Gene loci information

Transcript annotation

  • This transcript has been annotated as E3 ubiquitin-protein ligase Nedd-4.

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_2 g7674 g7674.t4 isoform g7674.t4 25211373 25212264
chr_2 g7674 g7674.t4 exon g7674.t4.exon1 25211373 25211436
chr_2 g7674 g7674.t4 cds g7674.t4.CDS1 25211375 25211436
chr_2 g7674 g7674.t4 exon g7674.t4.exon2 25211495 25211630
chr_2 g7674 g7674.t4 cds g7674.t4.CDS2 25211495 25211630
chr_2 g7674 g7674.t4 exon g7674.t4.exon3 25211690 25211942
chr_2 g7674 g7674.t4 cds g7674.t4.CDS3 25211690 25211942
chr_2 g7674 g7674.t4 exon g7674.t4.exon4 25212003 25212264
chr_2 g7674 g7674.t4 cds g7674.t4.CDS4 25212003 25212085
chr_2 g7674 g7674.t4 TSS g7674.t4 NA NA
chr_2 g7674 g7674.t4 TTS g7674.t4 NA NA

Sequences

>g7674.t4 Gene=g7674 Length=715
CTGAAGATGCTGTTGATCATTCATCAGAGACATCATCAATCTCATCGACTCAACGCTCAG
TAGCTTCTGCACCAGGAAGTTCTTCACAATCACGACAAAGTTCCTTAGATAGTCCAGCAA
GTAGACAAGCGGCAGCAACAGCTCAATTATCTGATGCCGGTTTGCCACCAGGTTGGTCAA
TGCAACTCGCACCAAATGGTCGTGTATTTTTCATAGATCATCAACGTAAAACGACAAGTT
GGGTTGATCCCAGAACTGGATCTGCAAGTCCAATGCCAAATGCCACTCCATCCACATATG
AAGACCGATCAGAAGACAATCTTGGACCATTACCAGAAGGATGGGAAGAGCGAGTGCACA
CAGATGGAAGAATTTTCTTTATTGATCACAATACAAGAACTACACAATGGGATGATCCAA
GACTGTCAAATCCAAATGTCGCTGGTCAAGCTGTGCCGTATTCACGTGACTATAAACAGA
AATATGAATTCTTTAAGACACAACTTAGAAAACCGACTAATGTACCTAACAAAATTGAAA
TCAAAGTTCGTCGTGAATCTATTTTAGAAGATTCTTATAGAGTTATTAGTTCGGTAACAA
AAACTGATTTGCTGAAAACAAAATTATGGGTAGAATTTGAAGGTGAAACTGGTCTTGATT
ATGGTGGCTTAGCTAGAGAATGGTTCTTTTTATTATCAAAACAAATGTTCAATCC

>g7674.t4 Gene=g7674 Length=178
MQLAPNGRVFFIDHQRKTTSWVDPRTGSASPMPNATPSTYEDRSEDNLGPLPEGWEERVH
TDGRIFFIDHNTRTTQWDDPRLSNPNVAGQAVPYSRDYKQKYEFFKTQLRKPTNVPNKIE
IKVRRESILEDSYRVISSVTKTDLLKTKLWVEFEGETGLDYGGLAREWFFLLSKQMFN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g7674.t4 CDD cd00201 WW 1 25 2.00784E-4
10 g7674.t4 CDD cd00201 WW 52 82 7.64173E-12
8 g7674.t4 Gene3D G3DSA:2.20.70.10 - 1 30 3.9E-10
9 g7674.t4 Gene3D G3DSA:2.20.70.10 - 41 86 3.2E-24
7 g7674.t4 Gene3D G3DSA:3.90.1750.10 Hect 87 178 4.0E-33
15 g7674.t4 MobiDBLite mobidb-lite consensus disorder prediction 20 46 -
16 g7674.t4 MobiDBLite mobidb-lite consensus disorder prediction 21 43 -
2 g7674.t4 PANTHER PTHR11254:SF420 E3 UBIQUITIN-PROTEIN LIGASE NEDD-4 1 178 6.6E-88
3 g7674.t4 PANTHER PTHR11254 HECT DOMAIN UBIQUITIN-PROTEIN LIGASE 1 178 6.6E-88
1 g7674.t4 Pfam PF00397 WW domain 51 80 3.7E-13
12 g7674.t4 ProSitePatterns PS01159 WW/rsp5/WWP domain signature. 55 80 -
17 g7674.t4 ProSiteProfiles PS50020 WW/rsp5/WWP domain profile. 1 26 10.561
18 g7674.t4 ProSiteProfiles PS50020 WW/rsp5/WWP domain profile. 49 82 18.658
19 g7674.t4 ProSiteProfiles PS50237 HECT domain profile. 141 178 19.258
13 g7674.t4 SMART SM00456 ww_5 1 26 1.1
14 g7674.t4 SMART SM00456 ww_5 50 82 1.5E-14
6 g7674.t4 SUPERFAMILY SSF51045 WW domain 3 27 1.41E-6
5 g7674.t4 SUPERFAMILY SSF51045 WW domain 45 83 6.38E-15
4 g7674.t4 SUPERFAMILY SSF56204 Hect, E3 ligase catalytic domain 100 178 1.31E-17

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:0005515 protein binding MF
GO:0004842 ubiquitin-protein transferase activity MF

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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