General information for g17250.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Toll-like receptor 7.
Parent gene
- The parent gene g17250 is located on chr_4: 12944291..12946128 (- 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_4 | g17250 | g17250.t3 | TTS | g17250.t3 | 12944227 | 12944227 |
| chr_4 | g17250 | g17250.t3 | isoform | g17250.t3 | 12944291 | 12945823 |
| chr_4 | g17250 | g17250.t3 | exon | g17250.t3.exon1 | 12944291 | 12945429 |
| chr_4 | g17250 | g17250.t3 | cds | g17250.t3.CDS1 | 12944291 | 12945220 |
| chr_4 | g17250 | g17250.t3 | exon | g17250.t3.exon2 | 12945808 | 12945823 |
| chr_4 | g17250 | g17250.t3 | TSS | g17250.t3 | 12945864 | 12945864 |
Sequences
>g17250.t3 Gene=g17250 Length=1155
ATAATTATTTAATTTGATTAAAAATGAAATCATTTTGTTTACTTCTTTTAATTTTAACAA
TTTTTTTGATTGATTTAACTGAATCAAACAATTTGTATCAACAAAAATTCGATAATGAAA
AAGATCAAGCTACAATAAGTAATTAAATAAAAAAAAGTTGAATTTTAAGTTTTTTTGGAC
TTTTCTAATTACAAATTTTATATTTTAGATCTCATTGACGGCGAAATGACAGAAGGAAGT
TGTTTTCAATATTTACAATGTGAAAATGAAAATGAAAAAAAATTAAAGCAATTCAAAGTT
AATGAAAATACAAAAATTCTTACAAATGATGCAAAAATAATGCAAAAGCATAAAAGTAAT
GAAATTGAATGGTTTGAAATTTATTTTGTCATAACAATGGAAATTTTTTATTTTCCAATC
AATGTTAATGAAATTTTTCCAAATTTACTTGTTTTTTATGTTTCGAATACTAAAATTAAA
ATGTTAAATTATGAAAATTTTAAGGATATGAAAAAACTTCTTGAATTGACACTTTCTTAT
AATCAAATTGAAGAAATTAATGAAGACACTTTTGATGATTTACAAGAATTAAAAATTTTA
GACTTAAGAGGGAATAAATTGAAAATTTTAAATTCAAGAACTTTCAACAATATTTCGAAT
TTGAAAGTTTTATCTTTACAAGAAAATGAAATTTCATCAATTATGGGACAATTTGGAAAT
TTAAAAAATTTGTCTACTTTAGATTTGTACGAAAATCAATTGGTTTCGATTCCATCAAAT
ATTTTTGAAAATTTAAGTAACCTTCAATTTTTAGATTTATCTAAGAACAAACTCACAAAT
CTACCAAATGAAATTTTTGAAAAAATAAGCAACCTCAAATATCTTGAACTTTATCGTAAT
CAATTGCAAACACTCGATGAAAATATTTTTAAAAATAATCACAAACTTGATGGAATTGAC
TTAAGTTTTAACAAAATTACAAAATTGAGTTTCAAAATTTTTGAAGAAAAAATTATTTTG
TATTATGTAAATTTAGAAAGAAATTTATGCACAAATTTATTACTTGGTGAATATTTATAT
GATGACAATGTTAATCCATTAACTGACGAAGATAAAAACAAATTAAAAAATGAACTAGAA
AAAAATTGTTCATAA
>g17250.t3 Gene=g17250 Length=309
MTEGSCFQYLQCENENEKKLKQFKVNENTKILTNDAKIMQKHKSNEIEWFEIYFVITMEI
FYFPINVNEIFPNLLVFYVSNTKIKMLNYENFKDMKKLLELTLSYNQIEEINEDTFDDLQ
ELKILDLRGNKLKILNSRTFNNISNLKVLSLQENEISSIMGQFGNLKNLSTLDLYENQLV
SIPSNIFENLSNLQFLDLSKNKLTNLPNEIFEKISNLKYLELYRNQLQTLDENIFKNNHK
LDGIDLSFNKITKLSFKIFEEKIILYYVNLERNLCTNLLLGEYLYDDNVNPLTDEDKNKL
KNELEKNCS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 24 | g17250.t3 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 9 | 307 | 0.000e+00 |
| 3 | g17250.t3 | PANTHER | PTHR45617:SF42 | LEUCINE RICH REPEAT CONTAINING G PROTEIN-COUPLED RECEPTOR 6 | 69 | 159 | 0.000e+00 |
| 6 | g17250.t3 | PANTHER | PTHR45617 | - | 69 | 159 | 0.000e+00 |
| 4 | g17250.t3 | PANTHER | PTHR45617:SF42 | LEUCINE RICH REPEAT CONTAINING G PROTEIN-COUPLED RECEPTOR 6 | 78 | 205 | 0.000e+00 |
| 7 | g17250.t3 | PANTHER | PTHR45617 | - | 78 | 205 | 0.000e+00 |
| 5 | g17250.t3 | PANTHER | PTHR45617:SF42 | LEUCINE RICH REPEAT CONTAINING G PROTEIN-COUPLED RECEPTOR 6 | 137 | 273 | 0.000e+00 |
| 8 | g17250.t3 | PANTHER | PTHR45617 | - | 137 | 273 | 0.000e+00 |
| 9 | g17250.t3 | PRINTS | PR00019 | Leucine-rich repeat signature | 169 | 182 | 4.900e-05 |
| 10 | g17250.t3 | PRINTS | PR00019 | Leucine-rich repeat signature | 190 | 203 | 4.900e-05 |
| 2 | g17250.t3 | Pfam | PF13855 | Leucine rich repeat | 72 | 132 | 0.000e+00 |
| 1 | g17250.t3 | Pfam | PF13855 | Leucine rich repeat | 191 | 251 | 0.000e+00 |
| 29 | g17250.t3 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 97 | 118 | 7.042e+00 |
| 26 | g17250.t3 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 121 | 142 | 6.026e+00 |
| 28 | g17250.t3 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 145 | 167 | 7.019e+00 |
| 25 | g17250.t3 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 168 | 189 | 7.689e+00 |
| 31 | g17250.t3 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 192 | 213 | 8.898e+00 |
| 30 | g17250.t3 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 216 | 237 | 6.680e+00 |
| 27 | g17250.t3 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 240 | 261 | 6.372e+00 |
| 14 | g17250.t3 | SMART | SM00369 | LRR_typ_2 | 95 | 118 | 1.400e-01 |
| 18 | g17250.t3 | SMART | SM00365 | LRR_sd22_2 | 95 | 113 | 4.100e+02 |
| 15 | g17250.t3 | SMART | SM00369 | LRR_typ_2 | 119 | 142 | 1.600e-01 |
| 20 | g17250.t3 | SMART | SM00365 | LRR_sd22_2 | 119 | 145 | 3.200e+01 |
| 16 | g17250.t3 | SMART | SM00369 | LRR_typ_2 | 143 | 165 | 3.900e+01 |
| 13 | g17250.t3 | SMART | SM00369 | LRR_typ_2 | 166 | 189 | 3.700e-04 |
| 23 | g17250.t3 | SMART | SM00365 | LRR_sd22_2 | 166 | 188 | 1.400e+02 |
| 17 | g17250.t3 | SMART | SM00369 | LRR_typ_2 | 190 | 213 | 1.200e-04 |
| 22 | g17250.t3 | SMART | SM00365 | LRR_sd22_2 | 190 | 208 | 7.200e+01 |
| 12 | g17250.t3 | SMART | SM00369 | LRR_typ_2 | 214 | 237 | 1.600e-01 |
| 19 | g17250.t3 | SMART | SM00365 | LRR_sd22_2 | 214 | 236 | 3.200e+02 |
| 21 | g17250.t3 | SMART | SM00365 | LRR_sd22_2 | 238 | 256 | 2.500e+02 |
| 11 | g17250.t3 | SUPERFAMILY | SSF52058 | L domain-like | 59 | 273 | 0.000e+00 |
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:0005515 | protein binding | MF |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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