General information for g17250.t2
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.t2 | TTS | g17250.t2 | 12944227 | 12944227 |
| chr_4 | g17250 | g17250.t2 | isoform | g17250.t2 | 12944291 | 12945823 |
| chr_4 | g17250 | g17250.t2 | exon | g17250.t2.exon1 | 12944291 | 12945237 |
| chr_4 | g17250 | g17250.t2 | cds | g17250.t2.CDS1 | 12944291 | 12945237 |
| chr_4 | g17250 | g17250.t2 | exon | g17250.t2.exon2 | 12945308 | 12945429 |
| chr_4 | g17250 | g17250.t2 | cds | g17250.t2.CDS2 | 12945308 | 12945422 |
| chr_4 | g17250 | g17250.t2 | exon | g17250.t2.exon3 | 12945652 | 12945823 |
| chr_4 | g17250 | g17250.t2 | TSS | g17250.t2 | 12945864 | 12945864 |
Sequences
>g17250.t2 Gene=g17250 Length=1241
ATAATTATTTAATTTGGTAATTTTCATTCTGTGGTTCTTCAATATTTTAAATTGTTATTA
ATACTTATGAGACTGATATTTTAAACTAGCGAGAGTAGTTTGCTTTGCAGCCCTTTCTTG
TCTAGAAATATTTATACCCATCATTTTCTAACGTAAACGTAAGACATAAAACATTAAAAA
TGAAATCATTTTGTTTACTTCTTTTAATTTTAACAATTTTTTTGATTGATTTAACTGAAT
CAAACAATTTGTATCAACAAAAATTCGATAATGAAAAAGATCAAGCTACAATAAATCTCA
TTGACGGCGAAATGACAGAAGGAAGTTGTTTTCAATATTTACAATGTGAAAATGAAAATG
AAAAAAAATTAAAGCAATTCAAAGTTAATGAAAATACAAAAATTCTTACAAATGATGCAA
AAATAATGCAAAAGCATAAAAGTAATGAAATTGAATGGTTTGAAATTTATTTTGTCATAA
CAATGGAAATTTTTTATTTTCCAATCAATGTTAATGAAATTTTTCCAAATTTACTTGTTT
TTTATGTTTCGAATACTAAAATTAAAATGTTAAATTATGAAAATTTTAAGGATATGAAAA
AACTTCTTGAATTGACACTTTCTTATAATCAAATTGAAGAAATTAATGAAGACACTTTTG
ATGATTTACAAGAATTAAAAATTTTAGACTTAAGAGGGAATAAATTGAAAATTTTAAATT
CAAGAACTTTCAACAATATTTCGAATTTGAAAGTTTTATCTTTACAAGAAAATGAAATTT
CATCAATTATGGGACAATTTGGAAATTTAAAAAATTTGTCTACTTTAGATTTGTACGAAA
ATCAATTGGTTTCGATTCCATCAAATATTTTTGAAAATTTAAGTAACCTTCAATTTTTAG
ATTTATCTAAGAACAAACTCACAAATCTACCAAATGAAATTTTTGAAAAAATAAGCAACC
TCAAATATCTTGAACTTTATCGTAATCAATTGCAAACACTCGATGAAAATATTTTTAAAA
ATAATCACAAACTTGATGGAATTGACTTAAGTTTTAACAAAATTACAAAATTGAGTTTCA
AAATTTTTGAAGAAAAAATTATTTTGTATTATGTAAATTTAGAAAGAAATTTATGCACAA
ATTTATTACTTGGTGAATATTTATATGATGACAATGTTAATCCATTAACTGACGAAGATA
AAAACAAATTAAAAAATGAACTAGAAAAAAATTGTTCATAA
>g17250.t2 Gene=g17250 Length=353
MKSFCLLLLILTIFLIDLTESNNLYQQKFDNEKDQATINLIDGEMTEGSCFQYLQCENEN
EKKLKQFKVNENTKILTNDAKIMQKHKSNEIEWFEIYFVITMEIFYFPINVNEIFPNLLV
FYVSNTKIKMLNYENFKDMKKLLELTLSYNQIEEINEDTFDDLQELKILDLRGNKLKILN
SRTFNNISNLKVLSLQENEISSIMGQFGNLKNLSTLDLYENQLVSIPSNIFENLSNLQFL
DLSKNKLTNLPNEIFEKISNLKYLELYRNQLQTLDENIFKNNHKLDGIDLSFNKITKLSF
KIFEEKIILYYVNLERNLCTNLLLGEYLYDDNVNPLTDEDKNKLKNELEKNCS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g17250.t2 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 52 | 351 | 6.7E-49 |
| 3 | g17250.t2 | PANTHER | PTHR46473:SF10 | GH08155P | 124 | 250 | 4.7E-41 |
| 5 | g17250.t2 | PANTHER | PTHR46473 | GH08155P | 124 | 250 | 4.7E-41 |
| 4 | g17250.t2 | PANTHER | PTHR46473:SF10 | GH08155P | 210 | 329 | 4.7E-41 |
| 6 | g17250.t2 | PANTHER | PTHR46473 | GH08155P | 210 | 329 | 4.7E-41 |
| 8 | g17250.t2 | PRINTS | PR00019 | Leucine-rich repeat signature | 213 | 226 | 6.1E-5 |
| 7 | g17250.t2 | PRINTS | PR00019 | Leucine-rich repeat signature | 234 | 247 | 6.1E-5 |
| 1 | g17250.t2 | Pfam | PF13855 | Leucine rich repeat | 116 | 176 | 3.4E-13 |
| 2 | g17250.t2 | Pfam | PF13855 | Leucine rich repeat | 235 | 295 | 4.6E-11 |
| 13 | g17250.t2 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 21 | - |
| 14 | g17250.t2 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 15 | g17250.t2 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 16 | - |
| 16 | g17250.t2 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 17 | 21 | - |
| 12 | g17250.t2 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 22 | 353 | - |
| 33 | g17250.t2 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 141 | 162 | 7.042 |
| 35 | g17250.t2 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 165 | 186 | 6.026 |
| 32 | g17250.t2 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 189 | 211 | 7.019 |
| 31 | g17250.t2 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 212 | 233 | 7.689 |
| 34 | g17250.t2 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 236 | 257 | 8.898 |
| 30 | g17250.t2 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 260 | 281 | 6.68 |
| 29 | g17250.t2 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 284 | 305 | 6.372 |
| 17 | g17250.t2 | SMART | SM00369 | LRR_typ_2 | 139 | 162 | 0.14 |
| 26 | g17250.t2 | SMART | SM00365 | LRR_sd22_2 | 139 | 157 | 410.0 |
| 19 | g17250.t2 | SMART | SM00369 | LRR_typ_2 | 163 | 186 | 0.16 |
| 27 | g17250.t2 | SMART | SM00365 | LRR_sd22_2 | 163 | 189 | 32.0 |
| 22 | g17250.t2 | SMART | SM00369 | LRR_typ_2 | 187 | 209 | 39.0 |
| 20 | g17250.t2 | SMART | SM00369 | LRR_typ_2 | 210 | 233 | 3.7E-4 |
| 28 | g17250.t2 | SMART | SM00365 | LRR_sd22_2 | 210 | 232 | 140.0 |
| 18 | g17250.t2 | SMART | SM00369 | LRR_typ_2 | 234 | 257 | 1.2E-4 |
| 23 | g17250.t2 | SMART | SM00365 | LRR_sd22_2 | 234 | 252 | 72.0 |
| 21 | g17250.t2 | SMART | SM00369 | LRR_typ_2 | 258 | 281 | 0.16 |
| 25 | g17250.t2 | SMART | SM00365 | LRR_sd22_2 | 258 | 280 | 320.0 |
| 24 | g17250.t2 | SMART | SM00365 | LRR_sd22_2 | 282 | 300 | 250.0 |
| 9 | g17250.t2 | SUPERFAMILY | SSF52058 | L domain-like | 103 | 317 | 1.09E-43 |
| 10 | g17250.t2 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 21 | - |
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