Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Toll-like receptor 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_2 g8289 g8289.t5 isoform g8289.t5 29564006 29565476
chr_2 g8289 g8289.t5 exon g8289.t5.exon1 29564006 29564320
chr_2 g8289 g8289.t5 cds g8289.t5.CDS1 29564086 29564320
chr_2 g8289 g8289.t5 exon g8289.t5.exon2 29564391 29565476
chr_2 g8289 g8289.t5 cds g8289.t5.CDS2 29564391 29565295
chr_2 g8289 g8289.t5 TSS g8289.t5 29565846 29565846
chr_2 g8289 g8289.t5 TTS g8289.t5 NA NA

Sequences

>g8289.t5 Gene=g8289 Length=1401
ATATCTTGCCATCGGTTCTAATGATTATATTTGTGCTTGTAATTTACGCGATTTTATAGA
TCGTGCAACGAGAAATGCTCTATATCACTATTGTTCAGAGAGAAATAAAAGATCGATTGA
AGAAACTCTTACATGGAATAATCCTGAACATCAATACAATGTCTTTCTTCGAGAATTCCA
TATGATAGTTGCATACTATGAAGAGAGCTATAGAAACATGATCCTAAATTCATTAAATCC
TGTTGAAGTAAAAATGCGCAGTGTTTCAAAAAATTTAAATACAGGAGGACTTTCATCTTT
CAGTGAAAGAGATTGTTACAATTTTGATAGTGATGAAGTCACACGCATGAATTTTAATTT
TCTTCTTCTCGATTATAATGAAAATGATTATGAATGTTTGGAAGAAGCTTATGGTTATAG
TACTTCACGAAGGGTACGTTTTCATGATGTTGAATCATGTTACAGCGATGAAAAAGATAC
GACTGAACCCTATGATGGAAGTTCAGACGATGAATCAAATGAAGAACCAACCGATGATCC
CGATAATGTGACTACGGATTCCTCCAAAATTTCTTCAACTACAACTGAAGGTTCTAAAGA
AGATGACTTTTTTAGACCAATTTTTGCTATCTTTAAAATGAATTATTTATACATTCTTCT
ATTTATTCCTGTATCATTATTCGCATTTTTCTGGTACAGGAAGCGAGCAGATATTAAATA
TTTTTGTACACTTTTTAAAAATTCCATTATATTGAGCCTTGATAATGAAGATAAGAAAAC
ATTGATGATGACAAATAGAAAAAAATCTCTTACTTCTGGAGGCATAATTGATGAATATCA
GTATGATGTATTTGTTTCTTATTCTGATAAAGACCGTTCTTGGGTGCTTGATGAGTTGAT
TCCAAATATTGAAAAGAGAGCTGAAATCAATATATGTCTACATGAAAGAGATTTTCAGGT
TGGATTAAGCATTCTCGAAAATATTATACAATGCATGGACAGAAGTCGCTGTCTATTACT
AGTTGTTTCAGAATCGTTTCTAAAGTCGAATTGGTGTGCTTTTGAAATGCATTTGGCACA
ACACAGATTAATTGAAACTCGAAGAGAACAATTGATACTCGTGCTTTTGCAAGACATTCC
TCGTTCAAAAAGAACTCGAACACTACAATTTTTAATGAGAACAAAAACGTATATTCAATG
GCCGCACGATGATAAAGAAGAGTCAAAGTTGACTTTTTGGAAGCGTTTAAGAAAAGCTAT
TATACTTAACAATTGGGAACCAGAAAAAAAAGTTAGTAAACCTCGTCATAGTATTGTTTA
AGTTATACAAAAAAGATTATAAATTTATTATTGTAATTGTATAAAGATATATATAAAGAG
AATATATTTTTGTTAGAACTT

>g8289.t5 Gene=g8289 Length=379
MIVAYYEESYRNMILNSLNPVEVKMRSVSKNLNTGGLSSFSERDCYNFDSDEVTRMNFNF
LLLDYNENDYECLEEAYGYSTSRRVRFHDVESCYSDEKDTTEPYDGSSDDESNEEPTDDP
DNVTTDSSKISSTTTEGSKEDDFFRPIFAIFKMNYLYILLFIPVSLFAFFWYRKRADIKY
FCTLFKNSIILSLDNEDKKTLMMTNRKKSLTSGGIIDEYQYDVFVSYSDKDRSWVLDELI
PNIEKRAEINICLHERDFQVGLSILENIIQCMDRSRCLLLVVSESFLKSNWCAFEMHLAQ
HRLIETRREQLILVLLQDIPRSKRTRTLQFLMRTKTYIQWPHDDKEESKLTFWKRLRKAI
ILNNWEPEKKVSKPRHSIV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g8289.t5 Gene3D G3DSA:3.40.50.10140 - 215 364 7.5E-49
15 g8289.t5 MobiDBLite mobidb-lite consensus disorder prediction 96 134 -
16 g8289.t5 MobiDBLite mobidb-lite consensus disorder prediction 103 121 -
2 g8289.t5 PANTHER PTHR24365:SF530 MSTPROX-RELATED 160 360 1.9E-56
3 g8289.t5 PANTHER PTHR24365 TOLL-LIKE RECEPTOR 160 360 1.9E-56
7 g8289.t5 PRINTS PR01537 Interleukin-1 receptor type I family signature 216 230 7.1E-7
5 g8289.t5 PRINTS PR01537 Interleukin-1 receptor type I family signature 257 284 7.1E-7
6 g8289.t5 PRINTS PR01537 Interleukin-1 receptor type I family signature 295 320 7.1E-7
4 g8289.t5 PRINTS PR01537 Interleukin-1 receptor type I family signature 345 364 7.1E-7
1 g8289.t5 Pfam PF01582 TIR domain 221 368 2.1E-22
10 g8289.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 154 -
12 g8289.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 155 172 -
11 g8289.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 173 379 -
17 g8289.t5 ProSiteProfiles PS50104 TIR domain profile. 219 363 30.333
14 g8289.t5 SMART SM00255 till_3 220 363 9.3E-24
8 g8289.t5 SUPERFAMILY SSF52200 Toll/Interleukin receptor TIR domain 212 361 2.09E-42
13 g8289.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 153 172 -

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:0016021 integral component of membrane CC
GO:0006955 immune response BP
GO:0004888 transmembrane signaling receptor activity MF
GO:0002224 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. There were no conditions that were differentially expressed