RetrogeneDB ID: | retro_mmus_1650 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 17:58579027..58579620(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Lgals8 | ||
| Ensembl ID: | ENSMUSG00000057554 | ||
| Aliases: | Lgals8, 1200015E08Rik, AI326142, D13Ertd524e, Lgals-8 | ||
| Description: | lectin, galactose binding, soluble 8 [Source:MGI Symbol;Acc:MGI:1928481] |
Retrocopy-Parental alignment summary:
>retro_mmus_1650
AAGCACATTCTGCTGCACACCCACAGGATTAGCCCAGAGAAGATAGACACACTAGTCATCTATGGCAAAGTGAACATTCA
CTCCATTGAGTTCAGATTCAGATCAGATTTACAGCATATGGAAACGTCTACTCTGGAACTGACACAGATAAACAGAGAAA
ATATACAATAGTCTGTCAAGCTCCAGTTGAGCCTGCCATTTGAAGCAAGGTTGAATGCCTCCATGGGCCCTGGACAAACC
ATTGTCATTAAAGGAGAAGTGAATACCAATGCCAGAAACATTTAACATTGACCTAGTGGAAGAAAAATCAAGGGATATCG
CTCTATACTTGAATCCATGCCTGACTGTGAAAGCATTTATAAGAAATTCCTTTCTTCAGGATGCCTGGGGAGAAGAGGAG
AGAAATATTACCTGCTTCCCATTTAGTTCTGGGATGTACTTTGAGATGACAATTTACTGGGATGTCCAAGAATTTAAGGT
TGCCGTAAATGGTGTGTACAGCCTGGAGTACAATCACAGATTTAAAGACCATAGCAGTATTGATGCACTTATCAGTTGAT
GGTGATATCCGTTTGCTGGATATAAGGAGCTGG
ORF - retro_mmus_1650 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 81.41 % |
| Parental protein coverage: | 88.34 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | RHVLLYAHRISPEQIDTVGIYGKVNIHSIGFRFSSDLQSMETSALGLTQINRENIQKPGKLQLSLPFEAR |
| .H.LL..HRISPE.IDT..IYGKVNIHSI.FRF.SDLQ.METS.L.LTQINRENIQ...KLQLSLPFEAR | |
| Retrocopy | KHILLHTHRISPEKIDTLVIYGKVNIHSIEFRFRSDLQHMETSTLELTQINRENIQ*SVKLQLSLPFEAR |
| Parental | LNASMGPGRTVVIKGEVNTNARS-FNVDLVAGKTRDIALHLNPRLNVKAFVRNSFLQDAWGEEERNITCF |
| LNASMGPG.T.VIKGEVNTNAR..FN.DLV..K.RDIAL.LNP.L.VKAF.RNSFLQDAWGEEERNITCF | |
| Retrocopy | LNASMGPGQTIVIKGEVNTNARN>FNIDLVEEKSRDIALYLNPCLTVKAFIRNSFLQDAWGEEERNITCF |
| Parental | PFSSGMYFEMIIYCDVREFKVAINGVHSLEYKHRFKDLSSIDT-LSVDGDIRLLDVRSW |
| PFSSGMYFEM.IY.DV.EFKVA.NGV.SLEY.HRFKD.SSID..LSVDGDIRLLD.RSW | |
| Retrocopy | PFSSGMYFEMTIYWDVQEFKVAVNGVYSLEYNHRFKDHSSIDA>LSVDGDIRLLDIRSW |
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 |
|---|---|---|
| SRP007412_brain | 0 .02 RPM | 28 .48 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 57 .97 RPM |
| SRP007412_heart | 0 .00 RPM | 41 .19 RPM |
| SRP007412_kidney | 0 .02 RPM | 69 .47 RPM |
| SRP007412_liver | 0 .00 RPM | 112 .62 RPM |
| SRP007412_testis | 0 .05 RPM | 183 .73 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1650 was not detected
No EST(s) were mapped for retro_mmus_1650 retrocopy.
No TSS is located nearby retro_mmus_1650 retrocopy 5' end.
retro_mmus_1650 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_1650 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000042363 | 3 retrocopies | |
| Mus musculus | ENSMUSG00000057554 | 1 retrocopy |
retro_mmus_1650 ,
|
| Rattus norvegicus | ENSRNOG00000018046 | 1 retrocopy |