General information for g16486.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Toll-like receptor Tollo.
Parent gene
- The parent gene g16486 is located on chr_4: 9672686..9673938 (- 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 | g16486 | g16486.t1 | TTS | g16486.t1 | 9671993 | 9671993 |
| chr_4 | g16486 | g16486.t1 | isoform | g16486.t1 | 9672073 | 9673938 |
| chr_4 | g16486 | g16486.t1 | exon | g16486.t1.exon1 | 9672073 | 9672151 |
| chr_4 | g16486 | g16486.t1 | cds | g16486.t1.CDS1 | 9672073 | 9672151 |
| chr_4 | g16486 | g16486.t1 | exon | g16486.t1.exon2 | 9672209 | 9672578 |
| chr_4 | g16486 | g16486.t1 | cds | g16486.t1.CDS2 | 9672209 | 9672578 |
| chr_4 | g16486 | g16486.t1 | exon | g16486.t1.exon3 | 9672680 | 9673615 |
| chr_4 | g16486 | g16486.t1 | cds | g16486.t1.CDS3 | 9672680 | 9673615 |
| chr_4 | g16486 | g16486.t1 | exon | g16486.t1.exon4 | 9673758 | 9673938 |
| chr_4 | g16486 | g16486.t1 | cds | g16486.t1.CDS4 | 9673758 | 9673938 |
| chr_4 | g16486 | g16486.t1 | TSS | g16486.t1 | 9673961 | 9673961 |
Sequences
>g16486.t1 Gene=g16486 Length=1566
ATGAAGTTTGCAGTTGGAATTTTTATTCTTTCACTTTTTGGTTCTTCTTTTGCTCAATCT
ATTGATTGTGTTTATTCAACTACAGTTATTAATAATGTTCAACATTATGCTTGTAATTTA
GAAATTGAAAATCCAAATGGTTTTGATGAATTCCAGGAAATTATAGGCACGCATTTAGAA
GGTCGAACAAATGCTGATGTCACTTATATTTCTCATTATCATGGTTCAACAACAATCGTC
CCACAAATCATTTGTAGCCAATTTCCCAACCTCGAAATTATTGATTTTGATGGTTTTGGT
GTCAGAACTTTAACTGATACTTCATTTGGTGGCTGTCGAAATGCAAGATCAATAAATTTA
TTCACAAATCAAATCAGTGAAATTTCAGAAAACGCTTTTGCAAATAATCCAAATTTGACT
TTTATCGATCTCAGTGGAAATCAATTGCGAACTCTTCATGTAAATTTATTTGTTAATCAA
CAACAACTTGATATGCTTGAACTTAACAATAATTCATTTACTGAAAATTTCCCTGCAGGA
CTTTTTAGAAATTTAGTCAATTTGAGGATGCTTTTATTGAATGAATGCAGATTAACAGCA
ATAAACCCAAATTGGTTCACAAATCTTGGAAATTTATTCATGTTGAATATGTTCAGAAAT
GAAATTCTTGAAATTAATGAAGATGCATTTGTTGGACTTGAAAATTTGAATATTTTGAAT
TTAAATCATAATTTTATTCAAACAATTCATCCAAATGCTTTCAGTTCACTTGGCAATCTT
CGTGTGATTTATATGGAAGACAACCAAATTTCTGAACTTCCTATTGGTGTTTTTGCTCCA
TTTACTGCAATAAGCTATGTTGATTTGAGACTAAATAGAATCAAAACTGTAAATAGAGAC
ATTTTTGGATCATTGAGTGCTTTAGGAACACTTGACTTAGATTTTAATGTTGTTAATGCA
ATGGATGAAAGAATTTTTAGAGAAGCTGATGCTCTTTATCTTTTCTATTTTGGAAATAAC
TTGTGTGCAAGCGGATTTTTCAATAACTTTGTTGGAAATCGTGATTTTTATATTGGAAGA
TTGTCAAGATGCTTTAGAAATTTTGAATTTACTGTTGAAATAACAACAGAAAGTGACAAT
CCAAACTATCAATTTTTCTCTGGTCCTGCACCTGGAATTCAATTGCGTGTAATGACAGCA
AATGAAGTTCACATTGCATTGACACCATTCAATTTTCCATGGACACCAATGATTGAAATT
ATTATTGGTGCAGCAAACAACACACGATCAATTGTTAGACGCAATCAAGAAACTGATGTA
GCTGTTGTACCAACACCAGGAATTTTGAATGAAAACTTTTGGAATGGATTTAGAATTACT
TGGGCAAATCATATTGTGCTGATATTTAGAGAAGGTGATCAATTTCCTTTCCTAGCTTTC
ACTATGATGGACTTTTTCAATGTAAACTTTTATGGATTAAGAACACCTGAAAACAGAGCT
TCATGGGTTATTCAACCAGTTGATGCTGATGAAATTGGTGTATCTCCTGCTGCTCTTTCA
AATTAA
>g16486.t1 Gene=g16486 Length=521
MKFAVGIFILSLFGSSFAQSIDCVYSTTVINNVQHYACNLEIENPNGFDEFQEIIGTHLE
GRTNADVTYISHYHGSTTIVPQIICSQFPNLEIIDFDGFGVRTLTDTSFGGCRNARSINL
FTNQISEISENAFANNPNLTFIDLSGNQLRTLHVNLFVNQQQLDMLELNNNSFTENFPAG
LFRNLVNLRMLLLNECRLTAINPNWFTNLGNLFMLNMFRNEILEINEDAFVGLENLNILN
LNHNFIQTIHPNAFSSLGNLRVIYMEDNQISELPIGVFAPFTAISYVDLRLNRIKTVNRD
IFGSLSALGTLDLDFNVVNAMDERIFREADALYLFYFGNNLCASGFFNNFVGNRDFYIGR
LSRCFRNFEFTVEITTESDNPNYQFFSGPAPGIQLRVMTANEVHIALTPFNFPWTPMIEI
IIGAANNTRSIVRRNQETDVAVVPTPGILNENFWNGFRITWANHIVLIFREGDQFPFLAF
TMMDFFNVNFYGLRTPENRASWVIQPVDADEIGVSPAALSN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g16486.t1 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 26 | 213 | 3.2E-28 |
| 9 | g16486.t1 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 214 | 363 | 3.3E-25 |
| 5 | g16486.t1 | PANTHER | PTHR24373 | SLIT RELATED LEUCINE-RICH REPEAT NEURONAL PROTEIN | 80 | 244 | 4.5E-47 |
| 4 | g16486.t1 | PANTHER | PTHR24373 | SLIT RELATED LEUCINE-RICH REPEAT NEURONAL PROTEIN | 177 | 341 | 4.5E-47 |
| 2 | g16486.t1 | Pfam | PF13306 | BspA type Leucine rich repeat region (6 copies) | 90 | 209 | 6.1E-11 |
| 1 | g16486.t1 | Pfam | PF13855 | Leucine rich repeat | 219 | 270 | 2.0E-13 |
| 3 | g16486.t1 | Pfam | PF12248 | Farnesoic acid 0-methyl transferase | 404 | 495 | 2.3E-19 |
| 12 | g16486.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 18 | - |
| 13 | g16486.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 14 | g16486.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 13 | - |
| 15 | g16486.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 14 | 18 | - |
| 11 | g16486.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 19 | 521 | - |
| 27 | g16486.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 114 | 135 | 5.756 |
| 30 | g16486.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 138 | 159 | 6.58 |
| 26 | g16486.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 187 | 208 | 4.693 |
| 29 | g16486.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 211 | 232 | 5.425 |
| 25 | g16486.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 235 | 256 | 7.473 |
| 28 | g16486.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 259 | 280 | 6.403 |
| 18 | g16486.t1 | SMART | SM00369 | LRR_typ_2 | 116 | 135 | 250.0 |
| 20 | g16486.t1 | SMART | SM00369 | LRR_typ_2 | 137 | 159 | 3.2 |
| 21 | g16486.t1 | SMART | SM00369 | LRR_typ_2 | 185 | 208 | 4.6 |
| 17 | g16486.t1 | SMART | SM00369 | LRR_typ_2 | 209 | 232 | 39.0 |
| 22 | g16486.t1 | SMART | SM00369 | LRR_typ_2 | 233 | 256 | 0.0046 |
| 19 | g16486.t1 | SMART | SM00369 | LRR_typ_2 | 257 | 280 | 0.0061 |
| 24 | g16486.t1 | SMART | SM00369 | LRR_typ_2 | 281 | 304 | 220.0 |
| 23 | g16486.t1 | SMART | SM00369 | LRR_typ_2 | 305 | 328 | 18.0 |
| 6 | g16486.t1 | SUPERFAMILY | SSF52058 | L domain-like | 85 | 342 | 3.15E-46 |
| 8 | g16486.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
| 16 | g16486.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
| 7 | g16486.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 20 | - |
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