Gene loci information

Transcript annotation

  • This transcript has been annotated as Ubiquitin conjugation factor E4 B.

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 g10975 g10975.t1 TSS g10975.t1 13102495 13102495
chr_1 g10975 g10975.t1 isoform g10975.t1 13102664 13106554
chr_1 g10975 g10975.t1 exon g10975.t1.exon1 13102664 13102717
chr_1 g10975 g10975.t1 cds g10975.t1.CDS1 13102664 13102717
chr_1 g10975 g10975.t1 exon g10975.t1.exon2 13102908 13103103
chr_1 g10975 g10975.t1 cds g10975.t1.CDS2 13102908 13103103
chr_1 g10975 g10975.t1 exon g10975.t1.exon3 13103180 13105088
chr_1 g10975 g10975.t1 cds g10975.t1.CDS3 13103180 13105088
chr_1 g10975 g10975.t1 exon g10975.t1.exon4 13105147 13105321
chr_1 g10975 g10975.t1 cds g10975.t1.CDS4 13105147 13105321
chr_1 g10975 g10975.t1 exon g10975.t1.exon5 13105387 13105949
chr_1 g10975 g10975.t1 cds g10975.t1.CDS5 13105387 13105949
chr_1 g10975 g10975.t1 exon g10975.t1.exon6 13106013 13106431
chr_1 g10975 g10975.t1 cds g10975.t1.CDS6 13106013 13106431
chr_1 g10975 g10975.t1 exon g10975.t1.exon7 13106487 13106554
chr_1 g10975 g10975.t1 cds g10975.t1.CDS7 13106487 13106554
chr_1 g10975 g10975.t1 TTS g10975.t1 13106670 13106670

Sequences

>g10975.t1 Gene=g10975 Length=3384
ATGGATGAAGATAGAAATCAAGAGCAACAAAATCAACAATTGAGTCAACAAGAGATTCGA
TTGCGTCGTTTGAGAAAATTAGGTGTCAACACTGCTTCCGTGAATAATGAAAAAACTGAT
GAGTCAGCTAACCAAAAAAGAGAGAGCAGTTTGAATAACAATAACTGCACAACTTCATCA
CCTGAAACAACTGAAAGTAGCTGTAATAGTAATGATAAAAAAGATGATAACAAGAACACA
ATATTCTCTGATACGACTTCAGTCGCGAACGATAAAGTTGAGAACAATATGAATATCAGT
AATCAGAGTTTAAGTGAAATTATTCATATGGAAACATGCGACAAAGATAAGATCTCAGCT
ATAGCAGTACCACCTGATCAAATGGACATCGATGAAAATGAGACTGCAGAAAGTGAAATT
TTAAAAAGTATTTCACGTATATTAGATGCAACTTGGACTGAAAACTATAATGCATCATTT
ATCGTAAAAAAGACTGCAGAAGCAATTTTAGATGGTTTCCTTCAACCAACCAACTATTCA
GAACTGATTTCTGAAATTCTCAATGAAGTTATACGACAATATATGGTCGGAGATTTAGTA
CAAGAAATCGAAGTAAATTCATTATCAGATCAAATTTTGAGCTCACGAATGCGCAACGAT
GATATTGAAATGGATTTCGATGAAGATGCATTGAACGATGCTTTTCGAGTTAAACAAACA
AAAACTTGCACACCCAAGGAAGCTATACTGTATTATCTTATTCAATGCTTCAACCGTACT
TTAACTGAACGACAGCATAAAGAAATAAGCACAGAATGCAAAAAGCAAATTATTCAAAAT
GCTATTTTTCTTCTTGATCACGACTGGTTATTTATTGAAATCTCTGATTTATCTCCATCT
GATATGCGATCACGTTCTGCAATTCTTCAAATTATGTATGATGAAACAATTTCATATCAA
GATTTCTTGAAAAACCTAATAACAGAACTCTATAATTATCACCCGAAGCTGTTTACAAAA
ATTTTCAATATCGTACTAGAAGATATTTTCTTAGATATGCGCTGCAAACAGATAAAACAT
TGTATTTATTCACTACCCACTCATTCAATCGATCGTTTAATAGAGTTAATCTCAATGGGT
CTTACAAACAATGAGAGTGTCAAACCAGTTTGCAATTTAGTTGTTGGTCATCGTACTTTC
TTACCAAAATTATCAACTGATATTCCAGGACGAGAAATATCACAAATTTCTTACTTAGCA
CCGTTTCTTTCATTATCTATTGTAGTTTACGATAGATTTTATGACGAAGACAACTCAATT
GATAACGTTGTTCAAAGTGATCTTCAAAATAAACTTGACTATGTAAGAACTTTGTTGCAT
AAATTATTCTACACATTTATTGCGAACAAAGATACACGTGAAATTGCACTTAAATATATC
GCAGAATTGCTCAAGCATAATGCAAAGAGAGAGCAATATAATGCTGATGAAAGGAGTTTA
GCTCAGGATGGATTTATGCTCAATCTTATGGCAGTTATGCAACAACTTTCAATCAAAGTA
AAATTAGAAAGAATCGATCCGCTTTATCCATTTCATCCACAAGCACTGGTGTCAATTGCT
GACGATACAAAGCTTAAATTTGAAACTAATGAATATATCAAGCATTGTGAAAAATTGAAA
AATGAAATAAAATGGGAAGAACCAAAATTTGTAAGTCATTGTTGGTTCTTTACATTGCAT
AGTCATCATTTAGGGATTTTGCCAGCAATTTCACGCTATCATAAAAGACTTCGTGCAATC
AAAGAGTTACAACGTATGGTTGACGAGTTAAATGCTACAGAATCTCGTTGGAAAAATACA
CCTATTTCACGCAGAAACGCTAATGCTCGAAACAAGTGGACTAATCGTATAAAGAAACTT
ACAAAGGCGAAAAATACTATGGAAATCGTTATTTTAGATCCTAATTTGAATCGCAATTGC
TTACAATTTTATAGTACAGTTTGTGAATTTGTTCTTCATCACATCGAAGGACGACAACAG
ATTGAAGTTCCATTCTACAATAAAATTACACCTAGTGCTCTTACTTCATCTGATGAATTC
TCGTCCCTACCTGTTTGGTACATAGAAGATGTTGCTGATTATTTACTTTTCTTACTTCAA
AATCGTGTTGAAGTAATAATTGATTACATGGATAATTCAATAATCACATGGCTTTTGACT
CTTGTTTGTGCTCCTCATTTGATCAAAAATCCATATCTTACTGCCAAATTGATTGAAGTA
CTTTTTGTCATATGTCCATCAATTCAATCAACAACAACTAAAATTTATAATATGATAATG
AACCATGAACTTGCACAAAATAGTTTGATACCTGCATTGATGAAATTTTATGTTGATGTG
GAGACAACAGGACAATCAACTGAATTTTACGATAAATTTACTATTCGATATCATATTTCT
CATATTTTTAAGAGTTTATGGAATAGTAGTCTTCATCGTCAAATGATCATTAGCGAATCA
AAGAATGGAAAGCAATTTGTAAAATTTGTCAACATGCTCATGAATGATACAACTTTCTTG
CTCGACGAAAGCTTGGAAAATTTAAAAAAGATTCATGAAGTGCAAACACTTATGATGCAA
GAAAAAGAATGGTCAAAACTCGATCCTGAAGATCAAGCACAACGACAGCGACAACTTATT
CAAGATGAACGTCAATGTCGTTCATATCTTACACTTGCGCGTGAAACTGTTGATATGTTT
CACTATCTTACAACTGATATTAAAGAGCCGTTTTTACGAAAAGAATTGGTTGATCGTCTC
AGTTCAATGCTTAATTACAACTTACATCAATTATGTGGGCCAAAGTGTAGTGACCTGCGT
GTTCGCAATCCATCAAGATATGGATGGGAACCACGACGTCTGCTTGGACAAATTATTGAT
ATCTATATTCATTTGAGTTCAGATGAGTTTGCTGCAAGTCTTGCACGAGATGAGCGATCA
TTTGAGAAACATCTTTTTGAATATGCAGCTGAGAAGATTGAAAAAAATGCTATTCGATCT
GCTATTGAAGTAGAGAAATTTAGAAGTTTGATACAAAAAGCAGGAGAAATTTATACTATG
AATCAGAAGAATGAAGACGATTTTGCTGATGCACCAGATGAATTTAAAGATCCTCTTATG
GATATTGTTATGAGTGATCCTGTCAAATTACCTAGCGGTCTAATTATGGAACGATCGATT
ATAGTAAGACACTTGTTGAACAGTCAAACAGATCCTTTCAATCGTCAGCCATTGACAGAA
GAAGAATTAAAACCAGTGCCTGAACTGAAAGCTAGGATTGAGAATTGGAAACGAGAAAAG
ACGGAAAAGAAGAATATCGATTAA

>g10975.t1 Gene=g10975 Length=1127
MDEDRNQEQQNQQLSQQEIRLRRLRKLGVNTASVNNEKTDESANQKRESSLNNNNCTTSS
PETTESSCNSNDKKDDNKNTIFSDTTSVANDKVENNMNISNQSLSEIIHMETCDKDKISA
IAVPPDQMDIDENETAESEILKSISRILDATWTENYNASFIVKKTAEAILDGFLQPTNYS
ELISEILNEVIRQYMVGDLVQEIEVNSLSDQILSSRMRNDDIEMDFDEDALNDAFRVKQT
KTCTPKEAILYYLIQCFNRTLTERQHKEISTECKKQIIQNAIFLLDHDWLFIEISDLSPS
DMRSRSAILQIMYDETISYQDFLKNLITELYNYHPKLFTKIFNIVLEDIFLDMRCKQIKH
CIYSLPTHSIDRLIELISMGLTNNESVKPVCNLVVGHRTFLPKLSTDIPGREISQISYLA
PFLSLSIVVYDRFYDEDNSIDNVVQSDLQNKLDYVRTLLHKLFYTFIANKDTREIALKYI
AELLKHNAKREQYNADERSLAQDGFMLNLMAVMQQLSIKVKLERIDPLYPFHPQALVSIA
DDTKLKFETNEYIKHCEKLKNEIKWEEPKFVSHCWFFTLHSHHLGILPAISRYHKRLRAI
KELQRMVDELNATESRWKNTPISRRNANARNKWTNRIKKLTKAKNTMEIVILDPNLNRNC
LQFYSTVCEFVLHHIEGRQQIEVPFYNKITPSALTSSDEFSSLPVWYIEDVADYLLFLLQ
NRVEVIIDYMDNSIITWLLTLVCAPHLIKNPYLTAKLIEVLFVICPSIQSTTTKIYNMIM
NHELAQNSLIPALMKFYVDVETTGQSTEFYDKFTIRYHISHIFKSLWNSSLHRQMIISES
KNGKQFVKFVNMLMNDTTFLLDESLENLKKIHEVQTLMMQEKEWSKLDPEDQAQRQRQLI
QDERQCRSYLTLARETVDMFHYLTTDIKEPFLRKELVDRLSSMLNYNLHQLCGPKCSDLR
VRNPSRYGWEPRRLLGQIIDIYIHLSSDEFAASLARDERSFEKHLFEYAAEKIEKNAIRS
AIEVEKFRSLIQKAGEIYTMNQKNEDDFADAPDEFKDPLMDIVMSDPVKLPSGLIMERSI
IVRHLLNSQTDPFNRQPLTEEELKPVPELKARIENWKREKTEKKNID

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g10975.t1 CDD cd16658 RING-Ubox_UBE4B 1047 1121 7.73271E-45
9 g10975.t1 Coils Coil Coil 7 27 -
8 g10975.t1 Coils Coil Coil 600 620 -
7 g10975.t1 Coils Coil Coil 1106 1127 -
6 g10975.t1 Gene3D G3DSA:3.30.40.10 Zinc/RING finger domain 1032 1127 2.4E-22
13 g10975.t1 MobiDBLite mobidb-lite consensus disorder prediction 30 75 -
12 g10975.t1 MobiDBLite mobidb-lite consensus disorder prediction 46 67 -
3 g10975.t1 PANTHER PTHR13931:SF14 UBIQUITIN CONJUGATION FACTOR E4 B 131 1124 0.0
4 g10975.t1 PANTHER PTHR13931 UBIQUITINATION FACTOR E4 131 1124 0.0
2 g10975.t1 Pfam PF10408 Ubiquitin elongating factor core 421 1034 6.9E-179
1 g10975.t1 Pfam PF04564 U-box domain 1051 1121 7.0E-26
14 g10975.t1 ProSiteProfiles PS51698 U-box domain profile. 1050 1123 30.095
11 g10975.t1 SMART SM00504 Ubox_2 1054 1116 2.9E-24
5 g10975.t1 SUPERFAMILY SSF57850 RING/U-box 1038 1120 2.3E-23

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0034450 ubiquitin-ubiquitin ligase activity MF
GO:0006511 ubiquitin-dependent protein catabolic process BP
GO:0000151 ubiquitin ligase complex CC
GO:0016567 protein ubiquitination BP
GO:0004842 ubiquitin-protein transferase activity MF

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