General information for g16488.t3
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 g16488 is located on chr_4: 9677220..9678997 (+ 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 | g16488 | g16488.t3 | TSS | g16488.t3 | 9677196 | 9677196 |
| chr_4 | g16488 | g16488.t3 | isoform | g16488.t3 | 9677220 | 9678997 |
| chr_4 | g16488 | g16488.t3 | exon | g16488.t3.exon1 | 9677220 | 9678402 |
| chr_4 | g16488 | g16488.t3 | cds | g16488.t3.CDS1 | 9677220 | 9678402 |
| chr_4 | g16488 | g16488.t3 | exon | g16488.t3.exon2 | 9678527 | 9678997 |
| chr_4 | g16488 | g16488.t3 | cds | g16488.t3.CDS2 | 9678527 | 9678897 |
| chr_4 | g16488 | g16488.t3 | TTS | g16488.t3 | 9679067 | 9679067 |
Sequences
>g16488.t3 Gene=g16488 Length=1654
ATGAAGTTAATTTTTATATTTCTTGCTTTAATTTGTTTATCAAAAGCGCAAATAGTGTCA
ATATCATGTGAATTTACACCAATGACAATCAATAACAACCAAGAATATGGTTGTTGGCTG
ACTATTTCGAATTCAATTGGTTTTGATAATTTTCTGATAATCAATGGCGCTCATACTTTT
GGTTTTTCCAATGAAAACGTCACAATTTTACTACGTGAAGCTGGAACAACTTCAATTGTT
CCTCGTATAATTTGCGATCGATTTCCCAATCTAAAATGGGCAGAATTTTCAAATTATAGA
ATTTCCTCACTCAGTGAAACTTCATTTGGTGGCTGTGAAAGTCTAGAAGTGATTGAATTA
AATCAAAATTCAATAACCGAAATAACTGACAGAATATTTGAAAGAAATTCAAATTTGATT
AATTTAGATTTATCAGGAAATTTAATTACAAGTTTAAGTTCGTCAGTTTTTCAAAATAAT
CAAAATTTAGAGACAGTTAATTTTGCTAACAATCGTTTGACTTCACTTCCAAATGAAATT
TTTGACAATTTAACTCGACTTAGAATTTTAAATCTTCAAACTAATCAAATTACAAGTCTT
GAAAATGTTTTTGGTTCTCTTCCATCACTTGAGCGACTTTATTTGTATGAAAATAATTTG
ACAGTTCTTGCAGCTGATAGTTTTGGTATAATGGAAAATTTAATTTATCTCGATTTGAGT
TCAAATCCATTGATAAATATTGAAAATGGCGCATTTAGATCACTTGGAAATCTTGAATAT
TTCTACGCAATTGCTTGTCAACTTCGTAATTTAAACTCTGATTCATTTGAAGGCCTAACT
GGACTTTTGACATTAAATTTGAATTTTAATGAACTTGAAAATTTACCAACTGGAATTTTC
CGACATTTTGAGAGATTATTTTATTTAAGTTTATGGGGAAATCGATTGAAAACATTAAAA
AGAGATCAATTTGGTGATTTAAGTTTTTTAACAAGTGCTGATTTTGATAATAATGTGATT
AATGCAATTGAAAGAAATGTCATTGAAGATGCAACAAATTTAAATGCTTTGCTGCTTAGT
GAAAATCTTTGTGCTAGTGGAATTTTCAGTAATTTTTCTGCCAATCGAGTTCAACATATG
GAAAGACTTCAGAGATGTTTTAGGAATTTTGAGCTTTCAATTGAAACTACAACCGACAAC
AATGCAAATTATGAATATCATTCAGCACCTGAACCTGGAATTCAATTTCGTGTCTTAACT
GACAACATTATTCATATTGCTTTATCACCATCGAATACAACTCAACAACCTCTAGTTGAA
ATTTTCATTGGAACTGCCAATAACACAAGATCATCAATCAGGTGGAATCAAGAACAAGAA
GTTGCACTTGTTCCTACTCCAGAAATCATCAGAGTTGGTCAATGGAATGGTTTTAGAATT
TCGTGGGCTAATCATGTTGTACTTGTGTCAAGAGAAGGTGAACAATTTCCATTTATGGTT
TTTACAATTGCTGAAACTTTTGATGTTAATTTCTTTGGATTAAGAACACCGTGAGTTCTA
AAATTTCTTAAAAATAAAATACAATTACTTAGGTTTTTTTAATTTTTTTAGTGAATCAAG
AGGTGAATGGAGCATACAACCAGTTGACTTATAG
>g16488.t3 Gene=g16488 Length=517
MKLIFIFLALICLSKAQIVSISCEFTPMTINNNQEYGCWLTISNSIGFDNFLIINGAHTF
GFSNENVTILLREAGTTSIVPRIICDRFPNLKWAEFSNYRISSLSETSFGGCESLEVIEL
NQNSITEITDRIFERNSNLINLDLSGNLITSLSSSVFQNNQNLETVNFANNRLTSLPNEI
FDNLTRLRILNLQTNQITSLENVFGSLPSLERLYLYENNLTVLAADSFGIMENLIYLDLS
SNPLINIENGAFRSLGNLEYFYAIACQLRNLNSDSFEGLTGLLTLNLNFNELENLPTGIF
RHFERLFYLSLWGNRLKTLKRDQFGDLSFLTSADFDNNVINAIERNVIEDATNLNALLLS
ENLCASGIFSNFSANRVQHMERLQRCFRNFELSIETTTDNNANYEYHSAPEPGIQFRVLT
DNIIHIALSPSNTTQQPLVEIFIGTANNTRSSIRWNQEQEVALVPTPEIIRVGQWNGFRI
SWANHVVLVSREGEQFPFMVFTIAETFDVNFFGLRTP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g16488.t3 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 19 | 202 | 3.0E-30 |
| 12 | g16488.t3 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 203 | 389 | 9.0E-33 |
| 7 | g16488.t3 | PANTHER | PTHR45617 | - | 86 | 204 | 8.6E-62 |
| 5 | g16488.t3 | PANTHER | PTHR45617 | - | 132 | 277 | 8.6E-62 |
| 6 | g16488.t3 | PANTHER | PTHR45617 | - | 202 | 440 | 8.6E-62 |
| 3 | g16488.t3 | Pfam | PF13306 | BspA type Leucine rich repeat region (6 copies) | 90 | 204 | 1.2E-12 |
| 2 | g16488.t3 | Pfam | PF13855 | Leucine rich repeat | 208 | 262 | 4.9E-11 |
| 1 | g16488.t3 | Pfam | PF13855 | Leucine rich repeat | 267 | 316 | 2.4E-7 |
| 4 | g16488.t3 | Pfam | PF12248 | Farnesoic acid 0-methyl transferase | 425 | 516 | 3.5E-17 |
| 14 | g16488.t3 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 16 | - |
| 15 | g16488.t3 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 16 | g16488.t3 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 11 | - |
| 17 | g16488.t3 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 12 | 16 | - |
| 13 | g16488.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 17 | 517 | - |
| 32 | g16488.t3 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 114 | 135 | 6.426 |
| 29 | g16488.t3 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 138 | 159 | 8.259 |
| 30 | g16488.t3 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 162 | 183 | 7.304 |
| 35 | g16488.t3 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 186 | 207 | 7.904 |
| 31 | g16488.t3 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 209 | 230 | 5.802 |
| 28 | g16488.t3 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 233 | 254 | 7.673 |
| 33 | g16488.t3 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 281 | 302 | 6.249 |
| 34 | g16488.t3 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 305 | 326 | 4.963 |
| 23 | g16488.t3 | SMART | SM00369 | LRR_typ_2 | 112 | 135 | 37.0 |
| 22 | g16488.t3 | SMART | SM00369 | LRR_typ_2 | 137 | 159 | 7.4 |
| 25 | g16488.t3 | SMART | SM00369 | LRR_typ_2 | 161 | 183 | 5.1 |
| 21 | g16488.t3 | SMART | SM00369 | LRR_typ_2 | 184 | 206 | 0.33 |
| 20 | g16488.t3 | SMART | SM00369 | LRR_typ_2 | 207 | 230 | 0.068 |
| 19 | g16488.t3 | SMART | SM00369 | LRR_typ_2 | 231 | 254 | 0.71 |
| 24 | g16488.t3 | SMART | SM00369 | LRR_typ_2 | 255 | 278 | 120.0 |
| 26 | g16488.t3 | SMART | SM00369 | LRR_typ_2 | 279 | 302 | 0.003 |
| 27 | g16488.t3 | SMART | SM00369 | LRR_typ_2 | 303 | 326 | 42.0 |
| 8 | g16488.t3 | SUPERFAMILY | SSF52058 | L domain-like | 53 | 366 | 8.28E-49 |
| 10 | g16488.t3 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 16 | - |
| 18 | g16488.t3 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
| 9 | g16488.t3 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 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