Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t5 isoform g7674.t5 25211918 25214130
chr_2 g7674 g7674.t5 exon g7674.t5.exon1 25211918 25211942
chr_2 g7674 g7674.t5 cds g7674.t5.CDS1 25211918 25211942
chr_2 g7674 g7674.t5 exon g7674.t5.exon2 25212003 25212265
chr_2 g7674 g7674.t5 cds g7674.t5.CDS2 25212003 25212265
chr_2 g7674 g7674.t5 exon g7674.t5.exon3 25212452 25212739
chr_2 g7674 g7674.t5 cds g7674.t5.CDS3 25212452 25212739
chr_2 g7674 g7674.t5 exon g7674.t5.exon4 25213692 25213782
chr_2 g7674 g7674.t5 cds g7674.t5.CDS4 25213692 25213782
chr_2 g7674 g7674.t5 exon g7674.t5.exon5 25213879 25214130
chr_2 g7674 g7674.t5 cds g7674.t5.CDS5 25213879 25214000
chr_2 g7674 g7674.t5 TSS g7674.t5 NA NA
chr_2 g7674 g7674.t5 TTS g7674.t5 NA NA

Sequences

>g7674.t5 Gene=g7674 Length=919
TGTAAGTGTATGTCACAAATATTATTAAATTTTTATCGTCTCTTATCAGTTGAGCTTGAA
ATAAGCAAGAGTGAAAACATAGACATTTTGAAATGAAATAAAAATACTTATTTTTTATTT
CCTCATTTAGATGATGAATCCATCAACTGCAGTTGAACCATTACCAAGTGGATGGGAAGA
GAGACAAGACGCAAACGGTCGAACTTATTATGTTGATCACGTCAGACGAACAACGCAATG
GGAGCGACCAACAACGGCACCACAATCATCTGTTGATAGCGACATCGCGACAGCATTCGG
ACGAAGATTTCATATTAGTGTCGATGAGTCAGAGCAAAATAATCAACAAGACGGTGTTAG
TGTTCATTCTGATGATTCCAATCTCGACAATCAGTCACTTCATTCAACATCTGAACAATC
AATTGCTAGTCCAACTTCTGAAAACTCAAGAATTAGACCAACTAGGCCAGCACCTTCAAT
TCCTAATAGTCTTACGCGCAATAACACGAGAAGATCTGCTCCAAATCCACCTGAAAGAAC
TCTTAGTAGTGCTATAACTTCAGCCCAACCACGTAGAAGTACACCAAATTTGCAGAGACA
AAATTCACTTGAAGATAATGCAGCTCAAAGTGCTGAAGATGCTGTTGATCATTCATCAGA
GACATCATCAATCTCATCGACTCAACGCTCAGTAGCTTCTGCACCAGGAAGTTCTTCACA
ATCACGACAAAGTTCCTTAGATAGTCCAGCAAGTAGACAAGCGGCAGCAACAGCTCAATT
ATCTGATGCCGGTTTGCCACCAGGTTGGTCAATGCAACTCGCACCAAATGGTCGTGTATT
TTTCATAGATCATCAACGTAAAACGACAAGTTGGGTTGATCCCAGAACTGGATCTGCAAG
TCCAATGCCAAATGCCACT

>g7674.t5 Gene=g7674 Length=263
MMNPSTAVEPLPSGWEERQDANGRTYYVDHVRRTTQWERPTTAPQSSVDSDIATAFGRRF
HISVDESEQNNQQDGVSVHSDDSNLDNQSLHSTSEQSIASPTSENSRIRPTRPAPSIPNS
LTRNNTRRSAPNPPERTLSSAITSAQPRRSTPNLQRQNSLEDNAAQSAEDAVDHSSETSS
ISSTQRSVASAPGSSSQSRQSSLDSPASRQAAATAQLSDAGLPPGWSMQLAPNGRVFFID
HQRKTTSWVDPRTGSASPMPNAT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g7674.t5 CDD cd00201 WW 12 41 2.06499E-12
10 g7674.t5 CDD cd00201 WW 223 252 5.1438E-9
8 g7674.t5 Gene3D G3DSA:2.20.70.10 - 7 55 8.0E-18
7 g7674.t5 Gene3D G3DSA:2.20.70.10 - 222 257 8.7E-16
17 g7674.t5 MobiDBLite mobidb-lite consensus disorder prediction 1 22 -
16 g7674.t5 MobiDBLite mobidb-lite consensus disorder prediction 63 226 -
15 g7674.t5 MobiDBLite mobidb-lite consensus disorder prediction 66 215 -
3 g7674.t5 PANTHER PTHR11254:SF420 E3 UBIQUITIN-PROTEIN LIGASE NEDD-4 8 256 1.4E-31
4 g7674.t5 PANTHER PTHR11254 HECT DOMAIN UBIQUITIN-PROTEIN LIGASE 8 256 1.4E-31
1 g7674.t5 Pfam PF00397 WW domain 11 40 7.3E-13
2 g7674.t5 Pfam PF00397 WW domain 222 251 3.1E-9
12 g7674.t5 ProSitePatterns PS01159 WW/rsp5/WWP domain signature. 15 40 -
11 g7674.t5 ProSitePatterns PS01159 WW/rsp5/WWP domain signature. 226 251 -
19 g7674.t5 ProSiteProfiles PS50020 WW/rsp5/WWP domain profile. 9 42 18.362
18 g7674.t5 ProSiteProfiles PS50020 WW/rsp5/WWP domain profile. 220 253 15.722
13 g7674.t5 SMART SM00456 ww_5 10 42 5.2E-14
14 g7674.t5 SMART SM00456 ww_5 221 253 1.2E-9
5 g7674.t5 SUPERFAMILY SSF51045 WW domain 3 42 3.48E-14
6 g7674.t5 SUPERFAMILY SSF51045 WW domain 219 254 6.68E-12

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

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