Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Myeloid differentiation primary response protein MyD88.

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 g8850 g8850.t2 TSS g8850.t2 33541220 33541220
chr_2 g8850 g8850.t2 isoform g8850.t2 33541312 33542518
chr_2 g8850 g8850.t2 exon g8850.t2.exon1 33541312 33541669
chr_2 g8850 g8850.t2 cds g8850.t2.CDS1 33541312 33541669
chr_2 g8850 g8850.t2 exon g8850.t2.exon2 33541940 33542518
chr_2 g8850 g8850.t2 cds g8850.t2.CDS2 33541940 33542517
chr_2 g8850 g8850.t2 TTS g8850.t2 33543102 33543102

Sequences

>g8850.t2 Gene=g8850 Length=937
ATGGCAATAAGAAACAATAATGAAGTGATAGAACATCGCATAAATTTCGAAGAAATTCCA
TTAAATGCATTAAGAAAAAGAACTCGTGAAAAATTGTCAGTTTTATTAAATCCAGAAAAA
GTATTGAGAAGTGAAGATGGATATTGTCGTGATTGGCGAGGTCTATTTTCATTTTCGGGC
TTATCACAATCTGAATACACTTTAATCTCTCAAAGTCATGATAAAATGAGTACACTTCTT
GATTTGTGGATAAGAAAAAATAGTGAAAATGACCATAAAGTGAATCTGAGTCAGTTACAG
CAATGTTTCGAGTTAATTGATAGATATGATATTTACGATGACACTCTGAGTTTACTCTCC
GATGATGCTCAAGCGTTCTTATCAAAATCGCAATCTATCAACTTAGAAAACAGAAGCAAA
TTTGAAGTTTTAAAGGCAGAGCCAGATAATGATATCATAACAATAAGAGACGTAGAATAT
ATTGAGAAAGGCTTATCGCTCCCAATATATGACGCGCTTGTTATTTACAGTGACAAAGAT
ATTGAATTTGCTTCCGAATTGATAGAAAGATTGGAAAAAGTTGGTTTTTTATTATGCGCT
AAAGATAGAGACCTTCTACCGGGACTATCATTTGAAAGTGACGCAATGCTGAATCTTTTA
TCGAAAAGATGCAAAAAATTAATTGTAATTATTTCTAAAGCATTCCTACAAAGTCCTATG
CAAATTTTTATGACTAACTTTGCACAAGCTCTCGGTATTGAGAATAAACAAAGAAAAATC
ATTCCATGCTTGTTAGAGCCCTGCGATTTGCCACAAATGCTGCGCTATTGTTTTCGACTT
GATTATTATAGAAATAACAAACTTTTTGATTTCTGGGAAAAGCTTGAAGTATCACTCAAA
GAACATAAAAGAGAAATCAAAATCGAAGCGATTGAAA

>g8850.t2 Gene=g8850 Length=312
MAIRNNNEVIEHRINFEEIPLNALRKRTREKLSVLLNPEKVLRSEDGYCRDWRGLFSFSG
LSQSEYTLISQSHDKMSTLLDLWIRKNSENDHKVNLSQLQQCFELIDRYDIYDDTLSLLS
DDAQAFLSKSQSINLENRSKFEVLKAEPDNDIITIRDVEYIEKGLSLPIYDALVIYSDKD
IEFASELIERLEKVGFLLCAKDRDLLPGLSFESDAMLNLLSKRCKKLIVIISKAFLQSPM
QIFMTNFAQALGIENKQRKIIPCLLEPCDLPQMLRYCFRLDYYRNNKLFDFWEKLEVSLK
EHKREIKIEAIE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g8850.t2 Gene3D G3DSA:1.10.533.10 Death Domain 18 137 0.0000
7 g8850.t2 Gene3D G3DSA:3.40.50.10140 - 170 301 0.0000
2 g8850.t2 PANTHER PTHR15079 MYD88 14 301 0.0000
3 g8850.t2 PANTHER PTHR15079:SF3 MYELOID DIFFERENTIATION PRIMARY RESPONSE PROTEIN MYD88 14 301 0.0000
1 g8850.t2 Pfam PF13676 TIR domain 174 284 0.0000
9 g8850.t2 ProSiteProfiles PS50017 Death domain profile. 51 119 9.9630
10 g8850.t2 ProSiteProfiles PS50104 TIR domain profile. 168 251 14.1470
6 g8850.t2 SMART SM00255 till_3 169 302 0.0014
5 g8850.t2 SUPERFAMILY SSF47986 DEATH domain 21 115 0.0000
4 g8850.t2 SUPERFAMILY SSF52200 Toll/Interleukin receptor TIR domain 169 297 0.0000

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:0043123 positive regulation of I-kappaB kinase/NF-kappaB signaling BP
GO:0007165 signal transduction BP
GO:0005515 protein binding MF
GO:0070976 TIR domain binding MF
GO:0002755 MyD88-dependent toll-like receptor signaling pathway 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