RetrogeneDB ID: | retro_cfam_1872 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 7:28858644..28859149(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PTN | ||
| Ensembl ID: | ENSCAFG00000003369 | ||
| Aliases: | None | ||
| Description: | pleiotrophin [Source:HGNC Symbol;Acc:9630] |
Retrocopy-Parental alignment summary:
>retro_cfam_1872
ATGCAGTCCCAACAGTACGTGCAGCAGCGTCGAAAATTTGCAGCTGCCTTCCCGGCATTCATTTTCATCTTGGCAGCTGT
GGGCACTGCTGAAGCCGGAAAGAAAGAGAAGCCAGAAAAAAAAAGTGAAGAGGTCTGACTGTGGAGAATGGCAGTGGAGT
GTGTGCGTGCCCACCAGTGGGGACTGTGGCCTGGGCACCGGGGAGGGCACCCGGACTGGAGCTGAGTGTAAGCACACCAG
GAAGACCCAGAGATGTAAGATCCCCTGCAACTGGAAAAAGCAATTTGGAGCGGAGTGCAAATACCAGTTCCAGGCCTGGG
GAGAATGTGACCTGAATACGGCCTTGAAGACCAGAACCTGAAGTCTGAAGCGAGCCCTCCACAATGCGGACTGCCAGAAG
ACAGTCACCATCTCCAAGCCTTGTGGCAAACTGACTAAGCCCAAACCTCAAGCAGAATCCAAGAAGAAGAAAAAGGAAGG
CAAGAAACAAGAGAAGATGCTGGAC
ORF - retro_cfam_1872 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.49 % |
| Parental protein coverage: | 92.82 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MQSQQYVQQRRKFAAAFLAFIFILAAVDTAEAGKKEKPEKK-VKKSDCGEWQWSVCVPTSGDCGLGTREG |
| MQSQQYVQQRRKFAAAF.AFIFILAAV.TAEAGKKEKP....VK.SDCGEWQWSVCVPTSGDCGLGT.EG | |
| Retrocopy | MQSQQYVQQRRKFAAAFPAFIFILAAVGTAEAGKKEKPXXX>VKRSDCGEWQWSVCVPTSGDCGLGTGEG |
| Parental | TRTGAECKQTMKTQRCKIPCNWKKQFGAECKYQFQAWGECDLNTALKTRTGSLKRALHNADCQKTVTISK |
| TRTGAECK.T.KTQRCKIPCNWKKQFGAECKYQFQAWGECDLNTALKTRT.SLKRALHNADCQKTVTISK | |
| Retrocopy | TRTGAECKHTRKTQRCKIPCNWKKQFGAECKYQFQAWGECDLNTALKTRT*SLKRALHNADCQKTVTISK |
| Parental | PCGKLTKPKPQAESKKKKKEGKKQEKMLD |
| PCGKLTKPKPQAESKKKKKEGKKQEKMLD | |
| Retrocopy | PCGKLTKPKPQAESKKKKKEGKKQEKMLD |
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 | 16 .80 RPM | 265 .98 RPM |
| SRP017611_brain | 12 .78 RPM | 143 .86 RPM |
| SRP017611_kidney | 0 .00 RPM | 0 .00 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .07 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1872 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1872 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_1872 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 | ENSCAFG00000003369 | 1 retrocopy |
retro_cfam_1872 ,
|
| Callithrix jacchus | ENSCJAG00000012786 | 1 retrocopy |