RetrogeneDB ID: | retro_mmus_2330 | ||
Retrocopylocation | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 4:20073372..20073542(+) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | Smagp | ||
| Ensembl ID: | ENSMUSG00000053559 | ||
| Aliases: | None | ||
| Description: | small cell adhesion glycoprotein [Source:MGI Symbol;Acc:MGI:2448476] |
Retrocopy-Parental alignment summary:
>retro_mmus_2330
ATGAACAACCTACCGGCCACACCTTCTCTTTAAGAATTGATGACCATGCCAGTTTTTCAGGCCCCCGTGACCCTGTCCGC
ACAAGCTGAAGAGGCCAGCATCGCATTCATTGCAGCTGTTATCACCGTGGTGTTCCTTACCCTGCTCTCAGTGTGACCTT
GATCTTCTTT
ATGAACAACCTACCGGCCACACCTTCTCTTTAAGAATTGATGACCATGCCAGTTTTTCAGGCCCCCGTGACCCTGTCCGC
ACAAGCTGAAGAGGCCAGCATCGCATTCATTGCAGCTGTTATCACCGTGGTGTTCCTTACCCTGCTCTCAGTGTGACCTT
GATCTTCTTT
ORF - retro_mmus_2330 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 84.48 % |
| Parental protein coverage: | 58.76 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MNNLPATPSPEELMTTPVFQAPETLSPQAEEASTALIAVVITVVFLTLLSV-VTLIFF |
| MNNLPATPS..ELMT.PVFQAP.TLS.QAEEAS.A.IA.VITVVFLTLLSV.VTLIFF | |
| Retrocopy | MNNLPATPSL*ELMTMPVFQAPVTLSAQAEEASIAFIAAVITVVFLTLLSV<VTLIFF |
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 | 0 .96 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 0 .87 RPM |
| SRP007412_heart | 0 .00 RPM | 6 .41 RPM |
| SRP007412_kidney | 0 .00 RPM | 25 .56 RPM |
| SRP007412_liver | 0 .00 RPM | 9 .83 RPM |
| SRP007412_testis | 0 .00 RPM | 1 .37 RPM |
RNA Polymerase II actvity near the 5' end of retro_mmus_2330 was not detected
No EST(s) were mapped for retro_mmus_2330 retrocopy.
No TSS is located nearby retro_mmus_2330 retrocopy 5' end.
retro_mmus_2330 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2330 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000001983 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000017680 | 1 retrocopy | |
| Dasypus novemcinctus | ENSDNOG00000024893 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000053559 | 2 retrocopies |
retro_mmus_2330 , retro_mmus_3329,
|