RetrogeneDB ID: | retro_mmus_3517 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | X:121913226..121913991(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000084110 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Trim5 | ||
| Ensembl ID: | ENSMUSG00000060441 | ||
| Aliases: | Trim5, EG667823, Gm8833 | ||
| Description: | tripartite motif-containing 5 [Source:MGI Symbol;Acc:MGI:3646853] |
Retrocopy-Parental alignment summary:
>retro_mmus_3517
TCAGACATAGAAATACTGCAGGGTGTGGAGAACATCATAAAACGGAGTCATACTTTTTCGATGAAGAAGCCCAAAACCAT
CGCCAGGGAACAAAGAAAGTTCAGAGCTCCTGACCTGCAAGGCATGCTGCAAGTGCTGCAAGAGGTCGCAGAGGCTCAAC
GCTACTGGGTTCAGGTGACCCTGGTTCAAAACAACCATCCAAACATTGCCATTACTGACGACAAAAGACAAGTACGATAT
GAAGACCACCAAGCAAGTAATCTTATACCCGGGTGTGAAAACTCTCATGAAGGCGTCCTGGGACATCCAGCTATCCAATC
TGGAAAACATTACTGGGAAGTAGATGTGTCTAGAAAAGGTGCTTGGGTTCTGGGGTTAAGTGATGGAAGCTACCTCTTCT
GTCCAATATTTCATTCAAATGCTGAAAGAAATCGTTTATTTTGTAGGGGGATTAAGAATGATTCACATTATCAACCAAAA
TATGGCTTCTGGGTTATAGGGCTGTGGAAAAAGTCTGAGTATAATGCTTTTGAGGAGTGTCCTTTCACAGGCAAGCCCAG
TGTCTTGTCCCTGTCTCTGATGGTCCCGCCCTGTCGTGTTGGTGTTTTCCTTGACTATGCAGCTGGCACTCTCTCATTTT
ACAATATTTCCAACAATGGGACTCTTATCTACAGATTCTGTACAGCTTCCTTTCCTGATAGGGTTTTTCCATATTTTAAT
CCCACGGGAAGTTCAGAGCCGATGACAATTTGCTGGCCAGACTCT
ORF - retro_mmus_3517 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 97.25 % |
| Parental protein coverage: | 51.31 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | SDIEILQGVENIIKRSLTFSMKKPKTIAREQRKFRAPDLQGMLQVLQEVTEAQRYWVQVTLVQNNHPNIA |
| SDIEILQGVENIIKRS.TFSMKKPKTIAREQRKFRAPDLQGMLQVLQEV.EAQRYWVQVTLVQNNHPNIA | |
| Retrocopy | SDIEILQGVENIIKRSHTFSMKKPKTIAREQRKFRAPDLQGMLQVLQEVAEAQRYWVQVTLVQNNHPNIA |
| Parental | ITDDKRQVRYEDHQASNLIHECENSHEGVLGHPAIQSGKHYWEVDVSGKGAWVLGLSDGSYLFCPIFHSN |
| ITDDKRQVRYEDHQASNLI..CENSHEGVLGHPAIQSGKHYWEVDVS.KGAWVLGLSDGSYLFCPIFHSN | |
| Retrocopy | ITDDKRQVRYEDHQASNLIPGCENSHEGVLGHPAIQSGKHYWEVDVSRKGAWVLGLSDGSYLFCPIFHSN |
| Parental | AERNRLFCRGIKNDSHYQPKYGFWVIGLWKKSVYNAFEECPFTGKPSVLTLSLMVPPCRVGVFLDYAAGT |
| AERNRLFCRGIKNDSHYQPKYGFWVIGLWKKS.YNAFEECPFTGKPSVL.LSLMVPPCRVGVFLDYAAGT | |
| Retrocopy | AERNRLFCRGIKNDSHYQPKYGFWVIGLWKKSEYNAFEECPFTGKPSVLSLSLMVPPCRVGVFLDYAAGT |
| Parental | LSFYNISNNGTLIYRFCTASFPDRVFPYFNPTGSSEPMTICWPDS |
| LSFYNISNNGTLIYRFCTASFPDRVFPYFNPTGSSEPMTICWPDS | |
| Retrocopy | LSFYNISNNGTLIYRFCTASFPDRVFPYFNPTGSSEPMTICWPDS |
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 | 0 .56 RPM |
| SRP007412_cerebellum | 0 .26 RPM | 1 .56 RPM |
| SRP007412_heart | 0 .03 RPM | 1 .56 RPM |
| SRP007412_kidney | 0 .31 RPM | 5 .79 RPM |
| SRP007412_liver | 0 .14 RPM | 3 .44 RPM |
| SRP007412_testis | 0 .00 RPM | 0 .69 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3517 was not detected
No EST(s) were mapped for retro_mmus_3517 retrocopy.
No TSS is located nearby retro_mmus_3517 retrocopy 5' end.
retro_mmus_3517 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_3517 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000060441 | 1 retrocopy |
retro_mmus_3517 ,
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