General information for g8850.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Myeloid differentiation primary response protein MyD88.
Parent gene
- The parent gene g8850 is located on chr_2: 33543031..33544806 (+ 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_2 | g8850 | g8850.t1 | TSS | g8850.t1 | 33541220 | 33541220 |
| chr_2 | g8850 | g8850.t1 | isoform | g8850.t1 | 33541312 | 33543031 |
| chr_2 | g8850 | g8850.t1 | exon | g8850.t1.exon1 | 33541312 | 33541669 |
| chr_2 | g8850 | g8850.t1 | cds | g8850.t1.CDS1 | 33541312 | 33541669 |
| chr_2 | g8850 | g8850.t1 | exon | g8850.t1.exon2 | 33541940 | 33542519 |
| chr_2 | g8850 | g8850.t1 | cds | g8850.t1.CDS2 | 33541940 | 33542519 |
| chr_2 | g8850 | g8850.t1 | exon | g8850.t1.exon3 | 33542575 | 33543031 |
| chr_2 | g8850 | g8850.t1 | cds | g8850.t1.CDS3 | 33542575 | 33543031 |
| chr_2 | g8850 | g8850.t1 | TTS | g8850.t1 | 33543102 | 33543102 |
Sequences
>g8850.t1 Gene=g8850 Length=1395
ATGGCAATAAGAAACAATAATGAAGTGATAGAACATCGCATAAATTTCGAAGAAATTCCA
TTAAATGCATTAAGAAAAAGAACTCGTGAAAAATTGTCAGTTTTATTAAATCCAGAAAAA
GTATTGAGAAGTGAAGATGGATATTGTCGTGATTGGCGAGGTCTATTTTCATTTTCGGGC
TTATCACAATCTGAATACACTTTAATCTCTCAAAGTCATGATAAAATGAGTACACTTCTT
GATTTGTGGATAAGAAAAAATAGTGAAAATGACCATAAAGTGAATCTGAGTCAGTTACAG
CAATGTTTCGAGTTAATTGATAGATATGATATTTACGATGACACTCTGAGTTTACTCTCC
GATGATGCTCAAGCGTTCTTATCAAAATCGCAATCTATCAACTTAGAAAACAGAAGCAAA
TTTGAAGTTTTAAAGGCAGAGCCAGATAATGATATCATAACAATAAGAGACGTAGAATAT
ATTGAGAAAGGCTTATCGCTCCCAATATATGACGCGCTTGTTATTTACAGTGACAAAGAT
ATTGAATTTGCTTCCGAATTGATAGAAAGATTGGAAAAAGTTGGTTTTTTATTATGCGCT
AAAGATAGAGACCTTCTACCGGGACTATCATTTGAAAGTGACGCAATGCTGAATCTTTTA
TCGAAAAGATGCAAAAAATTAATTGTAATTATTTCTAAAGCATTCCTACAAAGTCCTATG
CAAATTTTTATGACTAACTTTGCACAAGCTCTCGGTATTGAGAATAAACAAAGAAAAATC
ATTCCATGCTTGTTAGAGCCCTGCGATTTGCCACAAATGCTGCGCTATTGTTTTCGACTT
GATTATTATAGAAATAACAAACTTTTTGATTTCTGGGAAAAGCTTGAAGTATCACTCAAA
GAACATAAAAGAGAAATCAAAATCGAAGCGATTGAAAAATCAAAATTGCATACGCATACA
GAAGAACCACCGTCAATTTATAAATTTTCTGAATCAGTTTCAACAGATATTCCTAAAAAA
GAAATAAAACAGCAATTCATTCCGCTTCCAAAACTACGGTCTTCATCATCAGCTGTTAAT
TTAGATACAATTGGTAATGGAAGTGAATTAAAATATAAAAATAAACATTCTCAGAGCACA
CTTTGGCTCAATGGAACCACAGAGACTAATGAAGCTCAATCTATGGAAAGCAGTGTAAAA
TTAAAACGTAAAAAGTGGTACAGCATGTTCTTGCCACCAAAAGAGAAATTTAAAACAAAA
ATAAATGATGAATTTCCTGAGGAGGAAGAACAAAAACTCAAAGAAAAGAAAGAGAAGAAA
CCCAAGAAGCTATGGTTTGAAAGTAAGAAGAAACGTGATAAACAAAAGGAAAAGGTTGCA
GCTTTTGCAATATAA
>g8850.t1 Gene=g8850 Length=464
MAIRNNNEVIEHRINFEEIPLNALRKRTREKLSVLLNPEKVLRSEDGYCRDWRGLFSFSG
LSQSEYTLISQSHDKMSTLLDLWIRKNSENDHKVNLSQLQQCFELIDRYDIYDDTLSLLS
DDAQAFLSKSQSINLENRSKFEVLKAEPDNDIITIRDVEYIEKGLSLPIYDALVIYSDKD
IEFASELIERLEKVGFLLCAKDRDLLPGLSFESDAMLNLLSKRCKKLIVIISKAFLQSPM
QIFMTNFAQALGIENKQRKIIPCLLEPCDLPQMLRYCFRLDYYRNNKLFDFWEKLEVSLK
EHKREIKIEAIEKSKLHTHTEEPPSIYKFSESVSTDIPKKEIKQQFIPLPKLRSSSSAVN
LDTIGNGSELKYKNKHSQSTLWLNGTTETNEAQSMESSVKLKRKKWYSMFLPPKEKFKTK
INDEFPEEEEQKLKEKKEKKPKKLWFESKKKRDKQKEKVAAFAI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g8850.t1 | Gene3D | G3DSA:1.10.533.10 | Death Domain | 18 | 137 | 1.7E-17 |
| 8 | g8850.t1 | Gene3D | G3DSA:3.40.50.10140 | - | 170 | 301 | 4.6E-27 |
| 7 | g8850.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 421 | 441 | - |
| 2 | g8850.t1 | PANTHER | PTHR15079 | MYD88 | 14 | 419 | 1.5E-59 |
| 3 | g8850.t1 | PANTHER | PTHR15079:SF3 | MYELOID DIFFERENTIATION PRIMARY RESPONSE PROTEIN MYD88 | 14 | 419 | 1.5E-59 |
| 1 | g8850.t1 | Pfam | PF13676 | TIR domain | 174 | 284 | 3.0E-10 |
| 10 | g8850.t1 | ProSiteProfiles | PS50017 | Death domain profile. | 51 | 119 | 9.963 |
| 11 | g8850.t1 | ProSiteProfiles | PS50104 | TIR domain profile. | 168 | 251 | 14.147 |
| 6 | g8850.t1 | SMART | SM00255 | till_3 | 169 | 302 | 0.0014 |
| 5 | g8850.t1 | SUPERFAMILY | SSF47986 | DEATH domain | 21 | 115 | 1.7E-8 |
| 4 | g8850.t1 | SUPERFAMILY | SSF52200 | Toll/Interleukin receptor TIR domain | 169 | 297 | 4.45E-23 |
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
- This transcript has been annotated with K04729 (myeloid differentiation primary response protein MyD88)
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.
