General information for g16495.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Leucine-rich repeat-containing protein 15.
Parent gene
- The parent gene g16495 is located on chr_4: 9704375..9706081 (- 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 | g16495 | g16495.t1 | isoform | g16495.t1 | 9704375 | 9706081 |
| chr_4 | g16495 | g16495.t1 | exon | g16495.t1.exon1 | 9704375 | 9705402 |
| chr_4 | g16495 | g16495.t1 | cds | g16495.t1.CDS1 | 9704375 | 9705402 |
| chr_4 | g16495 | g16495.t1 | exon | g16495.t1.exon2 | 9705465 | 9705599 |
| chr_4 | g16495 | g16495.t1 | cds | g16495.t1.CDS2 | 9705465 | 9705599 |
| chr_4 | g16495 | g16495.t1 | exon | g16495.t1.exon3 | 9706015 | 9706081 |
| chr_4 | g16495 | g16495.t1 | cds | g16495.t1.CDS3 | 9706015 | 9706081 |
| chr_4 | g16495 | g16495.t1 | TSS | g16495.t1 | NA | NA |
| chr_4 | g16495 | g16495.t1 | TTS | g16495.t1 | NA | NA |
Sequences
>g16495.t1 Gene=g16495 Length=1230
ATGAAATCAGTTAATTTTGTAATTTATACTTCCATTGTTTTTGGAATTTTAATAAAAACT
TCAAAAGGTCAAAGTAATTCAAATCACTCTCAAAATGAACTTTGTGGATTAAAAGAAGAT
TGTAAGAAAAATAATCATCATGAAGGTTTTAAATGTCAACTTGGCTTCAGATTTGTGCAT
AATCAATGTGAAGAAAATCCAAATCAAATTGATGGAAAATTTGAAGTTCAAAAATGTAAA
AGTTTTTTTTTCTATAACTGTTCAAATGTTCTATTGACATTTCTACCGGAAAATGGATTA
AAAATTACAACATTTGACACTGAAATTTCATCAAAATATAAAAATGATTCTGTTAGTAGA
TTTAGAATTGAATTAGATGGTAATTGCGTCAATTGCAGGAATAAAAATGTAATTTATCTT
CCAATTAGAATAGCAGAAACGTTTCCAAATTTATCTGAATATTTTGCAAATCGACTTGAT
GTGAAAATATTAAAATATGAAAACTTTAAAAATATGAAAAATTTGAAAAAATTAACAATT
GATAACAATGAAATTGAAACAATTGACGAAAATTCTTTTGATGACTTAAATGAATTAGTT
TTTTTAGATTTAAGCCAAAATAAAATAAAAAACTTTGATCCAAGAATTTTTAAATCAACT
TTGAAGCTGACTTATTTAAATTTAAGTTTAAACCAAATAATTTCATTAATTGCAGACCAT
TTAAAATTTCTCTCTAAGCTGAAGTTTTTAGATTTGTCTTATAATAAAATTACAAATTTA
AATTCAAATGTTTTCGAAAACTCAAAAAATCTAGAAAATTTACGTTTAAATTCCAATCAA
ATCAAAAACCTTCCACTTGGAATTTTTGATAAAACCGAGAATTTAAAAGAAATAATTTTG
TCAAGCAATGAATTGACAACATTAAATTCTGATATTTTTAATAATTTGATCAATCTTAAA
TTCATTTCGTTGAGTTACAATAAATTTACAACACTTGATGAAAATTTATTTAAAAATAAT
AAAAATCTAGAGAGCATCATTTTACATGGTAACGATTTTTCATATTTACCTTGGAAATTG
TTTGAAGATAAAACTAATTTGACAAATTTTTATATAAAACTCAATAAATTTAATGAAAAA
CTTTATGTTGGTAGTAAAATACTTACAGAAGATGAAAGAAATGAGATAAAAAATGACCTG
AAGAAATATTTAGGAAATGGATTGAAATAA
>g16495.t1 Gene=g16495 Length=409
MKSVNFVIYTSIVFGILIKTSKGQSNSNHSQNELCGLKEDCKKNNHHEGFKCQLGFRFVH
NQCEENPNQIDGKFEVQKCKSFFFYNCSNVLLTFLPENGLKITTFDTEISSKYKNDSVSR
FRIELDGNCVNCRNKNVIYLPIRIAETFPNLSEYFANRLDVKILKYENFKNMKNLKKLTI
DNNEIETIDENSFDDLNELVFLDLSQNKIKNFDPRIFKSTLKLTYLNLSLNQIISLIADH
LKFLSKLKFLDLSYNKITNLNSNVFENSKNLENLRLNSNQIKNLPLGIFDKTENLKEIIL
SSNELTTLNSDIFNNLINLKFISLSYNKFTTLDENLFKNNKNLESIILHGNDFSYLPWKL
FEDKTNLTNFYIKLNKFNEKLYVGSKILTEDERNEIKNDLKKYLGNGLK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g16495.t1 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 125 | 248 | 1.5E-20 |
| 12 | g16495.t1 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 249 | 400 | 3.0E-29 |
| 5 | g16495.t1 | PANTHER | PTHR46473 | GH08155P | 127 | 233 | 5.9E-44 |
| 6 | g16495.t1 | PANTHER | PTHR46473 | GH08155P | 222 | 353 | 5.9E-44 |
| 4 | g16495.t1 | PANTHER | PTHR46473 | GH08155P | 276 | 378 | 5.9E-44 |
| 8 | g16495.t1 | PRINTS | PR00019 | Leucine-rich repeat signature | 199 | 212 | 5.7E-5 |
| 7 | g16495.t1 | PRINTS | PR00019 | Leucine-rich repeat signature | 244 | 257 | 5.7E-5 |
| 2 | g16495.t1 | Pfam | PF13855 | Leucine rich repeat | 167 | 209 | 6.5E-11 |
| 3 | g16495.t1 | Pfam | PF13855 | Leucine rich repeat | 222 | 281 | 1.6E-8 |
| 1 | g16495.t1 | Pfam | PF13855 | Leucine rich repeat | 294 | 353 | 2.0E-10 |
| 15 | g16495.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 23 | - |
| 16 | g16495.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 6 | - |
| 17 | g16495.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 7 | 18 | - |
| 18 | g16495.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 19 | 23 | - |
| 14 | g16495.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 24 | 409 | - |
| 32 | g16495.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 174 | 195 | 6.849 |
| 30 | g16495.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 198 | 219 | 6.811 |
| 27 | g16495.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 222 | 245 | 6.834 |
| 31 | g16495.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 246 | 267 | 8.058 |
| 29 | g16495.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 270 | 291 | 7.196 |
| 26 | g16495.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 294 | 315 | 6.434 |
| 28 | g16495.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 318 | 339 | 6.326 |
| 33 | g16495.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 342 | 363 | 4.816 |
| 24 | g16495.t1 | SMART | SM00369 | LRR_typ_2 | 172 | 195 | 0.8 |
| 25 | g16495.t1 | SMART | SM00369 | LRR_typ_2 | 196 | 219 | 2.3 |
| 23 | g16495.t1 | SMART | SM00369 | LRR_typ_2 | 244 | 267 | 0.0043 |
| 20 | g16495.t1 | SMART | SM00369 | LRR_typ_2 | 269 | 291 | 6.2 |
| 22 | g16495.t1 | SMART | SM00369 | LRR_typ_2 | 292 | 315 | 17.0 |
| 21 | g16495.t1 | SMART | SM00369 | LRR_typ_2 | 316 | 339 | 0.075 |
| 19 | g16495.t1 | SMART | SM00369 | LRR_typ_2 | 341 | 363 | 170.0 |
| 9 | g16495.t1 | SUPERFAMILY | SSF52058 | L domain-like | 128 | 379 | 4.85E-43 |
| 11 | g16495.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 23 | - |
| 10 | g16495.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 23 | - |
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