General information for g16624.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 g16624 is located on chr_4: 10297319..10298622 (- 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 | g16624 | g16624.t1 | isoform | g16624.t1 | 10296008 | 10298622 |
| chr_4 | g16624 | g16624.t1 | exon | g16624.t1.exon1 | 10296008 | 10296476 |
| chr_4 | g16624 | g16624.t1 | cds | g16624.t1.CDS1 | 10296008 | 10296476 |
| chr_4 | g16624 | g16624.t1 | exon | g16624.t1.exon2 | 10296673 | 10298101 |
| chr_4 | g16624 | g16624.t1 | cds | g16624.t1.CDS2 | 10296673 | 10298101 |
| chr_4 | g16624 | g16624.t1 | exon | g16624.t1.exon3 | 10298183 | 10298485 |
| chr_4 | g16624 | g16624.t1 | cds | g16624.t1.CDS3 | 10298183 | 10298485 |
| chr_4 | g16624 | g16624.t1 | exon | g16624.t1.exon4 | 10298541 | 10298622 |
| chr_4 | g16624 | g16624.t1 | cds | g16624.t1.CDS4 | 10298541 | 10298622 |
| chr_4 | g16624 | g16624.t1 | TSS | g16624.t1 | NA | NA |
| chr_4 | g16624 | g16624.t1 | TTS | g16624.t1 | NA | NA |
Sequences
>g16624.t1 Gene=g16624 Length=2283
ATGAGTTATTTATTTCTATGTAAATTGCTCTTTTTGATAACCTTTTTTGATTTGGTTTCA
TCTGATGCAATTGATGAAGTTGATTTTTGCAAAAATTCACCATGTGGACCAAATTCAAGT
TGTGTCAATTTTGAAAAATTTGCATCCTGCTATTGTCTTGATGGTTTTATTGGAAGTCCA
CCATACTGTCGACAACCTGAATGTTTTTATGATTCACAATGTCCATCAGATAGAGCTTGT
ATTAGATCCATTTGTACTGACGTTTGTGTAGCTCAAAAATGTCAACAAAATTCAAAATGT
GTAGTGAAAAATCATCGACCATTTTGTGAATGTCAAGCAGGATTTCTCAATAATGAAAAT
GATGGAGAATGTGAAGAAAACTTGAATCTTCTTGATGGTTCCATAATAACAGAAAGATTT
TACAACCAATATGAGGAAATCAAGAATTTTTGGGAAAAACATTCAAATGAAACTTTTGAA
ACATTTTTTATTAAAAATGGAACAAAAATGAAGGAAGAAAATTTTGAACTGTCAATTAAA
TTCAAAAATTTTAATGTTAAAGGTTTTGCAATAATGAATTCTGTTTGTAATGAATGGGAC
TTTTGTTACAAGAAATTCAACATAAAATTTCTACCCATAAGAATAGGCGAAATTTTTCCT
AATTTAATATCATATACAGCATTTGCATTTGATATTTCTGAAGTTAGAAAGATAAATTTG
GAAAATTTGACAAAATTAAAACTTTTGAGTTTGACATTGAGTGAGATTGAAAAAATTGAA
GAAGATTCTTTTGATGATCTTTCTCAATTACAATTTTTACTGATAATAGCAAGTAAGCTT
CAAAATATCAATAAAAAATGGTTCAAAAATACAAAGAAAATTGAATCCATTAATTTTAGT
CACAATCGTATCGAAACTATCACAGATCCAAAAACATTTGCTAATTTGAGAAACTTAAAA
GCATTAAATTTTGAAGGCAATAACATGAAAAGTTTAGATTCAAAAATTTTCAATAATTTA
AACAATTTGAAAACTCTCAAACTTAAAAATCTTGAATTGTCAATATTTGATGACAAAATT
TTTGACAGTTTACCAAAACTTGAAGAATTTTCAATTGGATCATTTGATTTTCAAAATTTA
CCAACGATTTCACTGCAAAAATTGAAAAATTTAAAGAAATTTAGTTGGACAGGAAGATTT
GACATTATTCAAAGCTCTGGAGTATTCAAAAGTCTATACCAACTTGAAGAAATTCATCTG
ACACGAAGTTCAATTGAAAGGCTACCGGAAGGGATTTTTAAAGATACAAAAAATCTTAAA
ATTCTTGATTTATCAAACAATAATTTGATTGAAATTACTTCAAATGATATTGGACACTTA
GAGAAACTTGAAGAACTTGATTTATCTTCTAATGAATTAACAGCTTTCCAAAGTAAATTT
TTTGACAATTTTTCAAATCTTAAAAAGCTAAAAATCAGCTCTAATCCTATACAATCATTT
GATGAAGAACTTTTAAAAAATTTACAAAATTTGGAAGAATTTGAACTTTATGATTTGGAA
TTTGTAAGAATTCCATCAAAAATCTTCCAAAATAACAAAAACCTAAAGTCAATTTCAATG
GTAAGAAACCAATTGGCTAAAAATGAATCAGAAATATTTACTAACCTTACAAAATTAACA
AAACTTGAACTCATTAGTAATGGTTTAACATCTTTGGAAAAAAAACTTTTTGCGCCTTTA
GAAAATTTGAAGAAATTGTCTCTTTCTGAAAACGATTTAAGTAAAATATCTGAAGAAGTT
TTCGAAAATTTGAGATCGCTTGAAATTTTAAACCTAAGAAATTGTAATTTGACAAATTTA
CAACCAAAATTATTGGAAAATACAAAAGAATTAAAGAAATTGGATCTCTCTCAAGAGAAT
CATTTGAAGTCAATTCCAATTGAATTTTTTTCTACTTTGAATAAATTAGAGGACCTTGAT
TTGTCTGACAATAAATTTGAAACTTTAGATGGTGATGTTTTTAGTAATTTAATCAATTTG
AAAATATTAAATATAAATTTTGCTGCATTAGGTTCATTGAATGAAAATATTTTCAAACAT
TTAATATCATTAAAAGAAGTTAGCTTAAATGGCAATAAAATTACAGAAATTTCACAAAAT
TTATTCGTCAACAATCAAAAACTTACCGAAATAAATTTAGATTCGAATGAAATCACAAAT
CTGGAACCTGAAGCATTTAATGGGACTTGCAAATTTGGAAACACTCAGTTTGGCAGGAAA
TAA
>g16624.t1 Gene=g16624 Length=760
MSYLFLCKLLFLITFFDLVSSDAIDEVDFCKNSPCGPNSSCVNFEKFASCYCLDGFIGSP
PYCRQPECFYDSQCPSDRACIRSICTDVCVAQKCQQNSKCVVKNHRPFCECQAGFLNNEN
DGECEENLNLLDGSIITERFYNQYEEIKNFWEKHSNETFETFFIKNGTKMKEENFELSIK
FKNFNVKGFAIMNSVCNEWDFCYKKFNIKFLPIRIGEIFPNLISYTAFAFDISEVRKINL
ENLTKLKLLSLTLSEIEKIEEDSFDDLSQLQFLLIIASKLQNINKKWFKNTKKIESINFS
HNRIETITDPKTFANLRNLKALNFEGNNMKSLDSKIFNNLNNLKTLKLKNLELSIFDDKI
FDSLPKLEEFSIGSFDFQNLPTISLQKLKNLKKFSWTGRFDIIQSSGVFKSLYQLEEIHL
TRSSIERLPEGIFKDTKNLKILDLSNNNLIEITSNDIGHLEKLEELDLSSNELTAFQSKF
FDNFSNLKKLKISSNPIQSFDEELLKNLQNLEEFELYDLEFVRIPSKIFQNNKNLKSISM
VRNQLAKNESEIFTNLTKLTKLELISNGLTSLEKKLFAPLENLKKLSLSENDLSKISEEV
FENLRSLEILNLRNCNLTNLQPKLLENTKELKKLDLSQENHLKSIPIEFFSTLNKLEDLD
LSDNKFETLDGDVFSNLINLKILNINFAALGSLNENIFKHLISLKEVSLNGNKITEISQN
LFVNNQKLTEINLDSNEITNLEPEAFNGTCKFGNTQFGRK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 31 | g16624.t1 | CDD | cd00054 | EGF_CA | 27 | 58 | 0.00193235 |
| 23 | g16624.t1 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 200 | 397 | 1.1E-26 |
| 22 | g16624.t1 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 398 | 519 | 4.2E-26 |
| 25 | g16624.t1 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 520 | 634 | 4.7E-25 |
| 24 | g16624.t1 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 635 | 757 | 8.5E-25 |
| 7 | g16624.t1 | PANTHER | PTHR45617:SF42 | LEUCINE RICH REPEAT CONTAINING G PROTEIN-COUPLED RECEPTOR 6 | 232 | 390 | 1.2E-90 |
| 12 | g16624.t1 | PANTHER | PTHR45617 | - | 232 | 390 | 1.2E-90 |
| 10 | g16624.t1 | PANTHER | PTHR45617:SF42 | LEUCINE RICH REPEAT CONTAINING G PROTEIN-COUPLED RECEPTOR 6 | 233 | 350 | 1.2E-90 |
| 15 | g16624.t1 | PANTHER | PTHR45617 | - | 233 | 350 | 1.2E-90 |
| 9 | g16624.t1 | PANTHER | PTHR45617:SF42 | LEUCINE RICH REPEAT CONTAINING G PROTEIN-COUPLED RECEPTOR 6 | 336 | 461 | 1.2E-90 |
| 14 | g16624.t1 | PANTHER | PTHR45617 | - | 336 | 461 | 1.2E-90 |
| 6 | g16624.t1 | PANTHER | PTHR45617:SF42 | LEUCINE RICH REPEAT CONTAINING G PROTEIN-COUPLED RECEPTOR 6 | 406 | 546 | 1.2E-90 |
| 11 | g16624.t1 | PANTHER | PTHR45617 | - | 406 | 546 | 1.2E-90 |
| 8 | g16624.t1 | PANTHER | PTHR45617:SF42 | LEUCINE RICH REPEAT CONTAINING G PROTEIN-COUPLED RECEPTOR 6 | 540 | 755 | 1.2E-90 |
| 13 | g16624.t1 | PANTHER | PTHR45617 | - | 540 | 755 | 1.2E-90 |
| 17 | g16624.t1 | PRINTS | PR00019 | Leucine-rich repeat signature | 439 | 452 | 2.8E-5 |
| 16 | g16624.t1 | PRINTS | PR00019 | Leucine-rich repeat signature | 460 | 473 | 2.8E-5 |
| 5 | g16624.t1 | Pfam | PF13306 | BspA type Leucine rich repeat region (6 copies) | 247 | 366 | 3.4E-11 |
| 4 | g16624.t1 | Pfam | PF13855 | Leucine rich repeat | 414 | 473 | 1.2E-13 |
| 2 | g16624.t1 | Pfam | PF13855 | Leucine rich repeat | 558 | 617 | 7.1E-13 |
| 1 | g16624.t1 | Pfam | PF13855 | Leucine rich repeat | 630 | 686 | 8.7E-10 |
| 3 | g16624.t1 | Pfam | PF13855 | Leucine rich repeat | 703 | 748 | 4.9E-9 |
| 27 | g16624.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 21 | - |
| 28 | g16624.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 29 | g16624.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 16 | - |
| 30 | g16624.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 17 | 21 | - |
| 26 | g16624.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 22 | 760 | - |
| 60 | g16624.t1 | ProSitePatterns | PS01186 | EGF-like domain signature 2. | 50 | 63 | - |
| 59 | g16624.t1 | ProSitePatterns | PS01186 | EGF-like domain signature 2. | 109 | 124 | - |
| 75 | g16624.t1 | ProSiteProfiles | PS50026 | EGF-like domain profile. | 26 | 64 | 12.468 |
| 70 | g16624.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 245 | 266 | 5.009 |
| 65 | g16624.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 293 | 314 | 5.979 |
| 64 | g16624.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 318 | 339 | 6.195 |
| 69 | g16624.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 438 | 459 | 7.358 |
| 62 | g16624.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 462 | 483 | 6.387 |
| 68 | g16624.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 486 | 507 | 6.418 |
| 67 | g16624.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 534 | 555 | 4.662 |
| 72 | g16624.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 558 | 579 | 6.441 |
| 63 | g16624.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 582 | 603 | 7.874 |
| 71 | g16624.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 606 | 627 | 6.156 |
| 74 | g16624.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 630 | 652 | 6.742 |
| 66 | g16624.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 655 | 676 | 7.358 |
| 61 | g16624.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 703 | 724 | 6.742 |
| 73 | g16624.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 727 | 748 | 7.35 |
| 47 | g16624.t1 | SMART | SM00179 | egfca_6 | 26 | 64 | 0.005 |
| 58 | g16624.t1 | SMART | SM00181 | egf_5 | 29 | 64 | 0.93 |
| 57 | g16624.t1 | SMART | SM00181 | egf_5 | 88 | 125 | 10.0 |
| 34 | g16624.t1 | SMART | SM00369 | LRR_typ_2 | 243 | 266 | 48.0 |
| 48 | g16624.t1 | SMART | SM00365 | LRR_sd22_2 | 243 | 264 | 190.0 |
| 49 | g16624.t1 | SMART | SM00365 | LRR_sd22_2 | 291 | 318 | 650.0 |
| 40 | g16624.t1 | SMART | SM00369 | LRR_typ_2 | 316 | 339 | 3.4 |
| 35 | g16624.t1 | SMART | SM00369 | LRR_typ_2 | 340 | 363 | 250.0 |
| 37 | g16624.t1 | SMART | SM00369 | LRR_typ_2 | 412 | 435 | 2.2 |
| 33 | g16624.t1 | SMART | SM00369 | LRR_typ_2 | 436 | 459 | 69.0 |
| 43 | g16624.t1 | SMART | SM00369 | LRR_typ_2 | 460 | 483 | 0.048 |
| 54 | g16624.t1 | SMART | SM00365 | LRR_sd22_2 | 460 | 481 | 56.0 |
| 38 | g16624.t1 | SMART | SM00369 | LRR_typ_2 | 484 | 507 | 32.0 |
| 56 | g16624.t1 | SMART | SM00365 | LRR_sd22_2 | 484 | 513 | 180.0 |
| 41 | g16624.t1 | SMART | SM00369 | LRR_typ_2 | 508 | 531 | 81.0 |
| 55 | g16624.t1 | SMART | SM00365 | LRR_sd22_2 | 532 | 558 | 100.0 |
| 39 | g16624.t1 | SMART | SM00369 | LRR_typ_2 | 556 | 579 | 0.45 |
| 46 | g16624.t1 | SMART | SM00369 | LRR_typ_2 | 580 | 603 | 0.0067 |
| 53 | g16624.t1 | SMART | SM00365 | LRR_sd22_2 | 580 | 606 | 120.0 |
| 32 | g16624.t1 | SMART | SM00369 | LRR_typ_2 | 604 | 627 | 4.2 |
| 42 | g16624.t1 | SMART | SM00369 | LRR_typ_2 | 653 | 676 | 0.066 |
| 52 | g16624.t1 | SMART | SM00365 | LRR_sd22_2 | 653 | 674 | 69.0 |
| 36 | g16624.t1 | SMART | SM00369 | LRR_typ_2 | 677 | 700 | 25.0 |
| 45 | g16624.t1 | SMART | SM00369 | LRR_typ_2 | 701 | 724 | 0.076 |
| 50 | g16624.t1 | SMART | SM00365 | LRR_sd22_2 | 701 | 723 | 650.0 |
| 51 | g16624.t1 | SMART | SM00365 | LRR_sd22_2 | 725 | 746 | 620.0 |
| 44 | g16624.t1 | SMART | SM00369 | LRR_typ_2 | 726 | 748 | 8.8 |
| 19 | g16624.t1 | SUPERFAMILY | SSF52058 | L domain-like | 212 | 501 | 4.91E-40 |
| 18 | g16624.t1 | SUPERFAMILY | SSF52058 | L domain-like | 458 | 746 | 4.42E-48 |
| 21 | g16624.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 21 | - |
| 20 | g16624.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 |
| GO:0005509 | calcium ion 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