General information for g16487.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 g16487 is located on chr_4: 9675936..9676467 (- 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 | g16487 | g16487.t1 | TTS | g16487.t1 | 9674142 | 9674142 |
| chr_4 | g16487 | g16487.t1 | isoform | g16487.t1 | 9674221 | 9676467 |
| chr_4 | g16487 | g16487.t1 | exon | g16487.t1.exon1 | 9674221 | 9674308 |
| chr_4 | g16487 | g16487.t1 | cds | g16487.t1.CDS1 | 9674221 | 9674308 |
| chr_4 | g16487 | g16487.t1 | exon | g16487.t1.exon2 | 9674372 | 9674738 |
| chr_4 | g16487 | g16487.t1 | cds | g16487.t1.CDS2 | 9674372 | 9674738 |
| chr_4 | g16487 | g16487.t1 | exon | g16487.t1.exon3 | 9674970 | 9675848 |
| chr_4 | g16487 | g16487.t1 | cds | g16487.t1.CDS3 | 9674970 | 9675848 |
| chr_4 | g16487 | g16487.t1 | exon | g16487.t1.exon4 | 9675933 | 9676467 |
| chr_4 | g16487 | g16487.t1 | cds | g16487.t1.CDS4 | 9675933 | 9676467 |
| chr_4 | g16487 | g16487.t1 | TSS | g16487.t1 | 9676496 | 9676496 |
Sequences
>g16487.t1 Gene=g16487 Length=1869
ATGAAATATTTTGCTGCTTTAATTTCTTTATTTTATATTTTAAATTCAGTGTCTGGACAA
GAATTTACTTGCGATTATAGAAATGGCACAATTAATTCTGTACCAGCTTACTATTGTTTA
TTGACAGCAAACAACCCAAATGGTGCTGAAAATATTACATCCATAGGTGGACAACATTTA
GAAGGTTTTACTGATGCTGACGTTTTTGGAGTTTTCAGTAGGGATGGAATTTCTACAAAT
GTTCCTACAGTCTTTTGTACACAATTTACAAACCTTGTTGAACTTGATTTATCTGGTCTG
AGAATTACAAATGTTGCTGCAAATTCATTTAATGCTTGCACAAATCTTCTTTGGCTTCGA
CTTTATTTCAATAATATTTCAAGTTTGCCAGCAAATGTATTTTCTAATACTCAAAGCTTG
GAATATTTAGATTTAGATACAAATCAATTGACAACATTGCCAGAGAACATTTTTGCTAAT
TTAGGACGATTAGACATGTTGGAATTGAGAAATAATCCTTTCCAAAATATTCCTGCTAGT
GTCTTCAATGGTCTGTCATTATTACAAACACTTTACCTTCAAAACACTCGTCTAACGGAA
ATTAATAATGCTTGGTTCCAAAGTCTTCCAAATCTTTCAACTCTCACAGTCTATGGCAAC
AATATCACATCAATTTCTGAGACAGCATTCAATGGTTTGTCACAACTTCGAGTTCTTGAA
ATCAGCAGAAACCCTCTTGGTCAAAATATTCATGTCAATGCATTTGCACCTTTGACAAAT
CTTCAAATTCTTTATATGTCAAATATCAATCTTAGTGTTATCAATCCACAACTATTTGCG
CCATTATCAAATCTTATAACACTTTATTTTTTTTGGAATAATATTGTGGAAATTCCAAGT
GGAACTTTTGATAATATGACAAATCTTTTTTCATTAGATATTGGTGGAAATTTGCTTGAT
GAAACATCAATTGCTGCTGATGCTTTTAGAAATTTACAAAATTTAGTTATTTTCTTCCTT
GATGACAATTACATTCAAAATTTAAATCCACAATGGTTTGCTAATCTCACAAATGTTGAA
GATTTATTCCTTGATTTTAATTTTATTGAAGATCTTCCAAATGGAATTTTCGCACCAATT
AGAGAACTCTGGCAAATTGGTTTATGGTTTAACGATTTAAAAACTATTAGAAGAAATGCT
TTTGGAAATTTAAATGGACTTTATGCAATTGATCTTGATCAAAATGTCATCAATGCTGTT
GATGAAAATTTCTTTAATGCATCATCAAATTTGTACATTATTTACTTCTTCCAAAACTTG
TGTGCAAGTATTTCAATTTATGGATTTAGTTTAAATAGAGAAAACAGCATGTCATGGTTT
AGACGATGTACTGAGAACTTTTTGTTTATTGTTGACGCTGAGACTGATGGAAATGAAAAT
TATGAATTCCATCCTGGACGTTCTCCTGGTATTCAAATGAGAGTTCAATCTAATGATGAA
GTTCATGTTGCATTAACACCTTTCAACTTCCCATGGACACCAATGATTGAAATTATCATC
GGTGCTGCAAACAACACAAGGTCAATCATTAGAAGAAATCAAGAAACTGATGTAGTTACA
GTTCCAACTCCAGGAATCATCAGAGCTGGTCAATGGAATGGATTTAGAATCACTTGGGCA
AATCATGCAATTCTTGTATGGAGAGAAGGTGAAGAATGGCCTTTCATGGGTTTCACAATG
ACTGACTTTTTTCCTGTCAATTTTTATGGATTAAGAGCACCATTAAGTCGAGCCTCTTGG
AGTGTTCAACCAGTTGATGGAATTGTTCCAACAATTGAAGAAAATTTAGAGTTGAATTTT
ATTAACTAG
>g16487.t1 Gene=g16487 Length=622
MKYFAALISLFYILNSVSGQEFTCDYRNGTINSVPAYYCLLTANNPNGAENITSIGGQHL
EGFTDADVFGVFSRDGISTNVPTVFCTQFTNLVELDLSGLRITNVAANSFNACTNLLWLR
LYFNNISSLPANVFSNTQSLEYLDLDTNQLTTLPENIFANLGRLDMLELRNNPFQNIPAS
VFNGLSLLQTLYLQNTRLTEINNAWFQSLPNLSTLTVYGNNITSISETAFNGLSQLRVLE
ISRNPLGQNIHVNAFAPLTNLQILYMSNINLSVINPQLFAPLSNLITLYFFWNNIVEIPS
GTFDNMTNLFSLDIGGNLLDETSIAADAFRNLQNLVIFFLDDNYIQNLNPQWFANLTNVE
DLFLDFNFIEDLPNGIFAPIRELWQIGLWFNDLKTIRRNAFGNLNGLYAIDLDQNVINAV
DENFFNASSNLYIIYFFQNLCASISIYGFSLNRENSMSWFRRCTENFLFIVDAETDGNEN
YEFHPGRSPGIQMRVQSNDEVHVALTPFNFPWTPMIEIIIGAANNTRSIIRRNQETDVVT
VPTPGIIRAGQWNGFRITWANHAILVWREGEEWPFMGFTMTDFFPVNFYGLRAPLSRASW
SVQPVDGIVPTIEENLELNFIN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g16487.t1 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 21 | 362 | 5.3E-71 |
| 15 | g16487.t1 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 363 | 479 | 3.5E-9 |
| 7 | g16487.t1 | PANTHER | PTHR46473:SF8 | ELRR (EXTRACELLULAR LEUCINE-RICH REPEAT) ONLY | 90 | 216 | 3.4E-82 |
| 11 | g16487.t1 | PANTHER | PTHR46473 | GH08155P | 90 | 216 | 3.4E-82 |
| 5 | g16487.t1 | PANTHER | PTHR46473:SF8 | ELRR (EXTRACELLULAR LEUCINE-RICH REPEAT) ONLY | 140 | 288 | 3.4E-82 |
| 9 | g16487.t1 | PANTHER | PTHR46473 | GH08155P | 140 | 288 | 3.4E-82 |
| 4 | g16487.t1 | PANTHER | PTHR46473:SF8 | ELRR (EXTRACELLULAR LEUCINE-RICH REPEAT) ONLY | 176 | 318 | 3.4E-82 |
| 8 | g16487.t1 | PANTHER | PTHR46473 | GH08155P | 176 | 318 | 3.4E-82 |
| 6 | g16487.t1 | PANTHER | PTHR46473:SF8 | ELRR (EXTRACELLULAR LEUCINE-RICH REPEAT) ONLY | 283 | 431 | 3.4E-82 |
| 10 | g16487.t1 | PANTHER | PTHR46473 | GH08155P | 283 | 431 | 3.4E-82 |
| 1 | g16487.t1 | Pfam | PF13855 | Leucine rich repeat | 116 | 173 | 6.8E-11 |
| 2 | g16487.t1 | Pfam | PF13306 | BspA type Leucine rich repeat region (6 copies) | 199 | 335 | 8.2E-13 |
| 3 | g16487.t1 | Pfam | PF12248 | Farnesoic acid 0-methyl transferase | 502 | 592 | 1.8E-19 |
| 18 | g16487.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 19 | - |
| 19 | g16487.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 20 | g16487.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 14 | - |
| 22 | g16487.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 19 | - |
| 17 | g16487.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 20 | 431 | - |
| 21 | g16487.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 432 | 452 | - |
| 16 | g16487.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 453 | 622 | - |
| 48 | g16487.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 91 | 112 | 5.81 |
| 52 | g16487.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 115 | 136 | 6.834 |
| 53 | g16487.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 139 | 160 | 7.65 |
| 49 | g16487.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 163 | 184 | 5.725 |
| 50 | g16487.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 187 | 208 | 5.779 |
| 51 | g16487.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 211 | 232 | 6.873 |
| 54 | g16487.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 235 | 257 | 4.693 |
| 47 | g16487.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 260 | 281 | 5.286 |
| 45 | g16487.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 284 | 305 | 5.964 |
| 55 | g16487.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 334 | 355 | 5.194 |
| 46 | g16487.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 358 | 379 | 6.418 |
| 32 | g16487.t1 | SMART | SM00369 | LRR_typ_2 | 89 | 112 | 37.0 |
| 44 | g16487.t1 | SMART | SM00365 | LRR_sd22_2 | 89 | 107 | 150.0 |
| 23 | g16487.t1 | SMART | SM00364 | LRR_bac_2 | 113 | 132 | 65.0 |
| 31 | g16487.t1 | SMART | SM00369 | LRR_typ_2 | 113 | 136 | 1.7 |
| 25 | g16487.t1 | SMART | SM00364 | LRR_bac_2 | 137 | 156 | 0.37 |
| 34 | g16487.t1 | SMART | SM00369 | LRR_typ_2 | 137 | 160 | 0.035 |
| 30 | g16487.t1 | SMART | SM00369 | LRR_typ_2 | 161 | 184 | 0.96 |
| 33 | g16487.t1 | SMART | SM00369 | LRR_typ_2 | 185 | 208 | 6.5 |
| 24 | g16487.t1 | SMART | SM00364 | LRR_bac_2 | 209 | 228 | 42.0 |
| 26 | g16487.t1 | SMART | SM00369 | LRR_typ_2 | 209 | 232 | 0.0067 |
| 42 | g16487.t1 | SMART | SM00365 | LRR_sd22_2 | 209 | 230 | 260.0 |
| 36 | g16487.t1 | SMART | SM00369 | LRR_typ_2 | 233 | 257 | 10.0 |
| 43 | g16487.t1 | SMART | SM00365 | LRR_sd22_2 | 233 | 252 | 390.0 |
| 39 | g16487.t1 | SMART | SM00369 | LRR_typ_2 | 258 | 281 | 7.7 |
| 29 | g16487.t1 | SMART | SM00369 | LRR_typ_2 | 282 | 305 | 0.16 |
| 38 | g16487.t1 | SMART | SM00369 | LRR_typ_2 | 306 | 331 | 13.0 |
| 27 | g16487.t1 | SMART | SM00369 | LRR_typ_2 | 332 | 355 | 13.0 |
| 40 | g16487.t1 | SMART | SM00365 | LRR_sd22_2 | 332 | 350 | 190.0 |
| 35 | g16487.t1 | SMART | SM00369 | LRR_typ_2 | 356 | 379 | 0.056 |
| 41 | g16487.t1 | SMART | SM00365 | LRR_sd22_2 | 356 | 374 | 57.0 |
| 37 | g16487.t1 | SMART | SM00369 | LRR_typ_2 | 380 | 403 | 73.0 |
| 28 | g16487.t1 | SMART | SM00369 | LRR_typ_2 | 404 | 427 | 210.0 |
| 12 | g16487.t1 | SUPERFAMILY | SSF52058 | L domain-like | 82 | 440 | 3.97E-56 |
| 13 | g16487.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 19 | - |
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 transcript has been annotated with K06260 (platelet glycoprotein V)
Pathway
- This transcript belongs to the following pathways
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