RetrogeneDB ID: | retro_ocun_525 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | 12:100181705..100182494(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSOCUG00000009673 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_ocun_525
ATGGCTAAGAACCTGCTAACACATACCACCTGTCCAATTTGCCTGGAAGATTTCCTAAATCCTGTCTCGCTTTCCTGTGG
ACATGTCTTCTGCTTTGATTGCATTCAAAGCTGGACTTCAGAAAGAGAGGAGGTCTGCCCCATCTGTCGCTCAGTCAATG
AGAAACCGCTTGTGGAAGAGTGGCAAATCAGAGCTTTCACGCATTACTTCAGGCAGCAGGGTCCTGTCCTGGGGCTGCGT
CTTAGTGAGGAGGTTCTGAGGTTCCAGGAGGACGAGGTCCTGGACACAGCTACCGCACACTCCCTCCTTGAGCTCTCCAG
CGACCTGAGGAGCGTTGAATGTGGGAAGACCTGCCACAACCTGCTGGAAGACCCCAGTAGTTTCCCTCACCTGGTCTGCA
TCCAGGGAAACACCTGCTTCTCCTGGGGCCGCCATTACTGGGAGGTTGAAGTAGGAGAAGCCAAGGAGTGGTCCCTGGGT
GTCTGGCAAGTGTCAGCTGACACAAAGAGAAATGGTGATTTAACCTCCGACCACGGTTTCTGGATCATCTTTGTAGAGGG
AGGACTCATTCACCCCAGCACCAACACAGAAGTAATCGTTCCTGCAAGCCCTAGTCTTCACCGCGTAGGAGTTTTCCTGG
ATGTGGATTTGGGAGAGATCAAGTTTTTTGATGTTGGAAATAAAGCTCTCATCTACATGCACAGGTTCCTCTCCACCGTG
GAGCCTTTTCATCCGTTCTTCTGTTTTGTACCTTTTTAATGTGCCACTGGTGCCCCCCTGAGCATCTGC
ORF - retro_ocun_525 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 73.98 % |
| Parental protein coverage: | 99.63 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAKNLLTATTCPICLGYFSCPVSLSCGHVFCLDCLHVWGLGREDFVLVCPTCRSVSERAPVEEWHIGKLT |
| MAKNLLT.TTCPICL..F..PVSLSCGHVFC.DC...W...RE....VCP.CRSV.E...VEEW.I...T | |
| Retrocopy | MAKNLLTHTTCPICLEDFLNPVSLSCGHVFCFDCIQSWTSEREE---VCPICRSVNEKPLVEEWQIRAFT |
| Parental | HLTRHHGGLLEQSLLLTEEVLRFQEDEVLDTATALSLIELSSNQRSVECGKTCHNPLEDPIRLSSLVCVL |
| H..R..G..L...L.L.EEVLRFQEDEVLDTATA.SL.ELSS..RSVECGKTCHN.LEDP.....LVC.. | |
| Retrocopy | HYFRQQGPVL--GLRLSEEVLRFQEDEVLDTATAHSLLELSSDLRSVECGKTCHNLLEDPSSFPHLVCIQ |
| Parental | GNTCFSWGRHYWEVEVGEAKEWTLGVWQESDNTKRNGDLTSDQGFWIICVEAGLIHPSTNIEVMVPASPS |
| GNTCFSWGRHYWEVEVGEAKEW.LGVWQ.S..TKRNGDLTSD.GFWII.VE.GLIHPSTN.EV.VPASPS | |
| Retrocopy | GNTCFSWGRHYWEVEVGEAKEWSLGVWQVSADTKRNGDLTSDHGFWIIFVEGGLIHPSTNTEVIVPASPS |
| Parental | LHRVGVFLDVDLGEIKFFDVGNKALIYMHRFLSTVEPFRPFYCFEIKHCHVTGNVVAVC |
| LHRVGVFLDVDLGEIKFFDVGNKALIYMHRFLSTVEPF.PF.CF....C..TG.....C | |
| Retrocopy | LHRVGVFLDVDLGEIKFFDVGNKALIYMHRFLSTVEPFHPFFCFVPF*C-ATGAPLSIC |
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 |
|---|---|---|
| SRP017611_brain | 0 .00 RPM | 0 .00 RPM |
| SRP017611_kidney | 0 .00 RPM | 0 .10 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .00 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_525 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_525 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_525 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Oryctolagus cuniculus | ENSOCUG00000009673 | 2 retrocopies |
retro_ocun_524, retro_ocun_525 ,
|