General information for g16596.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 g16596 is located on chr_4: 10159449..10160183 (+ 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 | g16596 | g16596.t1 | TSS | g16596.t1 | 10157673 | 10157673 |
| chr_4 | g16596 | g16596.t1 | isoform | g16596.t1 | 10157852 | 10160183 |
| chr_4 | g16596 | g16596.t1 | exon | g16596.t1.exon1 | 10157852 | 10158098 |
| chr_4 | g16596 | g16596.t1 | cds | g16596.t1.CDS1 | 10157852 | 10158098 |
| chr_4 | g16596 | g16596.t1 | exon | g16596.t1.exon2 | 10158388 | 10159798 |
| chr_4 | g16596 | g16596.t1 | cds | g16596.t1.CDS2 | 10158388 | 10159798 |
| chr_4 | g16596 | g16596.t1 | exon | g16596.t1.exon3 | 10159904 | 10160183 |
| chr_4 | g16596 | g16596.t1 | cds | g16596.t1.CDS3 | 10159904 | 10160183 |
| chr_4 | g16596 | g16596.t1 | TTS | g16596.t1 | 10160277 | 10160277 |
Sequences
>g16596.t1 Gene=g16596 Length=1938
ATGAAACTTTTACTGTTTCTAAATTTCTTCATTATTGCTACTTTAGCAGACGTTCATTCA
CCTGAATGCTTTATTGACTCTCAATGTCCAGATGACAAAGGATGCTTTAACCAACTTTGT
CTAGATTTCTGTTCAGCACAAAAATGTCCAGAAAATTCTAAATGTGTCATGAAAAATCAT
CGACCAGTTTGTGAATGTCAAGTTGGATTTATTGATGATGGATTTGGAGATTGTGACGAA
AATTCAAACATAATTTCTGGCACAATAAAGAATGAAAGCTGTTGCTCAATCAAGGATCCA
CTCAAACAAATTCATTCAATTACATTCGTCACTTTTAATGCTGAAGAAAGTATAAAAATT
CAGGAAGAAAATTTCGAAATTGCATTAACTCATAAGAGCGATGATGTTGAAAGTTTCAAA
TTAATTATTCCAAAATGTGTACCTTGGGAAAATTTCTGTTATGAAGAAAATGTAAAATTT
CTACCCGTAAAAGTTAATCAAATATTTCCAAATATTGCTACTTATGTTGTCAATAATGCT
GCAGTTGAAAAAGTTCAAAAGAAAAATTTCGAAAGACTTGGAAGTTTAGAAATTCTTGAT
TTATCATCAAATAGAATTAATAAAATCGATTTAAATGCGTTTGATGATTTGGCACGTTTG
AATTTCCTTGTTCTAAAAAATAATAAAATCAACACAATTTCACGACGATGGTTTAAGAAT
CTCATACAAATTAACTTAATTGATCTAAGTTCAAATCCACTTTCATTTCCTTATTTGAAT
GTTTTCAAAGGTTCACCAGTGAGACAACTTTCACTTTTTTCAATCGGTTTGAATAATTTC
AATCCAAAATTGTTTGAAAATGCCAAAAATTTAAATGCTCTTGATATCGGTGCAAATGAA
CTTAAAAATCTTGATGAAAATGCCTTTGAAAAATTAACAAATCTTAACTTTATTGGCTTA
CGTTACTGTAGATTGACAAATATTTCAAAAAATTTATTTAAAAGCCTTAAAAATCTCAAG
CAAATTGATCTTTCGGTAAATCAACTTAAATCATTACATGACGATATTTTTGAGAATCAA
AATTCACTTGAAGAAGTCATTTTTAGAGAAAGCTCACTGAATAAACTTCCAAAAAGTTTG
CTTAACAGCGCAGAAACTTTAAAAGTTCTAGCTGTTTCAGACAATAAATTGAAAACTCTT
GATAGCGAATTATTCAGTCGATTAAATCATTTAGAAGTTCTTGATGTAACAGAAACCTCA
TTGACAACTCTTGAAACAAAAGTTTTTAAAAATCTACCAAATTTAAAGAAACTTGTGCTC
AACTACAATCGTATTGAGTCTTTGAATCCTGAAATTTTTGAAAATTTGTTATCATTAGAA
GAACTTGATGCCACTGGACTTAGCTTAACTGAATTACCTGCAAATTTATTTAAAAACAAT
AAAAATCTTCAAAAGATCAATTTTAAATCAAATTATTTGAAAACACTTCCGACTGAAATT
TTCCAAAACATGTCAAAATTGACAGAAATTGATTTGACTTCAAACAGCATTACAAATTTG
GATGCACAAGTTTTTGGAGGTTTGAGTGGATTGAAAGAATTAAAAATGGACAACAACAAG
CTTACTGAATTACCAGAGGAAATTTTTCATGATTTGAGCTCACTTGAAAAAATTTCTATT
AATAACAACAAATTGAAAACAAAACTCTCTTCCAAATTGTTTGAAAATAAACCAAAATTA
GGTTTTGTTGGTTTAAGATCAAGTTGTGTTGATGAAACTTACGGTCACTGGCGGGGTGGT
GAAATTTTAACAAACAATGAGAAGGAGATATTGATAAATGATATTGATAAAAAATGTCAA
TATATTTTAAAATTTTTATTAAAGAAAAATTTTTTGGATTCCTGTGAAGAAAAAAAAATT
TTCAATTTAAATTCATAA
>g16596.t1 Gene=g16596 Length=645
MKLLLFLNFFIIATLADVHSPECFIDSQCPDDKGCFNQLCLDFCSAQKCPENSKCVMKNH
RPVCECQVGFIDDGFGDCDENSNIISGTIKNESCCSIKDPLKQIHSITFVTFNAEESIKI
QEENFEIALTHKSDDVESFKLIIPKCVPWENFCYEENVKFLPVKVNQIFPNIATYVVNNA
AVEKVQKKNFERLGSLEILDLSSNRINKIDLNAFDDLARLNFLVLKNNKINTISRRWFKN
LIQINLIDLSSNPLSFPYLNVFKGSPVRQLSLFSIGLNNFNPKLFENAKNLNALDIGANE
LKNLDENAFEKLTNLNFIGLRYCRLTNISKNLFKSLKNLKQIDLSVNQLKSLHDDIFENQ
NSLEEVIFRESSLNKLPKSLLNSAETLKVLAVSDNKLKTLDSELFSRLNHLEVLDVTETS
LTTLETKVFKNLPNLKKLVLNYNRIESLNPEIFENLLSLEELDATGLSLTELPANLFKNN
KNLQKINFKSNYLKTLPTEIFQNMSKLTEIDLTSNSITNLDAQVFGGLSGLKELKMDNNK
LTELPEEIFHDLSSLEKISINNNKLKTKLSSKLFENKPKLGFVGLRSSCVDETYGHWRGG
EILTNNEKEILINDIDKKCQYILKFLLKKNFLDSCEEKKIFNLNS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g16596.t1 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 152 | 261 | 1.0E-15 |
| 15 | g16596.t1 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 262 | 365 | 9.8E-18 |
| 17 | g16596.t1 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 366 | 591 | 9.0E-52 |
| 5 | g16596.t1 | PANTHER | PTHR24369:SF8 | LEUCINE-RICH REPEAT-CONTAINING PROTEIN 4C | 163 | 369 | 1.4E-81 |
| 9 | g16596.t1 | PANTHER | PTHR24369 | ANTIGEN BSP, PUTATIVE-RELATED | 163 | 369 | 1.4E-81 |
| 6 | g16596.t1 | PANTHER | PTHR24369:SF8 | LEUCINE-RICH REPEAT-CONTAINING PROTEIN 4C | 284 | 491 | 1.4E-81 |
| 10 | g16596.t1 | PANTHER | PTHR24369 | ANTIGEN BSP, PUTATIVE-RELATED | 284 | 491 | 1.4E-81 |
| 4 | g16596.t1 | PANTHER | PTHR24369:SF8 | LEUCINE-RICH REPEAT-CONTAINING PROTEIN 4C | 345 | 563 | 1.4E-81 |
| 8 | g16596.t1 | PANTHER | PTHR24369 | ANTIGEN BSP, PUTATIVE-RELATED | 345 | 563 | 1.4E-81 |
| 7 | g16596.t1 | PANTHER | PTHR24369:SF8 | LEUCINE-RICH REPEAT-CONTAINING PROTEIN 4C | 475 | 580 | 1.4E-81 |
| 11 | g16596.t1 | PANTHER | PTHR24369 | ANTIGEN BSP, PUTATIVE-RELATED | 475 | 580 | 1.4E-81 |
| 1 | g16596.t1 | Pfam | PF13855 | Leucine rich repeat | 177 | 230 | 7.1E-11 |
| 3 | g16596.t1 | Pfam | PF13306 | BspA type Leucine rich repeat region (6 copies) | 260 | 383 | 4.6E-11 |
| 2 | g16596.t1 | Pfam | PF13306 | BspA type Leucine rich repeat region (6 copies) | 447 | 580 | 7.5E-15 |
| 19 | g16596.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 16 | - |
| 20 | g16596.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 21 | g16596.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 12 | - |
| 22 | g16596.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 13 | 16 | - |
| 18 | g16596.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 17 | 645 | - |
| 53 | g16596.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 195 | 216 | 7.62 |
| 51 | g16596.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 219 | 240 | 5.356 |
| 48 | g16596.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 290 | 311 | 6.295 |
| 47 | g16596.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 314 | 335 | 4.716 |
| 52 | g16596.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 338 | 359 | 7.204 |
| 55 | g16596.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 386 | 407 | 6.303 |
| 58 | g16596.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 434 | 455 | 7.535 |
| 57 | g16596.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 458 | 479 | 4.524 |
| 49 | g16596.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 482 | 503 | 6.072 |
| 56 | g16596.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 506 | 527 | 5.987 |
| 50 | g16596.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 530 | 551 | 6.896 |
| 54 | g16596.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 554 | 576 | 4.878 |
| 34 | g16596.t1 | SMART | SM00369 | LRR_typ_2 | 193 | 216 | 0.0068 |
| 42 | g16596.t1 | SMART | SM00365 | LRR_sd22_2 | 193 | 213 | 59.0 |
| 38 | g16596.t1 | SMART | SM00369 | LRR_typ_2 | 217 | 240 | 8.5 |
| 27 | g16596.t1 | SMART | SM00364 | LRR_bac_2 | 288 | 307 | 520.0 |
| 45 | g16596.t1 | SMART | SM00365 | LRR_sd22_2 | 288 | 306 | 530.0 |
| 32 | g16596.t1 | SMART | SM00369 | LRR_typ_2 | 289 | 311 | 120.0 |
| 31 | g16596.t1 | SMART | SM00369 | LRR_typ_2 | 312 | 335 | 22.0 |
| 36 | g16596.t1 | SMART | SM00369 | LRR_typ_2 | 336 | 359 | 0.0039 |
| 41 | g16596.t1 | SMART | SM00365 | LRR_sd22_2 | 336 | 357 | 100.0 |
| 24 | g16596.t1 | SMART | SM00364 | LRR_bac_2 | 384 | 404 | 89.0 |
| 40 | g16596.t1 | SMART | SM00369 | LRR_typ_2 | 387 | 407 | 110.0 |
| 39 | g16596.t1 | SMART | SM00369 | LRR_typ_2 | 408 | 431 | 18.0 |
| 26 | g16596.t1 | SMART | SM00364 | LRR_bac_2 | 432 | 452 | 150.0 |
| 30 | g16596.t1 | SMART | SM00369 | LRR_typ_2 | 432 | 455 | 0.0015 |
| 46 | g16596.t1 | SMART | SM00365 | LRR_sd22_2 | 432 | 458 | 200.0 |
| 25 | g16596.t1 | SMART | SM00364 | LRR_bac_2 | 456 | 475 | 13.0 |
| 33 | g16596.t1 | SMART | SM00369 | LRR_typ_2 | 456 | 479 | 35.0 |
| 29 | g16596.t1 | SMART | SM00369 | LRR_typ_2 | 481 | 503 | 44.0 |
| 28 | g16596.t1 | SMART | SM00369 | LRR_typ_2 | 504 | 527 | 0.41 |
| 44 | g16596.t1 | SMART | SM00365 | LRR_sd22_2 | 504 | 522 | 59.0 |
| 23 | g16596.t1 | SMART | SM00364 | LRR_bac_2 | 528 | 547 | 5.0 |
| 37 | g16596.t1 | SMART | SM00369 | LRR_typ_2 | 528 | 551 | 8.6E-4 |
| 35 | g16596.t1 | SMART | SM00369 | LRR_typ_2 | 552 | 576 | 11.0 |
| 43 | g16596.t1 | SMART | SM00365 | LRR_sd22_2 | 552 | 579 | 130.0 |
| 13 | g16596.t1 | SUPERFAMILY | SSF52058 | L domain-like | 177 | 254 | 1.19E-13 |
| 12 | g16596.t1 | SUPERFAMILY | SSF52058 | L domain-like | 265 | 587 | 6.8E-50 |
| 14 | g16596.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 16 | - |
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.
