RetrogeneDB ID: | retro_mmus_1108 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 13:62670346..62670903(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Calcoco2 | ||
| Ensembl ID: | ENSMUSG00000006056 | ||
| Aliases: | Calcoco2, 2410154J16Rik, C77254, Ndp52, Ndp52l1 | ||
| Description: | calcium binding and coiled-coil domain 2 [Source:MGI Symbol;Acc:MGI:1343177] |
Retrocopy-Parental alignment summary:
>retro_mmus_1108
ATAGACCAGTGCCCCATACCTACCTTGCTAGAACATGGCAACTTCTCTCAGGTCCTGTTTAACAATGTTGAGAAGTTCTA
TGTTCCTGGAGGAGATGTCATGTGCTATTACACCCTCACTGAAAAGTTCATCCCTCATCCCAAGGCCTGGATCTGCATCT
TTAAAGTAGGATGGAAGACCACCCAGGAGTATTATACCTTCGTGTGGGCTCCCTTGCAGAGAAAGACCTAAACAAGGTGT
CAGCCACGCAGCAGGAAATCCAATTCAAAGCTTATTACCTTCCCAAGGATGAGGAGAGCTACCAGTTCTGCTATGTGGAT
GAAGATAGTTTGGTCTGGGGAACAAGTGTCCCTTTCCAGTTCTGTCCAGACCCTGACGAGGACATAATGGTTGCTATCAA
TAAGGAAAGGGTAGACGAGATGCAACAGCTCAGTGAGGAGCTTTACCAAGAAAACCAGGAACTGAAAGACAAGTACGCTG
ACCTCCATGAGCAGCTTCAGAGGAAGCAGATGGTACTGGAAACCACGCAGAGGATGAAAAAGACCTTAGAACAGGAA
ORF - retro_mmus_1108 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 79.14 % |
| Parental protein coverage: | 55.89 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MDQCPIPTLLEHGNFSQVLFNNVEKFYAPRGDIMCYYTLTEKFIPRRKDWIGIFKVGWK-TTQEY-YTFM |
| .DQCPIPTLLEHGNFSQVLFNNVEKFY.P.GD.MCYYTLTEKFIP..K.WI.IFKVGWK.T...Y.Y... | |
| Retrocopy | IDQCPIPTLLEHGNFSQVLFNNVEKFYVPGGDVMCYYTLTEKFIPHPKAWICIFKVGWKTTQEYY<YLRV |
| Parental | WAPLPKDQNKDSATQQEIQFKAYYLPKDVERYQFCYVDEDGLVRGTSVPFQFCPDPDEDIMVVINKEKVE |
| .....KD.NK.SATQQEIQFKAYYLPKD.E.YQFCYVDED.LV.GTSVPFQFCPDPDEDIMV.INKE.V. | |
| Retrocopy | GSLAEKDLNKVSATQQEIQFKAYYLPKDEESYQFCYVDEDSLVWGTSVPFQFCPDPDEDIMVAINKERVD |
| Parental | EMEQLSEELYQQNQELKDKYADLHEQLQRKQVALEATQRVNKTLEHK |
| EM.QLSEELYQ.NQELKDKYADLHEQLQRKQ..LE.TQR..KTLE.. | |
| Retrocopy | EMQQLSEELYQENQELKDKYADLHEQLQRKQMVLETTQRMKKTLEQE |
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 .14 RPM | 0 .02 RPM |
| SRP007412_cerebellum | 0 .17 RPM | 0 .00 RPM |
| SRP007412_heart | 0 .03 RPM | 0 .00 RPM |
| SRP007412_kidney | 0 .17 RPM | 0 .00 RPM |
| SRP007412_liver | 0 .00 RPM | 0 .00 RPM |
| SRP007412_testis | 0 .37 RPM | 0 .14 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1108 was not detected
No EST(s) were mapped for retro_mmus_1108 retrocopy.
No TSS is located nearby retro_mmus_1108 retrocopy 5' end.
retro_mmus_1108 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_1108 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000006056 | 3 retrocopies |
retro_mmus_1016, retro_mmus_1108 , retro_mmus_2097,
|
| Otolemur garnettii | ENSOGAG00000011709 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000031074 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000013395 | 1 retrocopy |