RetrogeneDB ID: | retro_mmus_1069 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 13:120046605..120047013(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Ctdsp1 | ||
| Ensembl ID: | ENSMUSG00000026176 | ||
| Aliases: | Ctdsp1, GIP, NLIIF, Nif3, SCP1 | ||
| Description: | CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 1 [Source:MGI Symbol;Acc:MGI:2654470] |
Retrocopy-Parental alignment summary:
>retro_mmus_1069
GACCAGAAGTCAGCAGTTTCCCAGAAGCCCCGGAGTCGGGGCATCCTCCACTCTCTCTTCTGCTGTGTCTGCCGGGATGA
TGGGGAGCCCCTACCTGCCCACAGTGGGGCTCCCCTGCTGGTGGAGGAAAATGGCGCCATCCCTAAGCACACCCCAGTCC
AGTACCTGCTTCCCGAGGCCAAGGCTCAGGACTCAGACAAGATCTGCGTAGTCATCGACCTGGACGAGACCCTGGTGCAC
AGCTCCTTCAAGCCAGTGAACAATGCGGACTTCATCATCCCGGTGGAGATAGATGGAGTGGTCCACCAGGTCTATGTGCT
GAAGCGGCCCCACGTAGATGAGTTCCTACAGCGAATGGGCAAGCTCTTTGAATGTGTGCTGTTCACTGCCAGCCTTGCCA
AGTACGCA
ORF - retro_mmus_1069 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 99.26 % |
| Parental protein coverage: | 52.11 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | DQKSAVSQKPRSRGILHSLFCCVCRDDGEPLPAHSGAPLLVEENGAIPKHTPVQYLLPEAKAQDSDKICV |
| DQKSAVSQKPRSRGILHSLFCCVCRDDGEPLPAHSGAPLLVEENGAIPKHTPVQYLLPEAKAQDSDKICV | |
| Retrocopy | DQKSAVSQKPRSRGILHSLFCCVCRDDGEPLPAHSGAPLLVEENGAIPKHTPVQYLLPEAKAQDSDKICV |
| Parental | VIDLDETLVHSSFKPVNNADFIIPVEIDGVVHQVYVLKRPHVDEFLQRMGELFECVLFTASLAKYA |
| VIDLDETLVHSSFKPVNNADFIIPVEIDGVVHQVYVLKRPHVDEFLQRMG.LFECVLFTASLAKYA | |
| Retrocopy | VIDLDETLVHSSFKPVNNADFIIPVEIDGVVHQVYVLKRPHVDEFLQRMGKLFECVLFTASLAKYA |
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 .00 RPM | 17 .20 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 22 .10 RPM |
| SRP007412_heart | 0 .03 RPM | 87 .13 RPM |
| SRP007412_kidney | 0 .04 RPM | 94 .13 RPM |
| SRP007412_liver | 0 .03 RPM | 101 .70 RPM |
| SRP007412_testis | 0 .00 RPM | 8 .74 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1069 was not detected
No EST(s) were mapped for retro_mmus_1069 retrocopy.
No TSS is located nearby retro_mmus_1069 retrocopy 5' end.
retro_mmus_1069 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_1069 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 | ENSMUSG00000026176 | 2 retrocopies |
retro_mmus_1069 , retro_mmus_1156,
|
| Mus musculus | ENSMUSG00000078429 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000015295 | 2 retrocopies |