Gene loci information

Transcript annotation

  • This transcript has been annotated as Ubiquitin-protein ligase E3C.

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 g534 g534.t3 isoform g534.t3 3967847 3968996
chr_3 g534 g534.t3 exon g534.t3.exon1 3967847 3968996
chr_3 g534 g534.t3 cds g534.t3.CDS1 3967881 3968996
chr_3 g534 g534.t3 TTS g534.t3 3969124 3969124
chr_3 g534 g534.t3 TSS g534.t3 NA NA

Sequences

>g534.t3 Gene=g534 Length=1150
TTTAGCTGCAGAGAAATTAAGGAGTCAAGGAGATATGCAAGGATTTCTGCAAGGACCACA
AACTCATTTGACTGTGCGAAGAACACATTTGTATGAAGATGCATTTGATAAATTATCACC
TGAAAATGAACCAAATCTAAGGACGAGATGGCGAGTTCAGATGGTTAATGAACAAGGACT
TGAAGAGGCTGGTATTGATGGTGGTGGTATTTTTAGAGAATTTCTCAGTGAATTAATTAA
AACAGCATTCGATCCTAATCGTGGATTTTTCATACTAACAAAGGATAACATGTTATATCC
AAATCCAAGTGCTAGTGTGATACAAGAAAACTATAAGAAACATTACTATTTTATTGGTCG
AATGCTAGGCAAAGCATTGTTTGAGAATCTTCTCGTTGAGCTTCCATTAGCTGAATTTTT
CTTATCAAAATTGGCTGGACGTCATGCAGACATAATTGACATTCATCAATTAATTTCACT
AGATCCCGATATGCACAAAAATTTAATGAAATTAAAAAGCTACAACGAAAATGATTTCAA
AGACCTTGGATTAGATTTCACTGTTGTTTGTGATGATTTGGGTGATACAAGAGTTGTTGA
ATTAAAACCTGATGGCGCTAATATAACTGTGAATTCAAGTAATTGGATTGAATATATTCA
AGTTATGGCAGATTTCAAACTTAATCGACAAATTCATGAGCAATGTTTAGCATTTAGACA
AGGTTTAGCCAACGTACTTCCAATCTCATGGCTTTACATGTTCAACACTAAAGAACTTCA
AGTGTTGATTTCTGGTGCAGAAATTCCTGTAGATGTTGATGATTTAATGGCACATACGAG
ATATGGAGGTGATTATACACCAGAACATGAAACAATAAAAATGTTTTGGAATGTCGTTAA
AAGTTTTGATGACTTAGAGAAACGACAATTGTTAAAATTTGTCACAAGTTGCTCACGACC
TCCCTTACTCGGTTTTAAAGATCTCGATCCACCATTCTGCATACAAAATTCAGGGGATGA
TAGTGATCGATTGGCAAGTGCATCAACTTGCATGAATTTACTTAAATTACCCACCTATTC
TGATGAAAACACTATGCGAGAGAAATTACTTTATTCCATAAATAGTGGCGTTGGTTTCGA
ATTGAGTTAA

>g534.t3 Gene=g534 Length=371
MQGFLQGPQTHLTVRRTHLYEDAFDKLSPENEPNLRTRWRVQMVNEQGLEEAGIDGGGIF
REFLSELIKTAFDPNRGFFILTKDNMLYPNPSASVIQENYKKHYYFIGRMLGKALFENLL
VELPLAEFFLSKLAGRHADIIDIHQLISLDPDMHKNLMKLKSYNENDFKDLGLDFTVVCD
DLGDTRVVELKPDGANITVNSSNWIEYIQVMADFKLNRQIHEQCLAFRQGLANVLPISWL
YMFNTKELQVLISGAEIPVDVDDLMAHTRYGGDYTPEHETIKMFWNVVKSFDDLEKRQLL
KFVTSCSRPPLLGFKDLDPPFCIQNSGDDSDRLASASTCMNLLKLPTYSDENTMREKLLY
SINSGVGFELS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g534.t3 CDD cd00078 HECTc 11 369 0.000
6 g534.t3 Gene3D G3DSA:3.90.1750.10 Hect 12 254 0.000
7 g534.t3 Gene3D G3DSA:3.30.2160.10 Hect 136 219 0.000
8 g534.t3 Gene3D G3DSA:3.30.2410.10 Hect 257 371 0.000
2 g534.t3 PANTHER PTHR45700:SF2 UBIQUITIN-PROTEIN LIGASE E3C 9 371 0.000
3 g534.t3 PANTHER PTHR45700 UBIQUITIN-PROTEIN LIGASE E3C 9 371 0.000
1 g534.t3 Pfam PF00632 HECT-domain (ubiquitin-transferase) 66 371 0.000
9 g534.t3 ProSiteProfiles PS50237 HECT domain profile. 31 371 87.197
5 g534.t3 SMART SM00119 hect_3 29 371 0.000
4 g534.t3 SUPERFAMILY SSF56204 Hect, E3 ligase catalytic domain 8 365 0.000

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g534/g534.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g534.t3.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
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