RetrogeneDB ID: | retro_mmus_3212 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 8:71704204..71704968(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Cnot8 | ||
| Ensembl ID: | ENSMUSG00000020515 | ||
| Aliases: | Cnot8, 1500015I04Rik, 1810022F04Rik, AA536816, AU015770, AU043059 | ||
| Description: | CCR4-NOT transcription complex, subunit 8 [Source:MGI Symbol;Acc:MGI:1916375] |
Retrocopy-Parental alignment summary:
>retro_mmus_3212
GCCAGGGACACAGAGTTCCCAGGTGTTGTTGTATGGCCGATCGGTGAATTTCAAAGCTCCATAGATTACCAGTATCAGCT
TCTGCGGTGCAATGTTGACCTTCTTAAAATCATCCAGCTGGGCCTTACGTTCACCAACGAGAAGGGGGAGTACCCATCTG
GAATCAACACGTGGCAGTTCAACTTCAAGTTCAACCTGACTGAGGATATGTACTCCCAGGATTCCATAGATCTGCTTGCA
AACTCAAGGCTGCAGTTCCAGAAACACGAGGAGAAAGGGATTGATACACTGCACTTTGCAGAGCTGCTTATGACATCGGG
AGTGGTTCTCTGTGACAACGTCAAGTGGCTTTCATTTCACAGTGGTTATGATTTTGGCTACATGGTAAAGCTGCTAACAG
ACTCTCGACTGCCGGAAGAAGAACACGAGTTCTTTCACATCCTGAATCTTTTCTTCCCGTCCATTTACAATGTGAAATAC
CTGATGAAGAGCTGCAAAATCTGAAGGGAGGCCTTCAGGAGGTGGCTGATCAGTTGGATCTGCAGAGGATTGGAAGGCAG
CATCAAGCAGGCTCAGACTCTCTGCTGACAGGGATGGCTTTCTTCAGGATGAAAGAGCTATTCTTTGAGGACAGTATTGA
CGATGCCAAGTATTGTGGGCGCCTCTATGGCCTGGGCACAGGGGTGGCCCAGAAGCAGAATGAGGATGTGGACTGTGCCC
AGGAGAAGATGAGCATCTTGGCCATGATCAACAACATGCAGCAG
ORF - retro_mmus_3212 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 97.27 % |
| Parental protein coverage: | 87.33 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | AMDTEFPGVVVRPIGEFRSSIDYQYQLLRCNVDLLKIIQLGLTFTNEKGEYPSGINTWQFNFKFNLTEDM |
| A.DTEFPGVVV.PIGEF.SSIDYQYQLLRCNVDLLKIIQLGLTFTNEKGEYPSGINTWQFNFKFNLTEDM | |
| Retrocopy | ARDTEFPGVVVWPIGEFQSSIDYQYQLLRCNVDLLKIIQLGLTFTNEKGEYPSGINTWQFNFKFNLTEDM |
| Parental | YSQDSIDLLANSGLQFQKHEEEGIDTLHFAELLMTSGVVLCDNVKWLSFHSGYDFGYMVKLLTDSRLPEE |
| YSQDSIDLLANS.LQFQKHEE.GIDTLHFAELLMTSGVVLCDNVKWLSFHSGYDFGYMVKLLTDSRLPEE | |
| Retrocopy | YSQDSIDLLANSRLQFQKHEEKGIDTLHFAELLMTSGVVLCDNVKWLSFHSGYDFGYMVKLLTDSRLPEE |
| Parental | EHEFFHILNLFFPSIYDVKYLMKSCK-NLKGGLQEVADQLDLQRIGRQHQAGSDSLLTGMAFFRMKELFF |
| EHEFFHILNLFFPSIY.VKYLMKSCK.NLKGGLQEVADQLDLQRIGRQHQAGSDSLLTGMAFFRMKELFF | |
| Retrocopy | EHEFFHILNLFFPSIYNVKYLMKSCK<NLKGGLQEVADQLDLQRIGRQHQAGSDSLLTGMAFFRMKELFF |
| Parental | EDSIDDAKYCGRLYGLGTGVAQKQNEDVDCAQEKMSILAMINNMQQ |
| EDSIDDAKYCGRLYGLGTGVAQKQNEDVDCAQEKMSILAMINNMQQ | |
| Retrocopy | EDSIDDAKYCGRLYGLGTGVAQKQNEDVDCAQEKMSILAMINNMQQ |
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 .40 RPM | 39 .51 RPM |
| SRP007412_cerebellum | 1 .65 RPM | 34 .87 RPM |
| SRP007412_heart | 0 .00 RPM | 31 .57 RPM |
| SRP007412_kidney | 1 .62 RPM | 28 .62 RPM |
| SRP007412_liver | 1 .78 RPM | 37 .03 RPM |
| SRP007412_testis | 1 .19 RPM | 13 .54 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3212 was not detected
No EST(s) were mapped for retro_mmus_3212 retrocopy.
No TSS is located nearby retro_mmus_3212 retrocopy 5' end.
retro_mmus_3212 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_3212 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 | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000020515 | 1 retrocopy |
retro_mmus_3212 ,
|
| Pan troglodytes | ENSPTRG00000017451 | 1 retrocopy |