RetrogeneDB ID: | retro_ocun_593 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | 13:2262697..2263458(+) | ||
| Located in intron of: | ENSOCUG00000026497 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FAM76B | ||
| Ensembl ID: | ENSOCUG00000014549 | ||
| Aliases: | None | ||
| Description: | family with sequence similarity 76, member B [Source:HGNC Symbol;Acc:28492] |
Retrocopy-Parental alignment summary:
>retro_ocun_593
GAGTTCTCCCAGGGCCAACAGCTCTGCAGGGAATGTCGGATCGCACATCCTACTGTAAAGTGTACTTACTGCAGATGAGA
ATTCCAACAAGAGAGCAAACGAACACAATCTGTAAGTGCACAAGATGTTAAGGGATTTGGGACACCCAAACCTTGTCGAC
ACTGTAACATGATTGCAGCATTCATTGGTACCAAGTGTCAGCGCTGTACACATTCAGAAAAAAATGCAGACCCCCTCAGA
CCTGTGAACAGTGCGAACGACAGAGAGCTTTTGATGCGAGGGAGGAAAGTAGAAAGGCGGATCGAAAGTAGTTATGCTGG
CGCTGTACTTTACCATACAAGAGTTTTACAGAAGACAAAAGAACAAAGGAAGGCTCTGGGATCCTCGCATTCAGATCCTC
CTCCTCCTCCTCTGAGAAAGACTAGCATCATTCAAAACCTCTCCACCAGCACCACCACCGCCATCCTCTCAGCAGTAGCC
ATCACCAAGTCAGCAGCTGAAGTCCAGAGCGAGAGCAGGGACTGTGGAAACGGCGCCATAAATCCTCTGAAGCAGTTCAG
AATGAAGCTCCAGAGAAACCCCAGCTGGAATCTAAGCCATCGGATGGAGACAGCTCTACAAGTCAGTCAGCACGTGGTGG
GGCAACAGACAGTTTCGTCCTAAGTCAACTGAAAGAAGTGATGTCGCTTAAGCATCTCTTAGAGCAGAGAGACCAGGCCA
TTGTAGAAAAAGACAGACAGTCAACTGAACTAAAGGCAGAT
ORF - retro_ocun_593 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 64.66 % |
| Parental protein coverage: | 74.08 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | QFELGTPL-QECRIAHPIVKCTYCRSEFQQESKTNTICKKCAQNVKQFGTPKPCQYCNIIAAFIGTKCQR |
| .F..G..L..ECRIAHP.VKCTYCR.EFQQESK........AQ.VK.FGTPKPC..CN.IAAFIGTKCQR | |
| Retrocopy | EFSQGQQLCRECRIAHPTVKCTYCR*EFQQESKRTQSVS--AQDVKGFGTPKPCRHCNMIAAFIGTKCQR |
| Parental | CTNSEK-KYGPPQTCEQCKQQCAFDRKEEGRRKVDGKLLCWLCTLSYKRVLQKTKEQRKTLGSSH-SNSS |
| CT.SEK.K..PPQTCEQC..Q.AFD..EE.R.K.D.K.LCW.CTL.YK.....T...R...GS......S | |
| Retrocopy | CTHSEK<KCRPPQTCEQCERQRAFDAREESR-KADRK*LCWRCTLPYKSF---TEDKRTKEGSGILAFRS |
| Parental | SSSLTEKDQHHSKHHHHHHHHHHRHSSSHHKISSLSPEQEQGLWKQSHKSSAAIQNETPKKKPKLESKPS |
| SSS..EKD.HHSK..H.HHH.H...SSSHH..SS.SPE.EQGLWK..HKSS.A.QNE.P..KP.LESKPS | |
| Retrocopy | SSSSSEKD*HHSKPLHQHHHRHPL-SSSHHQVSS*SPEREQGLWKRRHKSSEAVQNEAP-EKPQLESKPS |
| Parental | NGDSSSINQSADSGGTDNFVLISQLKEEVMSLKRLLQQRDQTILEKDKKLTELKAD |
| .GDSS...QSA..G.TD.FVL.SQLK.EVMSLK.LL.QRDQ.I.EKD...TELKAD | |
| Retrocopy | DGDSST-SQSARGGATDSFVL-SQLK-EVMSLKHLLEQRDQAIVEKDRQSTELKAD |
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 .11 RPM | 8 .66 RPM |
| SRP017611_kidney | 0 .41 RPM | 9 .22 RPM |
| SRP017611_liver | 0 .15 RPM | 3 .55 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_593 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_593 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_593 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 | |
|---|---|---|---|
| Erinaceus europaeus | ENSEEUG00000008119 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000014549 | 1 retrocopy |
retro_ocun_593 ,
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