RetrogeneDB ID: | retro_cfam_519 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 12:34783792..34784541(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MRPS9 | ||
| Ensembl ID: | ENSCAFG00000002122 | ||
| Aliases: | None | ||
| Description: | mitochondrial ribosomal protein S9 [Source:HGNC Symbol;Acc:14501] |
Retrocopy-Parental alignment summary:
>retro_cfam_519
CATTTCATTTTCTTTTATACTGGCAAACAGGCGTATTATTATTTATTAATGCATGAAGCATATGGAAAGCTACTAGAAGT
AGAAAAACGTCAGAATCAGTTGCAAGCCAAAGGTCTATTTTCAGAAAAAAACTAAAACCAAAGACCTGATTGGCAGCAGA
TGGCTGATTTAGGAAGAGCTAGAAGAAATGTTAGTGGAAAAACTGTCAGATCAAGATTATGCACAGTTCATTCGGCTGCT
AGAAGGGTTATTGACACTGCACTGTGGTTCCGAAGAAGAATTTGTGCAGAGATTTCGTAGGAGTGTAACTATCAATCAAA
AAAACAACTGATCGAACCTGTGCAATATGATGAGTAAGGAATGGCCTTCAGCACCAGCGAAGGTAAAAGAAAGAGTGTAA
AAACAGAAGCAATCATTTATGGGCATGGAAGTGGAAGAATAAAAGTAAATGGAATTGACTATCTTCTTTACTTCCCAGTG
ACACAAGACAAAGAACAGTTGATATTCCCCTTCCACTTCCTCGACCGGCTTGGAAAACACAACACAACCTGTACTGTCTC
CGGGGCGAGCAGTCATTGCAGGCTGGAGCCATACACTTGGCAGTGGTGAGAGCCTTGTGCAATTTCGTCACAGAGGAAGA
GGTCAAGTGGATGAGAGTAGCTGGACTGCTGACTGCTGATCCACACATCAAAGAATGGAAGAAGCCAGGCCAAGAGGGAG
CCTGAAGAAAGTTTACTTGGAAGAAGCGC
ORF - retro_cfam_519 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.54 % |
| Parental protein coverage: | 62.78 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | HFLF-YTGKQAYYSL-MHEAYGKLLEVEKRQNQLQAKGLFSEK-TKTKDLIDSRWLIKEELEEMLVEKLS |
| HF.F.YTGKQAYY.L.MHEAYGKLLEVEKRQNQLQAKGLFSEK.TKTKDLI.SRWLI.EELEEMLVEKLS | |
| Retrocopy | HFIFFYTGKQAYYYLLMHEAYGKLLEVEKRQNQLQAKGLFSEK>TKTKDLIGSRWLI*EELEEMLVEKLS |
| Parental | DQDYAQFIRLLERLLTLHCGSEEEFVQRFRRSVTI-QSKKQLIEPVQYDEQGMAFSTSEGKRKSAKAEAI |
| DQDYAQFIRLLE.LLTLHCGSEEEFVQRFRRSVTI.QSKKQLIEPVQYDE.GMAFSTSEGKRKS.K.EAI | |
| Retrocopy | DQDYAQFIRLLEGLLTLHCGSEEEFVQRFRRSVTI<QSKKQLIEPVQYDE*GMAFSTSEGKRKSVKTEAI |
| Parental | VYGHGSGRIKVNGIDYLLYFPVTQDREQLMFPFHFLDRLGKHDTTCTVSG-GGRSSQAGAIRLAVARALC |
| .YGHGSGRIKVNGIDYLLYFPVTQD.EQL.FPFHFLDRLGKH.TTCTVSG.G..S.QAGAI.LAV.RALC | |
| Retrocopy | IYGHGSGRIKVNGIDYLLYFPVTQDKEQLIFPFHFLDRLGKHNTTCTVSG<GEQSLQAGAIHLAVVRALC |
| Parental | SFVTEEEVEWMRQAGLLTADPRVKERKKPGQEGARRKFTWKKR |
| .FVTEEEV.WMR.AGLLTADP..KE.KKPGQEGA.RKFTWKKR | |
| Retrocopy | NFVTEEEVKWMRVAGLLTADPHIKEWKKPGQEGA*RKFTWKKR |
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 .00 RPM | 31 .50 RPM |
| SRP017611_brain | 0 .00 RPM | 30 .25 RPM |
| SRP017611_kidney | 0 .00 RPM | 89 .68 RPM |
| SRP017611_liver | 0 .07 RPM | 30 .31 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_519 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_519 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_519 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000002122 | 1 retrocopy |
retro_cfam_519 ,
|
| Callithrix jacchus | ENSCJAG00000008156 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000007255 | 1 retrocopy | |
| Pteropus vampyrus | ENSPVAG00000000927 | 1 retrocopy |