General information for g8289.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Toll-like receptor 6.
Parent gene
- The parent gene g8289 is located on chr_2: 29564086..29567224 (- 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 | g8289 | g8289.t1 | isoform | g8289.t1 | 29564086 | 29567224 |
| chr_2 | g8289 | g8289.t1 | exon | g8289.t1.exon1 | 29564086 | 29564320 |
| chr_2 | g8289 | g8289.t1 | cds | g8289.t1.CDS1 | 29564086 | 29564320 |
| chr_2 | g8289 | g8289.t1 | exon | g8289.t1.exon2 | 29564391 | 29565476 |
| chr_2 | g8289 | g8289.t1 | cds | g8289.t1.CDS2 | 29564391 | 29565476 |
| chr_2 | g8289 | g8289.t1 | exon | g8289.t1.exon3 | 29565536 | 29565707 |
| chr_2 | g8289 | g8289.t1 | cds | g8289.t1.CDS3 | 29565536 | 29565707 |
| chr_2 | g8289 | g8289.t1 | exon | g8289.t1.exon4 | 29565873 | 29566325 |
| chr_2 | g8289 | g8289.t1 | cds | g8289.t1.CDS4 | 29565873 | 29566325 |
| chr_2 | g8289 | g8289.t1 | exon | g8289.t1.exon5 | 29566442 | 29566586 |
| chr_2 | g8289 | g8289.t1 | cds | g8289.t1.CDS5 | 29566442 | 29566586 |
| chr_2 | g8289 | g8289.t1 | exon | g8289.t1.exon6 | 29566724 | 29567224 |
| chr_2 | g8289 | g8289.t1 | cds | g8289.t1.CDS6 | 29566724 | 29567224 |
| chr_2 | g8289 | g8289.t1 | TSS | g8289.t1 | 29567465 | 29567465 |
| chr_2 | g8289 | g8289.t1 | TTS | g8289.t1 | NA | NA |
Sequences
>g8289.t1 Gene=g8289 Length=2592
ATGTATCTTATTAAGATTATGTTATGTACTCTAGTGTTAACAATTACTCAATTAAGGTGC
AGTGTTTATTGTCACCCATACGGGAAAAATATTGATGACGTGATATCTAAAAGGAATACG
TCCCTGTTTGACGATAAAACACAAATCGTAATAATTGACGAAAATGTTAATACCTTTCTA
CCTGATAACATTAATGTCGATGATAGCGCAGTAAATGCCAGAGAATCCCCTGAAACGTCA
AAAGAAGCACTTTATCAAGATCTTTTCAATGATTACGGCTCTTCTTATTCACTTTATGAT
CCAGGTGACGACGAACCCGAATGTATTTTAGCCCGTTCTGAATTTTATCTATCATGGTGG
GTGCATGAAAATGGTAGCTTACGTCTTCCTAGTTTTAATCGTCTCAACACATCAGGCATA
CTTGATTTATCTCTTCAATTCGATTCGGAAACCACACTGTTCAATCATGTATTGAATTTT
ACAAGCGACAACCCTCATGAAGTGATAAGATTTATGAGCGTCGCAAGTAATAAGTTAGAT
CAAATACCGGCATCAGTTTTAAATTTAACAAGTGCGACAATACAATACCTTTCGCTAGCT
GGTAACAATTTTTATGGAATGTTTGAATATGAAAATACTACATTTCAAAATTTTACATCA
TTTCCATTAATGTCACACTTGTTAGAGTTGGATTTACGAAGTTGCCATATAAGGAGTTTG
AGCAGTGATTATTTCAAAAATTTACCAAGATTAGACAAGCTATTTCTTTCACACAACAAT
TTTTTGATAATTGAAGCTTCTGCATTTGCACCATTAACAAAGTTGCGTCATCTTGACTTA
AGTTACAATACAATTCCATTTGAAATTGAAAATCGAATTGAAGGAATGATTCTAGAAGAG
TTTTTATTTGAAAAACTTGAACATTTGATGTTTCTTGATTTGTCACATTCAAAATTACGT
AGACGAAGCTTGCTGGCATTGAAGTCACTAGGACATGAAATGAAACAACTTTCATTGTGT
CATACTGGCATTGTTTCATTTCCTGAAGGAATGCTTAACAACACTTCACTTAATGTTCTA
GATTTGAGTGGAAATTTAGAAAATTTTAAAGAATTGGCTGAATTAGAAATTTTAGATTTG
GGATCAAATAATATCAATAATTGGTACGAACGAGTTTTTACTGAAAATGAAAAACTTCGT
ATTGTAAATTTGCGTTCCAACAACATTACATTCATGCGAGAAGGAATGATTAGAGACTTT
TATGAGATCAGATATCTTGCCATCGGTTCTAATGATTATATTTGTGCTTGTAATTTACGC
GATTTTATAGATCGTGCAACGAGAAATGCTCTATATCACTATTGTTCAGAGAGAAATAAA
AGATCGATTGAAGAAACTCTTACATGGAATAATCCTGAACATCAATACAATGTCTTTCTT
CGAGAATTCCATATGATAGTTGCATACTATGAAGAGAGCTATAGAAACATGATCCTAAAT
TCATTAAATCCTGTTGAAGTAAAAATGCGCAGTGTTTCAAAAAATTTAAATACAGGAGGA
CTTTCATCTTTCAGTGAAAGAGATTGTTACAATTTTGATAGTGATGAAGTCACACGCATG
AATTTTAATTTTCTTCTTCTCGATTATAATGAAAATGATTATGAATGTTTGGAAGAAGCT
TATGGTTATAGTACTTCACGAAGGGTACGTTTTCATGATGTTGAATCATGTTACAGCGAT
GAAAAAGATACGACTGAACCCTATGATGGAAGTTCAGACGATGAATCAAATGAAGAACCA
ACCGATGATCCCGATAATGTGACTACGGATTCCTCCAAAATTTCTTCAACTACAACTGAA
GGTTCTAAAGAAGATGACTTTTTTAGACCAATTTTTGCTATCTTTAAAATGAATTATTTA
TACATTCTTCTATTTATTCCTGTATCATTATTCGCATTTTTCTGGTACAGGAAGCGAGCA
GATATTAAATATTTTTGTACACTTTTTAAAAATTCCATTATATTGAGCCTTGATAATGAA
GATAAGAAAACATTGATGATGACAAATAGAAAAAAATCTCTTACTTCTGGAGGCATAATT
GATGAATATCAGTATGATGTATTTGTTTCTTATTCTGATAAAGACCGTTCTTGGGTGCTT
GATGAGTTGATTCCAAATATTGAAAAGAGAGCTGAAATCAATATATGTCTACATGAAAGA
GATTTTCAGGTTGGATTAAGCATTCTCGAAAATATTATACAATGCATGGACAGAAGTCGC
TGTCTATTACTAGTTGTTTCAGAATCGTTTCTAAAGTCGAATTGGTGTGCTTTTGAAATG
CATTTGGCACAACACAGATTAATTGAAACTCGAAGAGAACAATTGATACTCGTGCTTTTG
CAAGACATTCCTCGTTCAAAAAGAACTCGAACACTACAATTTTTAATGAGAACAAAAACG
TATATTCAATGGCCGCACGATGATAAAGAAGAGTCAAAGTTGACTTTTTGGAAGCGTTTA
AGAAAAGCTATTATACTTAACAATTGGGAACCAGAAAAAAAAGTTAGTAAACCTCGTCAT
AGTATTGTTTAA
>g8289.t1 Gene=g8289 Length=863
MYLIKIMLCTLVLTITQLRCSVYCHPYGKNIDDVISKRNTSLFDDKTQIVIIDENVNTFL
PDNINVDDSAVNARESPETSKEALYQDLFNDYGSSYSLYDPGDDEPECILARSEFYLSWW
VHENGSLRLPSFNRLNTSGILDLSLQFDSETTLFNHVLNFTSDNPHEVIRFMSVASNKLD
QIPASVLNLTSATIQYLSLAGNNFYGMFEYENTTFQNFTSFPLMSHLLELDLRSCHIRSL
SSDYFKNLPRLDKLFLSHNNFLIIEASAFAPLTKLRHLDLSYNTIPFEIENRIEGMILEE
FLFEKLEHLMFLDLSHSKLRRRSLLALKSLGHEMKQLSLCHTGIVSFPEGMLNNTSLNVL
DLSGNLENFKELAELEILDLGSNNINNWYERVFTENEKLRIVNLRSNNITFMREGMIRDF
YEIRYLAIGSNDYICACNLRDFIDRATRNALYHYCSERNKRSIEETLTWNNPEHQYNVFL
REFHMIVAYYEESYRNMILNSLNPVEVKMRSVSKNLNTGGLSSFSERDCYNFDSDEVTRM
NFNFLLLDYNENDYECLEEAYGYSTSRRVRFHDVESCYSDEKDTTEPYDGSSDDESNEEP
TDDPDNVTTDSSKISSTTTEGSKEDDFFRPIFAIFKMNYLYILLFIPVSLFAFFWYRKRA
DIKYFCTLFKNSIILSLDNEDKKTLMMTNRKKSLTSGGIIDEYQYDVFVSYSDKDRSWVL
DELIPNIEKRAEINICLHERDFQVGLSILENIIQCMDRSRCLLLVVSESFLKSNWCAFEM
HLAQHRLIETRREQLILVLLQDIPRSKRTRTLQFLMRTKTYIQWPHDDKEESKLTFWKRL
RKAIILNNWEPEKKVSKPRHSIV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 18 | g8289.t1 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 122 | 293 | 4.0E-18 |
| 17 | g8289.t1 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 294 | 368 | 1.7E-6 |
| 16 | g8289.t1 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 369 | 503 | 4.1E-14 |
| 15 | g8289.t1 | Gene3D | G3DSA:3.40.50.10140 | - | 699 | 848 | 3.3E-48 |
| 34 | g8289.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 580 | 618 | - |
| 33 | g8289.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 587 | 605 | - |
| 4 | g8289.t1 | PANTHER | PTHR24365:SF530 | MSTPROX-RELATED | 160 | 286 | 5.7E-78 |
| 6 | g8289.t1 | PANTHER | PTHR24365 | TOLL-LIKE RECEPTOR | 160 | 286 | 5.7E-78 |
| 5 | g8289.t1 | PANTHER | PTHR24365:SF530 | MSTPROX-RELATED | 294 | 844 | 5.7E-78 |
| 7 | g8289.t1 | PANTHER | PTHR24365 | TOLL-LIKE RECEPTOR | 294 | 844 | 5.7E-78 |
| 9 | g8289.t1 | PRINTS | PR01537 | Interleukin-1 receptor type I family signature | 700 | 714 | 1.3E-5 |
| 10 | g8289.t1 | PRINTS | PR01537 | Interleukin-1 receptor type I family signature | 741 | 768 | 1.3E-5 |
| 11 | g8289.t1 | PRINTS | PR01537 | Interleukin-1 receptor type I family signature | 779 | 804 | 1.3E-5 |
| 8 | g8289.t1 | PRINTS | PR01537 | Interleukin-1 receptor type I family signature | 829 | 848 | 1.3E-5 |
| 2 | g8289.t1 | Pfam | PF13855 | Leucine rich repeat | 226 | 285 | 1.8E-13 |
| 1 | g8289.t1 | Pfam | PF13855 | Leucine rich repeat | 374 | 432 | 3.8E-7 |
| 3 | g8289.t1 | Pfam | PF01582 | TIR domain | 705 | 852 | 9.5E-22 |
| 21 | g8289.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 24 | - |
| 22 | g8289.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 7 | - |
| 23 | g8289.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 8 | 16 | - |
| 25 | g8289.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 17 | 24 | - |
| 20 | g8289.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 25 | 638 | - |
| 24 | g8289.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 639 | 656 | - |
| 19 | g8289.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 657 | 863 | - |
| 35 | g8289.t1 | ProSiteProfiles | PS50104 | TIR domain profile. | 703 | 847 | 30.333 |
| 27 | g8289.t1 | SMART | SM00369 | LRR_typ_2 | 224 | 247 | 6.8 |
| 29 | g8289.t1 | SMART | SM00369 | LRR_typ_2 | 248 | 271 | 2.7 |
| 30 | g8289.t1 | SMART | SM00369 | LRR_typ_2 | 272 | 296 | 46.0 |
| 31 | g8289.t1 | SMART | SM00369 | LRR_typ_2 | 372 | 395 | 15.0 |
| 28 | g8289.t1 | SMART | SM00369 | LRR_typ_2 | 397 | 419 | 160.0 |
| 32 | g8289.t1 | SMART | SM00255 | till_3 | 704 | 847 | 9.3E-24 |
| 13 | g8289.t1 | SUPERFAMILY | SSF52058 | L domain-like | 170 | 441 | 1.09E-29 |
| 12 | g8289.t1 | SUPERFAMILY | SSF52200 | Toll/Interleukin receptor TIR domain | 696 | 845 | 9.68E-42 |
| 14 | g8289.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 24 | - |
| 26 | g8289.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 637 | 656 | - |
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
- This transcript has been annotated with K10169 (toll-like receptor 6)
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