RetrogeneDB ID: | retro_ocun_1695 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | GL018779:207504..208295(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MMP1 | ||
| Ensembl ID: | ENSOCUG00000017958 | ||
| Aliases: | MMP1, MMP-1 | ||
| Description: | matrix metallopeptidase 1 (interstitial collagenase) (MMP1), mRNA [Source:RefSeq mRNA;Acc:NM_001171139] |
Retrocopy-Parental alignment summary:
>retro_ocun_1695
AAGAGTTTCAGAAATTACAACTTGTATCATGTTGTGGCTCATGAATCAGGCCATCCCCTTAGACTCTGTCATTCTTCGGA
TACTGAGTCTTTGATGTACCCCAGCTACATCATCAGTGGTGATGTTCACCTGCCTCAGCATGACACTGAGGGCATCCAGG
CTATATGTGGGCCTTTCCAAATCCCCACTTAAGCCAAGAGGCCCAGGAACTCCATAGATATGTGGCTATAAGTGAACATT
TCAAGCTGAAAGTCCAATTCAGAGAGAACCAACGTTCTTTAATGGAAGGTCCAATATGTGCACAGATTCCTTCCACCTGG
GAGTTGAGTTCAATTTCATTTCTGCTTTCTGGCTGTATCTGCCAAATGGACTTGACGCCACTTATGAACTTGCTGATAGA
GTGAAGTCTGGTTTTCCAAAGGTAGTAAGTGCTGGGTCTGAGCGGAACCAGATTGTGCTGTGCAGGTACCCTGAGGACAC
CCACATCTCCTCTGGCTGCCCTGGAAACCTGAAGCGTGTCGATGCTGCTGTTTCTGAGGAGGGTACTGGGAAGGCATCGT
TTGTTGTTGCCAAGGAGTTCTGGACGGTGTGATGGATAGAAAAGACCCATGGATGCAGGTTCTCCCCAAATGACGGCACT
GGGCTTGCCTGGAACTGGCAACCAGGTTGACACTGTTCTCAAGAAAGATGGATTTTTCTGTTTCCTTCATGGGAAAAGGC
GGAACAAATTTGATCCTAAGATGAGGATTTTGCCTCTCCAGAAAGCTAATAGCTGGTTCAAATGCCAAGAA
ORF - retro_ocun_1695 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 54.85 % |
| Parental protein coverage: | 56.41 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | KDFRNYNLYRVAAHELGHSLGLSHSTDIGALMYPNYMFSGDVQLAQDDIDGIQAIYGP-SQNPSQPVGPQ |
| K.FRNYNLY.V.AHE.GH.L.L.HS.D...LMYP.Y..SGDV.L.Q.D..GIQAI.GP.S..P..P.GP. | |
| Retrocopy | KSFRNYNLYHVVAHESGHPLRLCHSSDTESLMYPSYIISGDVHLPQHDTEGIQAICGP>SKSPLKPRGPG |
| Parental | TPKVCDSKLTFDAITTIRGEIMFFKDRFYMRANPYYSEVELNFISVFWPHLPNGLQAAYEVAHR-DEILF |
| TP..C..K.TF.A...I..E..FF..R..M........VE.NFIS.FW..LPNGL.A.YE.A.R..E..F | |
| Retrocopy | TP*ICGYK*TFQAESPIQREPTFFNGRSNMCTDSFHLGVEFNFISAFWLYLPNGLDATYELADR<SEVWF |
| Parental | FKGNKYW-TVQGQNELPGYPKDIHSSFGFPRSVNHIDAAVSEEDTGKTYFFVANKYW-RYDEYKRSMDAG |
| .KG.K.W.....Q..L..YP.D.H.S.G.P......DAAVSEE.TGK..F.VA...W.R.D..KR.MDAG | |
| Retrocopy | SKGSKCW>SERNQIVLCRYPEDTHISSGCPGNLKRVDAAVSEEGTGKASFVVAKEFW>RCDG*KRPMDAG |
| Parental | YPKMIEYDFPGIGNKVDAVFKKDGFFYFFHGTRQYKFDPKTKRILTLQKANSWFNCRK |
| .P.M.....PG.GN.VD.V.KKDGFF.F.HG.R..KFDPK..RIL.LQKANSWF.C.. | |
| Retrocopy | SPQMTALGLPGTGNQVDTVLKKDGFFCFLHGKRRNKFDPK-MRILPLQKANSWFKCQE |
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 .06 RPM | 0 .06 RPM |
| SRP017611_kidney | 0 .00 RPM | 2 .64 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_1695 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_1695 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_1695 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Oryctolagus cuniculus | ENSOCUG00000017958 | 1 retrocopy |
retro_ocun_1695 ,
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