACGTTGGTCAACAACTCATTGGTCCAGTAAATGAACTCGAAAATGCAAAA
TGGATCGTTCAAACACCAGAAATGCGTGCAAGTCGAAAGCACAAGGCAGAAAGGAAATTT
ACAGTGCAATCAGTTGAAATTGATGGAGTTTATGTACATTGGCAATGTAAAGCATCGTGT
GAGGAAAATTCAAGTTCAAATGACTCGGGAATTCCTAAACGATACATAACTGGTGATGAT
TTGAAAAGAATGAAGAGATTAAATTTATTTGAAAGCTGCATGTTACAAATTAACGATAAA
AATTACTTAAATATTGACGAAAACGATGTAATAGTTAGAAAATCACAATGGAAAAAAGAA
CAAAGCAATAAATATCGAATTTTAAGTAGTAAAACTAATCAAAATATGGAAATTAGTCAT
AATATAAACGAATCTATAACATTAACGGAAGAAGAAAATACAACTGAAAATAAACAAACT
TTAAAAGTTGAGTGTGATAGAACAAAACTTTGTCCATCGACACCAAAATTTCTTGAAAGT
GATGAATGGCAAACAGAAGAAGAAGAGGAAGAAATTTTATCTGATAGTGGAACAACTGCT
TCTTCATGCTCAAGCAATCCAACGCCAAAAGGTTCACCAAAAAAATCACCGCTGCTTTCG
CACAAAATTCGTAAGCTCAAAAAGCATAAACAACGTGATCCAAAAGAGCGACAAATTCCT
CAAGTTAATGATCGTGTTGTGACAGAAGCACTTGTTGTTTATAGTTGGGCAACTGTTGTA
TGGCAAGATGGCACAATTGAAAAAAATATTCCATCAACTGAACTTTGTCCAATTCATCAT
CTTGATGATCATGAATTTTTTCCAGCTGATTTTGTGCTTGCTGCCAATGACTCAGCTAAT
TTTAATCCTTCTTATCGTGATTATGGAGTGATACAGAAAGTTGATCATTTAGGAAGAATT
GCAAAGGTTAAATGGTTTAGTACTTATACAAATATTGAAGAACCAGTGCCATTTTATAAG
GGAGAATCAGAAGTTAGTGTTTATGACTTGAAAGATCATCCTGATTTTCAATATCGTCCA
GGCACAATTGTCATTCGTGTTGCAAACTTTCCAAGTGAAATGCGAACTGCAACAGCTGGT
CAAGTTGTCGATAATTATCCTGAAGGAAGAGTTAAAGTTTGGTGGGTTGATGGAAGTATT
TCAATGTGTTGGCCACAAGATTTATTTGAAGTTGGTCAATATGATTCAGAAAATAATTTC
TGGGGCAATGGTGGTGATTCAGAAGATGAAAGTTGGCAAACAGAGGATGAATTTAGTGAA
CCTGGTGGAATGCCACAACACCAACAACTCACAGCTAATTTAGAACGTGCAAGAAAAGCA
ATGGCAAGACTTGAAGAATTATTTATAAATTCAAATTTACAATCACAGGAAGTGATGAAA
AAATTATTGATGGTTTATAAAAAATGTCGCTATCTTGATCGATTAATGAATACAAATTTT
TTCCATGAATCAAATTTTATGGGATTAGTTGAAAGAGTTAGAAAAAGTGGATCACAAACG
ACTGCTGAACTTGTGCAAGAAAAGAAAAATCGTCTTTTTAATGAATCGCCAGGTGAAAAT
TCTTCAACGAAGCCAATAACGAAGAAAATTTCATTGCTTGAAGCAACAAAATCGTCTTCA
TCGAATTCAAATAGTCATGAAGATAACAGCAGCTATTGTAGCTTTGAGAGCACAAAATCA
TGCTTTCAACCATCAACAAGACAAGCAAGTCAAGAATCGCCAACAAAGAAACAAAATCTT
CTTGTTGTTGCATCAGAAACATGGAGCAAGCAAGGAAAATGTCATTCAACATCATCGGAT
ATTTCTAGTATTTTGGATGACAATATGAAATTATCCAATTGCTCATCGCCTTCTTCTTCT
GCCTATAAAGCTCCATCACCATCTAAAAAAGGTGATGAGACAGAAAAAAATAGCACCGAT
TCTGGTATTTTAATCACACTCGATAGTGGAACTAGTGAAAATTCACAAAAAATTATTGAA
ACTTCTGATTCAGCGAATGGAAGCTTTGTTATAACTGTTTGTGCAAAACTTTGTTCACTT
ATAAAAATTCAACTTGTAAAAGCATTACAAGAAATTAATAATCGTTATTGCCCAAGTGAC
ACCTTTAAAGAAATTGTTGAACTTGAAATGGATTCAAATGCCATTGCTAAAATTGATAGT
GAATTTGAAGAAGAAGAAGAAGAGGAAACAAAAACTCCTGATGATGCTAAAATTATTGAA
CCAGAAATTCCAACAATTGATAATTTTCAAATTATAAGCCATGTTCCAAGCACACACAAA
TATTATCTTACAGTTTTTAATCCAGCCAATCCACATGCCTTTTTTAAAGCTGTTCAACGT
GAACATAAATTGCTCAAAACTTCATTGCCTTCGGGCGTTTGGGTAAAAACTTTTGAAGAT
CGTTTAGACTTGCTAAGTGTGCTCATTGAAGGACCTAAAAAAACTCCTTATGAAGACGGT
CTTTTTGCTTTTGATATTCAATTAAGTCACGATTATCCTAAAACACCACCGCTGTGTCAT
TTTATAAGCTATTGTAGAGATCGATTGAATCCAAATTTATATGAAGATGGAAAAGTTTGT
GTGAGTTTGCTTGGAACATGGACTGGGCGTGGAACTGAAGTATGGTGTCCAAGTAGTAGT
GGAGTTTTGCAAGTTATTGTTTCAATTCAAGGATTAATTTTAGTCGATGAGCCTTATTAC
AATGAAGCTGGCTATGAAAAACAAAGAGGAACTCAACAAGGTAAAGAAAATTCAAGAATG
TATAATGAAATGGTCGTTTTAAAAGTAGTTCAATCGATGACTAAATTAATAACATCGCCG
CCCGAAGTATTTAGTGATATTATACAAGAACATTTTCGTAAAAACGGTAAAATATTTTAT
AATCGAATTAAATCATGGATGGAATTAAGTGAAAATTCAAATAATGAAGCTGCAAAAAAC
GAATTTGAAATTCCTGAATTTCCATTAATTCCAGCATCGAAAGGTTTCTGCTTAACTTTA
GTGTCAGTTTTAGAAGGATTTAATCATAAACTTCAGGAAATTAATACTTAA

>g15001.t1 Gene=g15001 Length=1216
MNQYFYEDQVFTVDKKGNIKFGLVVENEVPSDGEENQTETEKFLRKGELRVVWYPEGKDE
VVLEKNVGLADRTLMPGDVVRRMTDTDTQRGYCREIHVKADLKIIGNSRYVVKDVASERL
VPIVSMPRDNAVCLDSWVGSTKNIDEKLTLRSTCGSILELRPDIDYFPFKDKNNRSVFSN
NLFYVGQQLIGPVNELENAKWIVQTPEMRASRKHKAERKFTVQSVEIDGVYVHWQCKASC
EENSSSNDSGIPKRYITGDDLKRMKRLNLFESCMLQINDKNYLNIDENDVIVRKSQWKKE
QSNKYRILSSKTNQNMEISHNINESITLTEEENTTENKQTLKVECDRTKLCPSTPKFLES
DEWQTEEEEEEILSDSGTTASSCSSNPTPKGSPKKSPLLSHKIRKLKKHKQRDPKERQIP
QVNDRVVTEALVVYSWATVVWQDGTIEKNIPSTELCPIHHLDDHEFFPADFVLAANDSAN
FNPSYRDYGVIQKVDHLGRIAKVKWFSTYTNIEEPVPFYKGESEVSVYDLKDHPDFQYRP
GTIVIRVANFPSEMRTATAGQVVDNYPEGRVKVWWVDGSISMCWPQDLFEVGQYDSENNF
WGNGGDSEDESWQTEDEFSEPGGMPQHQQLTANLERARKAMARLEELFINSNLQSQEVMK
KLLMVYKKCRYLDRLMNTNFFHESNFMGLVERVRKSGSQTTAELVQEKKNRLFNESPGEN
SSTKPITKKISLLEATKSSSSNSNSHEDNSSYCSFESTKSCFQPSTRQASQESPTKKQNL
LVVASETWSKQGKCHSTSSDISSILDDNMKLSNCSSPSSSAYKAPSPSKKGDETEKNSTD
SGILITLDSGTSENSQKIIETSDSANGSFVITVCAKLCSLIKIQLVKALQEINNRYCPSD
TFKEIVELEMDSNAIAKIDSEFEEEEEEETKTPDDAKIIEPEIPTIDNFQIISHVPSTHK
YYLTVFNPANPHAFFKAVQREHKLLKTSLPSGVWVKTFEDRLDLLSVLIEGPKKTPYEDG
LFAFDIQLSHDYPKTPPLCHFISYCRDRLNPNLYEDGKVCVSLLGTWTGRGTEVWCPSSS
GVLQVIVSIQGLILVDEPYYNEAGYEKQRGTQQGKENSRMYNEMVVLKVVQSMTKLITSP
PEVFSDIIQEHFRKNGKIFYNRIKSWMELSENSNNEAAKNEFEIPEFPLIPASKGFCLTL
VSVLEGFNHKLQEINT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g15001.t1 CDD cd00195 UBCc 976 1125 4.00691E-32
7 g15001.t1 Coils Coil Coil 627 654 -
6 g15001.t1 Coils Coil Coil 908 928 -
5 g15001.t1 Gene3D G3DSA:3.10.110.10 Ubiquitin Conjugating Enzyme 943 1186 1.6E-77
11 g15001.t1 MobiDBLite mobidb-lite consensus disorder prediction 356 400 -
10 g15001.t1 MobiDBLite mobidb-lite consensus disorder prediction 375 393 -
12 g15001.t1 MobiDBLite mobidb-lite consensus disorder prediction 708 728 -
13 g15001.t1 MobiDBLite mobidb-lite consensus disorder prediction 816 841 -
2 g15001.t1 PANTHER PTHR46116 (E3-INDEPENDENT) E2 UBIQUITIN-CONJUGATING ENZYME 40 1205 3.3E-143
3 g15001.t1 PANTHER PTHR46116:SF6 (E3-INDEPENDENT) E2 UBIQUITIN-CONJUGATING ENZYME 40 1205 3.3E-143
1 g15001.t1 Pfam PF00179 Ubiquitin-conjugating enzyme 978 1125 2.0E-27
14 g15001.t1 ProSiteProfiles PS50127 Ubiquitin-conjugating enzymes family profile. 976 1098 20.341
9 g15001.t1 SMART SM00212 ubc_7 976 1134 2.1E-22
4 g15001.t1 SUPERFAMILY SSF54495 UBC-like 964 1141 4.64E-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

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