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:

ParentalKDFRNYNLYRVAAHELGHSLGLSHSTDIGALMYPNYMFSGDVQLAQDDIDGIQAIYGP-SQNPSQPVGPQ
K.FRNYNLY.V.AHE.GH.L.L.HS.D...LMYP.Y..SGDV.L.Q.D..GIQAI.GP.S..P..P.GP.
RetrocopyKSFRNYNLYHVVAHESGHPLRLCHSSDTESLMYPSYIISGDVHLPQHDTEGIQAICGP>SKSPLKPRGPG
ParentalTPKVCDSKLTFDAITTIRGEIMFFKDRFYMRANPYYSEVELNFISVFWPHLPNGLQAAYEVAHR-DEILF
TP..C..K.TF.A...I..E..FF..R..M........VE.NFIS.FW..LPNGL.A.YE.A.R..E..F
RetrocopyTP*ICGYK*TFQAESPIQREPTFFNGRSNMCTDSFHLGVEFNFISAFWLYLPNGLDATYELADR<SEVWF
ParentalFKGNKYW-TVQGQNELPGYPKDIHSSFGFPRSVNHIDAAVSEEDTGKTYFFVANKYW-RYDEYKRSMDAG
.KG.K.W.....Q..L..YP.D.H.S.G.P......DAAVSEE.TGK..F.VA...W.R.D..KR.MDAG
RetrocopySKGSKCW>SERNQIVLCRYPEDTHISSGCPGNLKRVDAAVSEEGTGKASFVVAKEFW>RCDG*KRPMDAG
ParentalYPKMIEYDFPGIGNKVDAVFKKDGFFYFFHGTRQYKFDPKTKRILTLQKANSWFNCRK
.P.M.....PG.GN.VD.V.KKDGFF.F.HG.R..KFDPK..RIL.LQKANSWF.C..
RetrocopySPQMTALGLPGTGNQVDTVLKKDGFFCFLHGKRRNKFDPK-MRILPLQKANSWFKCQE

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(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

ChIP-Seq - click to see more details

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ocun_1695 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

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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