Gene loci information

Transcript annotation

  • This transcript has been annotated as TNF receptor-associated factor 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_4 g17063 g17063.t1 TTS g17063.t1 12346270 12346270
chr_4 g17063 g17063.t1 isoform g17063.t1 12346577 12353257
chr_4 g17063 g17063.t1 exon g17063.t1.exon1 12346577 12347674
chr_4 g17063 g17063.t1 cds g17063.t1.CDS1 12346577 12347674
chr_4 g17063 g17063.t1 exon g17063.t1.exon2 12347870 12347974
chr_4 g17063 g17063.t1 cds g17063.t1.CDS2 12347870 12347974
chr_4 g17063 g17063.t1 exon g17063.t1.exon3 12353066 12353257
chr_4 g17063 g17063.t1 cds g17063.t1.CDS3 12353066 12353257
chr_4 g17063 g17063.t1 TSS g17063.t1 12353516 12353516

Sequences

>g17063.t1 Gene=g17063 Length=1395
ATGGTCCGAAGCCTTTCACACTGGACGAAAACATTAAGTTTTCCAAATCGCCACTCGAAA
GAATGCAATGTAAATGTTCATCCAATTCAAGCACCACCAACACCGGCACGTAATAAAACA
AGCAGCTCTTCACGATCTTCTTCACCACCAAGTTCACCATCAAATGTTCCAATCACTGAA
ATCAGTCAAATTATTTATCCTGATCCAGATTCTGAAAAAGTCATCATGGGATCACTTGTG
TTTTGTATTCATCACAAAGAAGGCTGCAAATGGTCTGATGAGCTTCGTAAATTAAAGGCT
CATTTAAACACATGCAAATTTGACGCAATTCCATGTCCAAATCAATGCAATTCTCAAATT
CCACGTGTCATGATGTCAGACCATCTCGCTTTCACATGCACTCTTCGTCGTGCTGTCTGT
GAATTTTGTAATGTTGAATTCTCAGGACAAGGACTTGAAGAGCATCAAGGATTTTGCAAT
CAAGAGCCAATTTATTGTGAATCAAAATGTGGAACAAGAGTACTTCGTGGTCGAATGTCA
ATTCATCGTGCCAAAGACTGTTTAAAACGCTTAAAACGCTGCAATCACTGCCAACGTGAA
TTTTCAGCTGATACATTGTCACTTCATGCAAGCACATGCCATAAAGTTCTCGTACAATGT
CCACAAAAATGCGATGTTAGTCCACTGCCACGTGGTGAAATTGATGCACATTTAAGAGAT
GAATGCAAAGCATTGCTTGTGCCATGTACATTTAGAGATGCTGGTTGTCGTTATAAAGGA
CCAAGAAATATGCTCGAATCACATCTTGAATCAAATACAGCATCACATTTATCACTCATG
TGTCAAATGTCAGTCAAACAAAATCAACAAATTTTGTCACTTAAAAATGCAGTTGCAAAA
TTAAGTACAAATTATACTGGAACATTATTATGGAAAATTACAGATTGGAGTTCAAAATTA
GCTGAAGCAAAAAGTAAAGAAGGTTTAGAATTAGTTAGTCCACCATTTTATACAAGTCAA
TATGGCTATAAATTGCAAGCTTCAGTTTTTCTTAATGGAAATGGACCAGGCGAAAAATCA
CATTTGTCAGTTTATATTAAAGTTTTACCAGGCGAATATGATGCATTACTTAAATGGCCA
TTTTCACATTCAATTACTTTCACACTTTTTGAACAGTCTTCAAATGGTGGTGGAGCACAA
GGTGGAATTGCTGAAAGTTTTGTTCCTGATCCATCATGGGATAATTTTCAACGACCATCA
ACTGAACCTGACTCACTTGGCTTTGGTTTTCCACGATTTGTCTCACATGAAATGCTCACT
CGAAGACCTTTCATTAAAGATGACACAATTTTCTTAAGAATCAAAGCTGATGCAAGTAAA
GTTGTTGCTGTCTAA

>g17063.t1 Gene=g17063 Length=464
MVRSLSHWTKTLSFPNRHSKECNVNVHPIQAPPTPARNKTSSSSRSSSPPSSPSNVPITE
ISQIIYPDPDSEKVIMGSLVFCIHHKEGCKWSDELRKLKAHLNTCKFDAIPCPNQCNSQI
PRVMMSDHLAFTCTLRRAVCEFCNVEFSGQGLEEHQGFCNQEPIYCESKCGTRVLRGRMS
IHRAKDCLKRLKRCNHCQREFSADTLSLHASTCHKVLVQCPQKCDVSPLPRGEIDAHLRD
ECKALLVPCTFRDAGCRYKGPRNMLESHLESNTASHLSLMCQMSVKQNQQILSLKNAVAK
LSTNYTGTLLWKITDWSSKLAEAKSKEGLELVSPPFYTSQYGYKLQASVFLNGNGPGEKS
HLSVYIKVLPGEYDALLKWPFSHSITFTLFEQSSNGGGAQGGIAESFVPDPSWDNFQRPS
TEPDSLGFGFPRFVSHEMLTRRPFIKDDTIFLRIKADASKVVAV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g17063.t1 Gene3D G3DSA:3.30.40.10 Zinc/RING finger domain 100 159 6.1E-18
11 g17063.t1 Gene3D G3DSA:3.30.40.10 Zinc/RING finger domain 160 212 2.9E-10
10 g17063.t1 Gene3D G3DSA:3.30.40.10 Zinc/RING finger domain 213 276 4.3E-11
13 g17063.t1 Gene3D G3DSA:2.60.210.10 Apoptosis 282 463 1.5E-58
18 g17063.t1 MobiDBLite mobidb-lite consensus disorder prediction 28 55 -
19 g17063.t1 MobiDBLite mobidb-lite consensus disorder prediction 34 55 -
4 g17063.t1 PANTHER PTHR10131 TNF RECEPTOR ASSOCIATED FACTOR 17 173 1.6E-99
6 g17063.t1 PANTHER PTHR10131:SF138 TNF RECEPTOR ASSOCIATED FACTOR (TRAF) HOMOLOG 17 173 1.6E-99
3 g17063.t1 PANTHER PTHR10131 TNF RECEPTOR ASSOCIATED FACTOR 169 456 1.6E-99
5 g17063.t1 PANTHER PTHR10131:SF138 TNF RECEPTOR ASSOCIATED FACTOR (TRAF) HOMOLOG 169 456 1.6E-99
14 g17063.t1 PIRSF PIRSF015614 TRAF 1 188 2.4E-39
16 g17063.t1 PIRSF PIRSF015614 TRAF 167 289 1.2E-23
15 g17063.t1 PIRSF PIRSF015614 TRAF 272 464 3.8E-76
2 g17063.t1 Pfam PF02176 TRAF-type zinc finger 101 155 1.9E-11
1 g17063.t1 Pfam PF02176 TRAF-type zinc finger 209 268 6.1E-13
22 g17063.t1 ProSiteProfiles PS50145 Zinc finger TRAF-type profile. 100 153 12.713
21 g17063.t1 ProSiteProfiles PS50145 Zinc finger TRAF-type profile. 155 206 11.106
23 g17063.t1 ProSiteProfiles PS50145 Zinc finger TRAF-type profile. 209 266 13.252
20 g17063.t1 ProSiteProfiles PS50144 MATH/TRAF domain profile. 306 456 19.343
17 g17063.t1 SMART SM00061 math_3 308 439 2.7E-9
8 g17063.t1 SUPERFAMILY SSF49599 TRAF domain-like 79 143 7.85E-12
9 g17063.t1 SUPERFAMILY SSF49599 TRAF domain-like 229 282 3.73E-8
7 g17063.t1 SUPERFAMILY SSF49599 TRAF domain-like 305 456 5.72E-41

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:0007165 signal transduction BP
GO:0005515 protein binding MF
GO:0008270 zinc ion binding MF
GO:0042981 regulation of apoptotic process BP

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