RetrogeneDB ID:

retro_ocun_1392

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:7:164456061..164456363(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL13A
Ensembl ID:ENSOCUG00000025258
Aliases:None
Description:ribosomal protein L13a [Source:HGNC Symbol;Acc:10304]


Retrocopy-Parental alignment summary:






>retro_ocun_1392
AAGGTGTTTAATGGGATCTCACTGCCCTGTGACAAGGAAAAGCAGATGGTAGTTCTTGCAGCCCTCAAGGTTGTGTACCT
GAAGCCTTTGAGAAAGTTTACCTACCTTGGTCTCCTGGCTTATGAAGTTGGCTGGAAGTACCAGGCAGTGACAGCTACAC
TGGAAGAAAAGAAAAGGAGAAAGCCAAGATCCATTACTGGAAGAAAAAACAGCTCATGAGGCCATAGAAACAGACCAAAA
AGAACTTGGAGAAGAAAATCAACACACTCACATGGGTCTTCAAGACCCATGGACTCCTGGTC

ORF - retro_ocun_1392 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.49 %
Parental protein coverage: 85.59 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalKVFDGIPPPYDKKKRMVVPAALKVVRLKPTRKFAYLGRLAHEVGWKYQAVTATLEEKR-KEKAKIHYRKK
KVF.GI..P.DK.K.MVV.AALKVV.LKP.RKF.YLG.LA.EVGWKYQAVTATLEEK..KEKAKIHY.KK
RetrocopyKVFNGISLPCDKEKQMVVLAALKVVYLKPLRKFTYLGLLAYEVGWKYQAVTATLEEKK<KEKAKIHYWKK
ParentalKQLMRLRKQAEKNVEKKISKFTDVLKTHGLLV
KQLMR..KQ..KN.EKKI...T.V.KTHGLLV
RetrocopyKQLMRP*KQTKKNLEKKINTLTWVFKTHGLLV

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 131 .02 RPM
SRP017611_kidney 0 .00 RPM 349 .17 RPM
SRP017611_liver 0 .00 RPM 66 .52 RPM
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_1392 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_1392 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_1392 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 21 parental genes, and 104 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000140272 retrocopies
Bos taurus ENSBTAG000000052963 retrocopies
Canis familiaris ENSCAFG000000298923 retrocopies
Callithrix jacchus ENSCJAG0000000007216 retrocopies
Cavia porcellus ENSCPOG000000124172 retrocopies
Equus caballus ENSECAG000000158323 retrocopies
Erinaceus europaeus ENSEEUG000000140716 retrocopies
Echinops telfairi ENSETEG000000170762 retrocopies
Felis catus ENSFCAG000000091944 retrocopies
Loxodonta africana ENSLAFG000000162133 retrocopies
Myotis lucifugus ENSMLUG0000000494510 retrocopies
Mustela putorius furoENSMPUG000000026043 retrocopies
Mus musculus ENSMUSG000000741293 retrocopies
Oryctolagus cuniculus ENSOCUG00000025258 9 retrocopies
Ochotona princeps ENSOPRG000000011943 retrocopies
Procavia capensis ENSPCAG000000040864 retrocopies
Pteropus vampyrus ENSPVAG000000109583 retrocopies
Rattus norvegicus ENSRNOG0000002061810 retrocopies
Sus scrofa ENSSSCG000000031664 retrocopies
Tarsius syrichta ENSTSYG000000087914 retrocopies
Tursiops truncatus ENSTTRG000000054857 retrocopies



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