RetrogeneDB ID: | retro_rnor_248 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 4:152666612..152667512(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSRNOG00000046199 | |
| Aliases: | Vom1r80, V1rc38 | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Vom1r71 | ||
| Ensembl ID: | ENSRNOG00000047851 | ||
| Aliases: | None | ||
| Description: | vomeronasal 1 receptor 71 [Source:RefSeq peptide;Acc:NP_001009523] |
Retrocopy-Parental alignment summary:
>retro_rnor_248
ATGTCCTCATTAGATAACTTCCTTTATATCCAAGCTGGGCTTGGAGTCCTGGCCAATATGTTTCTCCTTTTTTTCTATAC
TTCCATAATACTGCGTGACAGACCTAAGCCCATGGACCTGATCTCCTGTCAACTGACCTTCATTCACATAATGATGATCC
TCACTGAAGGAGATAATTTGCTTCCAAACATATTAGAGTCACTAAAATTTGAAAATGATTTCAAATGTAAGACAACATTT
TACATAAACAGAGTGATGAGAGGCCTCTCTGTCTGCATCACCTGCCTCCTGGGTGTGTTCCAGGCTGTCACAATCAGTCC
CAGTACCTCGCTGTTGGCAAAATTTAAGGGTAAAGTAAAAACAAACATCATCTATGCTTTCTTATATCTTTGGTCTTTCA
ATTTGTCATTCAGTAGTAGGTGGATCTTCTATGTGGCTGGTTTTAGCAATGTAAGTGAGAACCACCAGATGAGGGTCACT
AAATCCTGCTCACTCTTCCCCATGAACTACATCATCAGGGGATTAACTTTAATAGTAACAATGTCCAGAGATGTATTTCT
CATAGGAGTCATGTTGACCACAAGTGTATACGTAGTGATTATCCTGTATAGACATCAGAGGCAATGTAAGCATCTTCATA
GCATTAGCCACCTGAGAGCATCCCCTGAGAAAAGGGCCACTCAGACTGTCTTGCTGCTGGTGATTTTCTTTGTGGTCATT
TACTGGGTGGACTTTATCATCTCATTCACCTCAATCCTGTTATGGATGTATGACCCAGTTGTCCTGAGAGTTCAGAAGTT
TGTGATGTGTGCCTATCCCACAATTACTCCTTTGGTACAAATCAATTCTGATAAAAGAGTAATCAGTGTACTGAAAAACT
TGCACTCCAAGTGCCACTAG
ORF - retro_rnor_248 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 76.59 % |
| Parental protein coverage: | 96.45 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MFSLKNVLYFQTGLGVLANMFLVCFYIYVILGHRPKPTDLISCQLTFIHIMMFLTGGDIWLTDLFELLNI |
| M.SL.N.LY.Q.GLGVLANMFL..FY...IL..RPKP.DLISCQLTFIHIMM.LT.GD..L....E.L.. | |
| Retrocopy | MSSLDNFLYIQAGLGVLANMFLLFFYTSIILRDRPKPMDLISCQLTFIHIMMILTEGDNLLPNILESLKF |
| Parental | ENDFKCKTIFYTSRVMRGLSICTTCLLSVFQAVTISPNTSFLAKFKQKLKKYMVYVFLCIWSFNLSFSTN |
| ENDFKCKT.FY..RVMRGLS.C.TCLL.VFQAVTISP.TS.LAKFK.K.K....Y.FL..WSFNLSFS.. | |
| Retrocopy | ENDFKCKTTFYINRVMRGLSVCITCLLGVFQAVTISPSTSLLAKFKGKVKTNIIYAFLYLWSFNLSFSSR |
| Parental | RIFYVGGFINVSETNQMKITKSCSLFPMNYIIRGMIVTVTTSRDVFLVGIMLITSTYMVIILCRHQRQCK |
| .IFYV.GF.NVSE..QM..TKSCSLFPMNYIIRG....VT.SRDVFL.G.ML.TS.Y.VIIL.RHQRQCK | |
| Retrocopy | WIFYVAGFSNVSENHQMRVTKSCSLFPMNYIIRGLTLIVTMSRDVFLIGVMLTTSVYVVIILYRHQRQCK |
| Parental | HLHRISHLSASPEKRATQTILLLVVFFVVIYWEDFIISFTSILLWMYDPVVLRVQKFVIYAYPTITPLVQ |
| HLH.ISHL.ASPEKRATQT.LLLV.FFVVIYW.DFIISFTSILLWMYDPVVLRVQKFV..AYPTITPLVQ | |
| Retrocopy | HLHSISHLRASPEKRATQTVLLLVIFFVVIYWVDFIISFTSILLWMYDPVVLRVQKFVMCAYPTITPLVQ |
| Parental | ISSDKRIISVLKNLHSKCH |
| I.SDKR.ISVLKNLHSKCH | |
| Retrocopy | INSDKRVISVLKNLHSKCH |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP017611_brain | 0 .00 RPM | 0 .00 RPM |
| SRP017611_kidney | 0 .00 RPM | 0 .00 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .00 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_248 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_248 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_248 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Rattus norvegicus | ENSRNOG00000047851 | 3 retrocopies |
retro_rnor_1989, retro_rnor_1992, retro_rnor_248 ,
|