Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative TNF receptor-associated factor 6.

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 g444 g444.t1 TSS g444.t1 3374302 3374302
chr_3 g444 g444.t1 isoform g444.t1 3374424 3375672
chr_3 g444 g444.t1 exon g444.t1.exon1 3374424 3374620
chr_3 g444 g444.t1 cds g444.t1.CDS1 3374424 3374620
chr_3 g444 g444.t1 exon g444.t1.exon2 3374690 3374722
chr_3 g444 g444.t1 cds g444.t1.CDS2 3374690 3374722
chr_3 g444 g444.t1 exon g444.t1.exon3 3374778 3375672
chr_3 g444 g444.t1 cds g444.t1.CDS3 3374778 3375672
chr_3 g444 g444.t1 TTS g444.t1 NA NA

Sequences

>g444.t1 Gene=g444 Length=1125
ATGTCAGCAGAGGAATCGACAATAGCTCAAACACAAACTAGTGAAAACAGTGATTCTCCT
CCCAAAAAGAAAACTGGTGAAATTTTAAAAGAGACCTTGAGAACAAAAAGTCTTGAGCCA
GTACCTCAAGAAAATTATGAATGTCCAATTTGTTTAAATCTTCTAAAAGATCCAGTTCTA
ACGAAATGCGGTCACAGATATTGCAAAAATTGTCTCGAAGAATGGAGAATGAAAAAGAAT
ACTAAATGTCCACTTGATGATATGACTCTGTCTGTCGAAGATATTTTTCCAGACAATTTT
ACTAAAAGAGAAATTGAACAGATTAGAAAAAGCTTTCCTGATCAATTTGAACCACCAGCA
GTTGTATTATTTGAATGCCGTTTTTCAACAATATCATGTGAATTTAAAACAACAGAGCCG
GAAGAAATGGATCGACACATGGAAAGTGCACATAAGGAACATTTAGAAATGCTTCTTAGT
TCTTATTTAAAAACTCAATATCAAGCATGGGAACCTTTAGAGAAAACTAAGAATGGAGAA
AAAGAAGCATACCTTCGACAGCAATCGACAACACGTGATCTTGTAAATGCCATGTATGAG
AGAATCGTTATACTTGAGCAATTAACTCGCGAGCAAGCAATTAAAATTGACAAACTTCAA
TCAATGGAGACCAGAAAGCATGGCACTCTTGTGTGGAAAATAGAAGACTTTAAAAAGAAA
ATTGAAATAATGCAAAGCAATCCAAATATGATGTTTTACAGTACAGAAGCATTTACCAGC
CCAGATGGTTATAGATTTTGTGCTCGTATTAATTTATCAAATAAAATGAGAGATTGTTTA
AGTCTTCATGTGCATCTGATGCGATCTGAAAATGATTATCATCTTTCTTGGCCATTTATT
GGGAGAATAAGAATCTCAATGATTCACACAAAAGACTCTTCACTTACTCAAACTGATTGC
ATTATGAGCAAACCAGAGATTCTTGCTTTTCATCGACCATGTGAAAGTGAAATTTCTCCA
AGAGGCTTTGGTTTCACAGAATATGCAGTCATTAGCGATATAATTAAACGAGGATTCATT
GAGAATGATTGTCTTATTATTAAAATTCAAATGAATATTGTCTAG

>g444.t1 Gene=g444 Length=374
MSAEESTIAQTQTSENSDSPPKKKTGEILKETLRTKSLEPVPQENYECPICLNLLKDPVL
TKCGHRYCKNCLEEWRMKKNTKCPLDDMTLSVEDIFPDNFTKREIEQIRKSFPDQFEPPA
VVLFECRFSTISCEFKTTEPEEMDRHMESAHKEHLEMLLSSYLKTQYQAWEPLEKTKNGE
KEAYLRQQSTTRDLVNAMYERIVILEQLTREQAIKIDKLQSMETRKHGTLVWKIEDFKKK
IEIMQSNPNMMFYSTEAFTSPDGYRFCARINLSNKMRDCLSLHVHLMRSENDYHLSWPFI
GRIRISMIHTKDSSLTQTDCIMSKPEILAFHRPCESEISPRGFGFTEYAVISDIIKRGFI
ENDCLIIKIQMNIV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g444.t1 Coils Coil Coil 205 225 -
8 g444.t1 Gene3D G3DSA:3.30.40.10 Zinc/RING finger domain 31 154 4.5E-22
9 g444.t1 Gene3D G3DSA:2.60.210.10 Apoptosis 203 374 1.3E-38
13 g444.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 27 -
14 g444.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 19 -
3 g444.t1 PANTHER PTHR10131:SF131 TNF RECEPTOR-ASSOCIATED FACTOR 6 39 108 6.1E-40
5 g444.t1 PANTHER PTHR10131 TNF RECEPTOR ASSOCIATED FACTOR 39 108 6.1E-40
2 g444.t1 PANTHER PTHR10131:SF131 TNF RECEPTOR-ASSOCIATED FACTOR 6 122 370 6.1E-40
4 g444.t1 PANTHER PTHR10131 TNF RECEPTOR ASSOCIATED FACTOR 122 370 6.1E-40
1 g444.t1 Pfam PF00097 Zinc finger, C3HC4 type (RING finger) 48 85 4.4E-11
11 g444.t1 ProSitePatterns PS00518 Zinc finger RING-type signature. 63 72 -
16 g444.t1 ProSiteProfiles PS50089 Zinc finger RING-type profile. 48 87 12.902
15 g444.t1 ProSiteProfiles PS50144 MATH/TRAF domain profile. 227 371 12.797
12 g444.t1 SMART SM00184 ring_2 48 86 5.6E-9
7 g444.t1 SUPERFAMILY SSF57850 RING/U-box 41 110 1.43E-20
6 g444.t1 SUPERFAMILY SSF49599 TRAF domain-like 227 374 3.27E-29

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:0005164 tumor necrosis factor receptor binding MF
GO:0046872 metal ion binding MF
GO:0005515 protein binding MF
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