RetrogeneDB ID: | retro_mmus_2402 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 4:144587243..144588629(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000070610 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Mcrs1 | ||
| Ensembl ID: | ENSMUSG00000037570 | ||
| Aliases: | Mcrs1, C78274, ICP22BP, MSP58, P78 | ||
| Description: | microspherule protein 1 [Source:MGI Symbol;Acc:MGI:1858420] |
Retrocopy-Parental alignment summary:
>retro_mmus_2402
ATGGACAAAGATTCTCAGGGGCTGCTAGACTCGTCCCTGATGGCGTCAGGCACAGCCAGCCGCTCCGAGGATGAGGAGTC
ACTGGCAGGGCAGAAGCGAGCATCCTCCCAGGCCCTGGGCACTATTCCCAAACGCAGAAGCTCCTCCAGGTTCATCAAAA
GGAAGAAATTCGACGATGAACTGGTAGAGAGCAGCCTGGCCAAATCCTCCACCCGGGTGAAGGGGGCCGGCGGGGTGGAG
TCAGGCCGCTGCTCAGGGAGCGAGCCCTCCTCTAGTGAGAAGAAGAAGGTATCCAAGGCTCCCAGTACTCCTGTACCTCC
CAGCCCTGCCCCAACCCCTGGGCTGACCAAGCGTGTGAAGAAAAGCAAACAGCCACTTCAGGTGACCAAGGATCTGGGCC
GATGGAAGCCTGCAGATGACCTCCTCCTCATCAATGCTGTGCTGCAGACTAACGACCTGACATCTGTCCACCTGGGTGTG
AAGTTCAGCTGCTGCTTCACCCTTCGGGAAGTTCAGGAGCGCTGGTACGCCCTGCTCTACGACCCTGTCATCTCCAAGCT
GGCTTGCCAGGCCATGAGGCAGTTACACCCAGAAGCCATTGCAGCCATTCAGAGCAAGGCCCTGTTCAGCAAGGCTGAGG
AGCAGCTGCTGAGCAAAGTCGGATCAAGCAGCCAGCGCACCTTGGAGACCTTCCAGGACTTGCTGCATACACACCCTGAT
GCCTTCTACCTGGCTCGTACTGCCAAGGCTCTGCAGGCCCACTGGCAGCTCATGAAACAGTATTACCTACTCGAGGATCA
GACAGTGCAGCCACTGCCTAAGGGGGACCAAGTGCTCAACTTCTCAGATGCAGAGGACCTGATTGACGACAGTAAGCTCA
AGGACATGCGAGATGAAGTCCTGGAACATGAGCTGACAGTGGCTGACCGGCGCCAGAAACGAGAGATCCGGCAGCTGGAA
CAGGAACTGCATAAGTGGCAGGTGCTAGTGGACAGCATCACAGGCATGGGCTCTCCAGACTTTGACAACCAGACCCTGGC
CGTGCTGCGGGGCCGCATGGTGCGGTACCTAATGCGCTCTCGTGAGATAACCCTGGGCAGAGCAACCAAGGACAACCAGA
TTGACGTGGACCTGTCTCTGGAGGGTCCGGCTTGGAAGATCTCCCGAAAGCAAGGTGTCATCAAGCTGAAAAACAATGGT
GACTTCTTCATTGCCAACGAGGGCCGGCGGCCTATCTATATCGATGGGCGACCAGTGCTGTGCGGCTCCAAGTGGCGCCT
TAGCAACAACTCTGTGGTAGAGATCGCCAGCCTGCGATTCGTCTTCCTCATCAACCAGGACCTCATTGCCCTCATCCGGG
CTGAGGCTGCCAAGATCACCCCACAG
ORF - retro_mmus_2402 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 99.57 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MDKDSQGLLDSSLMASGTASRSEDEESLAGQKRASSQALGTIPKRRSSSRFIKRKKFDDELVESSLAKSS |
| MDKDSQGLLDSSLMASGTASRSEDEESLAGQKRASSQALGTIPKRRSSSRFIKRKKFDDELVESSLAKSS | |
| Retrocopy | MDKDSQGLLDSSLMASGTASRSEDEESLAGQKRASSQALGTIPKRRSSSRFIKRKKFDDELVESSLAKSS |
| Parental | TRVKGAGGVESGRCSGSEPSSSEKKKVSKAPSTPVPPSPAPTPGLTKRVKKSKQPLQVTKDLGRWKPADD |
| TRVKGAGGVESGRCSGSEPSSSEKKKVSKAPSTPVPPSPAPTPGLTKRVKKSKQPLQVTKDLGRWKPADD | |
| Retrocopy | TRVKGAGGVESGRCSGSEPSSSEKKKVSKAPSTPVPPSPAPTPGLTKRVKKSKQPLQVTKDLGRWKPADD |
| Parental | LLLINAVLQTNDLTSVHLGVKFSCRFTLREVQERWYALLYDPVISKLACQAMRQLHPEAIAAIQSKALFS |
| LLLINAVLQTNDLTSVHLGVKFSC.FTLREVQERWYALLYDPVISKLACQAMRQLHPEAIAAIQSKALFS | |
| Retrocopy | LLLINAVLQTNDLTSVHLGVKFSCCFTLREVQERWYALLYDPVISKLACQAMRQLHPEAIAAIQSKALFS |
| Parental | KAEEQLLSKVGSSSQPTLETFQDLLHTHPDAFYLARTAKALQAHWQLMKQYYLLEDQTVQPLPKGDQVLN |
| KAEEQLLSKVGSSSQ.TLETFQDLLHTHPDAFYLARTAKALQAHWQLMKQYYLLEDQTVQPLPKGDQVLN | |
| Retrocopy | KAEEQLLSKVGSSSQRTLETFQDLLHTHPDAFYLARTAKALQAHWQLMKQYYLLEDQTVQPLPKGDQVLN |
| Parental | FSDAEDLIDDSKLKDMRDEVLEHELTVADRRQKREIRQLEQELHKWQVLVDSITGMGSPDFDNQTLAVLR |
| FSDAEDLIDDSKLKDMRDEVLEHELTVADRRQKREIRQLEQELHKWQVLVDSITGMGSPDFDNQTLAVLR | |
| Retrocopy | FSDAEDLIDDSKLKDMRDEVLEHELTVADRRQKREIRQLEQELHKWQVLVDSITGMGSPDFDNQTLAVLR |
| Parental | GRMVRYLMRSREITLGRATKDNQIDVDLSLEGPAWKISRKQGVIKLKNNGDFFIANEGRRPIYIDGRPVL |
| GRMVRYLMRSREITLGRATKDNQIDVDLSLEGPAWKISRKQGVIKLKNNGDFFIANEGRRPIYIDGRPVL | |
| Retrocopy | GRMVRYLMRSREITLGRATKDNQIDVDLSLEGPAWKISRKQGVIKLKNNGDFFIANEGRRPIYIDGRPVL |
| Parental | CGSKWRLSNNSVVEIASLRFVFLINQDLIALIRAEAAKITPQ |
| CGSKWRLSNNSVVEIASLRFVFLINQDLIALIRAEAAKITPQ | |
| Retrocopy | CGSKWRLSNNSVVEIASLRFVFLINQDLIALIRAEAAKITPQ |
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 .56 RPM | 20 .93 RPM |
| SRP007412_cerebellum | 0 .30 RPM | 14 .94 RPM |
| SRP007412_heart | 0 .62 RPM | 16 .84 RPM |
| SRP007412_kidney | 0 .42 RPM | 13 .96 RPM |
| SRP007412_liver | 0 .11 RPM | 3 .14 RPM |
| SRP007412_testis | 1 .78 RPM | 34 .81 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2402 was not detected
1 EST(s) were mapped to retro_mmus_2402 retrocopy
| EST ID | Start | End | Identity | Match | Mis-match | Score |
|---|---|---|---|---|---|---|
| BQ570550 | 144588079 | 144588220 | 100 | 141 | 0 | 141 |
No TSS is located nearby retro_mmus_2402 retrocopy 5' end.
retro_mmus_2402 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2402 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000008549 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000037570 | 1 retrocopy |
retro_mmus_2402 ,
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