General information for g444.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative TNF receptor-associated factor 6.
Parent gene
- The parent gene g444 is located on chr_3: 3375672..3379191 (+ strand)
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.t4 | TSS | g444.t4 | 3374302 | 3374302 |
| chr_3 | g444 | g444.t4 | isoform | g444.t4 | 3374778 | 3376330 |
| chr_3 | g444 | g444.t4 | exon | g444.t4.exon1 | 3374778 | 3376330 |
| chr_3 | g444 | g444.t4 | cds | g444.t4.CDS1 | 3374809 | 3375672 |
| chr_3 | g444 | g444.t4 | TTS | g444.t4 | NA | NA |
Sequences
>g444.t4 Gene=g444 Length=1553
GAAAAAGAATACTAAATGTCCACTTGATGATATGACTCTGTCTGTCGAAGATATTTTTCC
AGACAATTTTACTAAAAGAGAAATTGAACAGATTAGAAAAAGCTTTCCTGATCAATTTGA
ACCACCAGCAGTTGTATTATTTGAATGCCGTTTTTCAACAATATCATGTGAATTTAAAAC
AACAGAGCCGGAAGAAATGGATCGACACATGGAAAGTGCACATAAGGAACATTTAGAAAT
GCTTCTTAGTTCTTATTTAAAAACTCAATATCAAGCATGGGAACCTTTAGAGAAAACTAA
GAATGGAGAAAAAGAAGCATACCTTCGACAGCAATCGACAACACGTGATCTTGTAAATGC
CATGTATGAGAGAATCGTTATACTTGAGCAATTAACTCGCGAGCAAGCAATTAAAATTGA
CAAACTTCAATCAATGGAGACCAGAAAGCATGGCACTCTTGTGTGGAAAATAGAAGACTT
TAAAAAGAAAATTGAAATAATGCAAAGCAATCCAAATATGATGTTTTACAGTACAGAAGC
ATTTACCAGCCCAGATGGTTATAGATTTTGTGCTCGTATTAATTTATCAAATAAAATGAG
AGATTGTTTAAGTCTTCATGTGCATCTGATGCGATCTGAAAATGATTATCATCTTTCTTG
GCCATTTATTGGGAGAATAAGAATCTCAATGATTCACACAAAAGACTCTTCACTTACTCA
AACTGATTGCATTATGAGCAAACCAGAGATTCTTGCTTTTCATCGACCATGTGAAAGTGA
AATTTCTCCAAGAGGCTTTGGTTTCACAGAATATGCAGTCATTAGCGATATAATTAAACG
AGGATTCATTGAGAATGATTGTCTTATTATTAAAATTCAAATGAATATTGTCTAGAATGA
ATAATCTAAAGAATTTCAATAATATGTGCTCAAAAATTATTAAAAGTATTTTATACAAGT
GTGATTAGTAGATATTTTGTGTGAAATGAAAACAGTTCATTGTTCAAGTTGATGTTCAAA
TTATAGAATTATACATTCCTTAAGCAACAAAATTATAAGAATATCTATTTAATTTTAACC
CGTCCATTCAATCTTATTTTGTTTAAAATTCTTTTTTTTATTAAATTATTAGGATTTTAT
GTATTACACAAATATTGTATTTCAAACATTGTTTTTACTTTAAATAAAAAAGTAGAATAA
TGAAAGGAGAATATAGCAATCGAAATTCTCTCTAAATATATTTAATTTGTTTTAAAATTA
ATTTTTTAGATGTGTAAATTAAATTAATGGACAACAGGATTAAGTTGTTCACCTCGAATT
TTCTGATAATCAATTTCTTGTTCTACCGCTTCATCGATTAATCCAATTACTGCTACATTA
TCACCACGAATGATTTTTAACCCGAGATTTATTTGCTCCATTCCGGCAGTTGTTGAGTAT
ATTCTTTCATGCGTATCGACAAGAATTAAATTTATTAATTGATCAAAGCCTTAAATTTGA
AATAAAATATTAGGAATAAACTGTTTATTTATTTGAATTTAAATATCATTACC
>g444.t4 Gene=g444 Length=287
MTLSVEDIFPDNFTKREIEQIRKSFPDQFEPPAVVLFECRFSTISCEFKTTEPEEMDRHM
ESAHKEHLEMLLSSYLKTQYQAWEPLEKTKNGEKEAYLRQQSTTRDLVNAMYERIVILEQ
LTREQAIKIDKLQSMETRKHGTLVWKIEDFKKKIEIMQSNPNMMFYSTEAFTSPDGYRFC
ARINLSNKMRDCLSLHVHLMRSENDYHLSWPFIGRIRISMIHTKDSSLTQTDCIMSKPEI
LAFHRPCESEISPRGFGFTEYAVISDIIKRGFIENDCLIIKIQMNIV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g444.t4 | Coils | Coil | Coil | 118 | 138 | - |
| 4 | g444.t4 | Gene3D | G3DSA:2.60.210.10 | Apoptosis | 116 | 287 | 6.5E-39 |
| 1 | g444.t4 | PANTHER | PTHR10131:SF131 | TNF RECEPTOR-ASSOCIATED FACTOR 6 | 35 | 283 | 5.8E-25 |
| 2 | g444.t4 | PANTHER | PTHR10131 | TNF RECEPTOR ASSOCIATED FACTOR | 35 | 283 | 5.8E-25 |
| 6 | g444.t4 | ProSiteProfiles | PS50144 | MATH/TRAF domain profile. | 140 | 284 | 12.797 |
| 3 | g444.t4 | SUPERFAMILY | SSF49599 | TRAF domain-like | 140 | 287 | 1.8E-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:0005515 | protein binding | MF |
| GO:0016567 | protein ubiquitination | BP |
| 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.
