RetrogeneDB ID: | retro_cfam_659 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 15:34547058..34548059(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | NARF | ||
| Ensembl ID: | ENSCAFG00000012976 | ||
| Aliases: | None | ||
| Description: | nuclear prelamin A recognition factor [Source:HGNC Symbol;Acc:29916] |
Retrocopy-Parental alignment summary:
>retro_cfam_659
TGTGGCTTCCTCAAAAGTCTTGGGGGTGTGCACTGTCTTTGATACAGCAATAACTGTAGATTTCAGCACCCTGGAAAGTC
AGAAGGATCTGTGCCTTGATGCCACCAGCACAATGAGGAAGAGCCAGTGTTACCCAAGCTCACCTCCACCTGTCCAGGCT
GGGCCCCATATTCGGAACATAGGCTGGGCTACCCTTGTCACCCTTCCAACTCTACACCACCCACTCTCCCCAGCAGATCA
TGGGCTCCCTGGTGATGGATTACTTCGCCAGATAGCAGAACCTATCCCCAGACAAGATTTTCCACGTTATTGTGGCCCCT
TGCTACAACAATAAACTGGAGGTCCTCTGAGAAGATTTTCCCACAGCTTCACATGGTTTCCTGGGTGCTGACTGCATATT
AACCTCAGGTGAAATTTTTTCAGATAATGGAGGAAAGTGACCTCTTGGTGAAAAGACACTGCCATGTACACTCTGCTTGG
AGGCCTGAAGGAAAAGATGAGGCACCATGATGGAGCCAGCTCCAGCAGGTACCTGGCACACATCTTCAGGCATGCAGCCA
ACCAGCTGTTTAATGAGGATATGAGGGAAGTCACCTGCCACATCCCGAGGAACAAAGACTTGCAGGAGGTTAACTTTGAA
AAGAATGGGTAGGTTCTGTTATGCTTTGCTGCTGTGTACTGCTTTCAAAACATCCAGGATGGTTCTGAAACTGAAGAAGG
GCAATTTGTCATACCACTTGGTAGCAGTGCTTGCCTGGACCAGAGGATGTTTAAATGACGGAGGCCAAGCCCAGACCAAG
GATGGGCATGCAGACAAGGTGCTGCCATGGCAGATGGAAGGCATACACACTGATATCCCCATGCAGCCCCCTAGACCAGT
GCCCACATACAGGAGCTATACCAGGAGTGGATAAACAAAACCAACTGCCCCAGACTCCAAGAAGTTGTGCACAATGTACC
AGGGCCCAGCGCTTCCTGCCATCAGCTGAGACATCAAGTGG
ORF - retro_cfam_659 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 64.24 % |
| Parental protein coverage: | 73.46 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected: | 8 |
Retrocopy - Parental Gene Alignment:
| Parental | CGFLKSLG-VHYVFDTTIAADFSILESQKEF-VRRYQQHSEEEPALPMLTSACPGWVRYAERVLGHP-VT |
| CGFLKSLG.V..VFDT.I..DFS.LESQK...V....QH.EEEP.LP.LTS.CPGW..Y.E..LG.P... | |
| Retrocopy | CGFLKSLG>VCTVFDTAITVDFSTLESQKDL<VP*CHQHNEEEPVLPKLTSTCPGWAPYSEHRLGYP<LS |
| Parental | P-HLCTAKSPQQIMGSLVKDYFARQQNLSPDKIFHVIVAPCYDKKLEALREDFPTAPHGFRSADCVLTSG |
| P..L.T..SPQQIMGSLV.DYFAR.QNLSPDKIFHVIVAPCY..KLE.L.EDFPTA.HGF..ADC.LTSG | |
| Retrocopy | PFQLYTTHSPQQIMGSLVMDYFAR*QNLSPDKIFHVIVAPCYNNKLEVL*EDFPTASHGFLGADCILTSG |
| Parental | EI-AQIMEQSDLTV-KDAAVDTVFGGLKEEEVRRHDGASSDGYLAHVFRHAAKQLFDEDVGEVTYRTLRN |
| EI..QIME.SDL.V.KD.A..T..GGLK.E..R.HDGASS..YLAH.FRHAA.QLF.ED..EVT....RN | |
| Retrocopy | EI>FQIMEESDLLV>KDTAMYTLLGGLK-EKMRHHDGASSSRYLAHIFRHAANQLFNEDMREVTCHIPRN |
| Parental | KDFQEVTLEKNGEVLLRFAAAYGFRNIQNVVLKLKKGRF-PYHFVEVLACAGGCLNGRGQAQTEDGRADK |
| KD.QEV..EKNG.VLL.FAA.Y.F.NIQ........G.F..YH.V.VLA...GCLN..GQAQT.DG.ADK | |
| Retrocopy | KDLQEVNFEKNG*VLLCFAAVYCFQNIQD-GSETEEGQF>SYHLVAVLAWTRGCLNDGGQAQTKDGHADK |
| Parental | ALLRQMEGIYADIPVRPPE-SSAHVQELYQEWLDGADSPRAQEALHTKYQGP-GLPALSRDIKW |
| .L..QMEGI..DIP..PP...SAH.QELYQEW......PR.QE..H....GP..LPA.S.DIKW | |
| Retrocopy | VLPWQMEGIHTDIPMQPPR<TSAHIQELYQEWINKTNCPRLQEVVH-NVPGP>ALPAIS*DIKW |
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 | 4 .58 RPM | 59 .26 RPM |
| SRP017611_brain | 1 .11 RPM | 34 .62 RPM |
| SRP017611_kidney | 0 .53 RPM | 49 .20 RPM |
| SRP017611_liver | 0 .15 RPM | 11 .53 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_659 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_659 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_659 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 27 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000018178 | 1 retrocopy | |
| Canis familiaris | ENSCAFG00000012976 | 1 retrocopy |
retro_cfam_659 ,
|
| Dasypus novemcinctus | ENSDNOG00000011246 | 1 retrocopy | |
| Echinops telfairi | ENSETEG00000009329 | 1 retrocopy | |
| Myotis lucifugus | ENSMLUG00000017740 | 23 retrocopies |
retro_mluc_1006, retro_mluc_1012, retro_mluc_1083, retro_mluc_1091, retro_mluc_1124, retro_mluc_1256, retro_mluc_1282, retro_mluc_1457, retro_mluc_1573, retro_mluc_1622, retro_mluc_1632, retro_mluc_1700, retro_mluc_1718, retro_mluc_1898, retro_mluc_1973, retro_mluc_2365, retro_mluc_671, retro_mluc_688, retro_mluc_817, retro_mluc_825, retro_mluc_877, retro_mluc_879, retro_mluc_982,
|