RetrogeneDB ID: | retro_cfam_2100 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | X:76219466..76219964(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | BRMS1 | ||
| Ensembl ID: | ENSCAFG00000012784 | ||
| Aliases: | None | ||
| Description: | breast cancer metastasis suppressor 1 [Source:HGNC Symbol;Acc:17262] |
Retrocopy-Parental alignment summary:
>retro_cfam_2100
AGGGAACGGCTGAGTCAGCTGAGGGTGCCGCTGGAGGAAGTAGGGGCTGAGAGAGCACCTGAATACACAGAGCCTCTGGG
GGAGCTGCAGCAGAGCCTCAAGATCTTCATTCAGGTGACAGGGATCTACAAGGGCTTCTGTCTGGACGTGATCCGGAATA
AGTACGAATGTGAGCTGCAGGGAGCCAAACAGCACCCGGAGAGCAAGAAGCTGCTGTTCCACCACACGCTGCAGGGGGAG
CTGCAAGAGCAGATCCAAAGGCTGGAAGAGGACCGCCAGAGCCTGGACATCAGCTCTGAGTGGTGGGATGACAAACTGCA
CGTCAGAAGCAGCGCAAAGACCTGGGACTCCCTGCCACCCAGCAAGAGGAAGAAGGCACCTCTCATTTCTGGTCCTTACA
TCGTGTATATGCTGCAAGAGATCAACATCCTGGAGGACTGGACAGCCATCAAAAAGGCTACGGCAGCTGTGTCCCCTCAG
AAGAGAAAAGCAGATGGA
ORF - retro_cfam_2100 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.36 % |
| Parental protein coverage: | 66.67 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | RERLSQLRVRLEEVGAERAPEYTEPLGGLQRSLKIRIQVAGIYKGFCLDVIRNKYECELQGAKQHLESEK |
| RERLSQLRV.LEEVGAERAPEYTEPLG.LQ.SLKI.IQV.GIYKGFCLDVIRNKYECELQGAKQH.ES.K | |
| Retrocopy | RERLSQLRVPLEEVGAERAPEYTEPLGELQQSLKIFIQVTGIYKGFCLDVIRNKYECELQGAKQHPESKK |
| Parental | LLLYDTLQGELQERIQRLEEDRQSLDISSEWWDDKLHARSSAKTWDSLPPSKRKKAPLVSGPYMVYMLQE |
| LL...TLQGELQE.IQRLEEDRQSLDISSEWWDDKLH.RSSAKTWDSLPPSKRKKAPL.SGPY.VYMLQE | |
| Retrocopy | LLFHHTLQGELQEQIQRLEEDRQSLDISSEWWDDKLHVRSSAKTWDSLPPSKRKKAPLISGPYIVYMLQE |
| Parental | IDILEDWTAIKKARAAVSPQKRKADG |
| I.ILEDWTAIKKA.AAVSPQKRKADG | |
| Retrocopy | INILEDWTAIKKATAAVSPQKRKADG |
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 |
|---|---|---|
| SRP012049_cerebellum | 0 .08 RPM | 9 .95 RPM |
| SRP017611_brain | 0 .00 RPM | 6 .11 RPM |
| SRP017611_kidney | 0 .79 RPM | 22 .72 RPM |
| SRP017611_liver | 0 .29 RPM | 6 .45 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_2100 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_2100 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_2100 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000012784 | 1 retrocopy |
retro_cfam_2100 ,
|
| Myotis lucifugus | ENSMLUG00000014596 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000047683 | 1 retrocopy |