RetrogeneDB ID:

retro_ocun_21

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:X:86448915..86449782(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOCUG00000014778
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSOCUG00000015117
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ocun_21
ATGAGTTCCAGAAAGCAGGGTTCTCAAACTCGTGGACAACAATCTGCGGAAGAAGACAACTTCAAAAAGCCAACTAGAGG
CAACATGCAGAGAAGTAAGATGAGAGGCGCCTCCTCAGGAAAGAAGACAGCTGGCCAACAGCCGAAGAATGTTGAACAAG
CTCTCCCAGGAAGATGGGGGGGTCGCTCGGCTGAGAACCCCCCTTCAGGATCTGTGAGGAAGACAAGGAAGAACAAGCAG
AAGACTCCTGGGAATGGAGATGGCGGCAGTACCAGCGAAGCACCCCAGCCCCCTCGGAAGAAGAGGGCCCGGGCCGATCC
CACTGTCGAAAGTGAGGATGCATTCAAGAATAGGATGGAAGTGAAGGTCAAGATCCCTGAAGAATTAAAACCATGGCTTG
TTGAGGACTGGGACTTAGTAACCAGGCAGAAACAGCTCTTTCAACTCCCTGCCAAGAAGAATGTAGATGCTATTCTGGAA
GAGTATGCCAATTGCAAGAAGTCACAGGGAAACATCGACAACAAAGAATATGCCGTCAATGAAGTTGTGGGAGGTATAAA
AGAGTATTTCAATGTGATGTTGGGCACTCAGCTGCTCTATAAGTTTGAGAGGCCCCAGTATGCTGAAATCCTGTTGGCTC
ACCCTGATGCGCCGATGTCCCAGGTTTATGGAGCACCACACCTACTGAGATTATTTGTGAGAATTGGAGCAATGTTGGCT
TATACGCCCCTTGATGAAAAGAGCCTTGCTCTATTGTTGGGCTATTTGCATGATTTCCTAAAATATCTGGCAAAGAATTC
TGCTTCTCTGTTTACTGCCAGTGATTATAAAGTGGCTTCTGCTGAGTACCACCGCAAAGCCCTGTGA

ORF - retro_ocun_21 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.91 %
Parental protein coverage: 61.78 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalKTKKNKQKTPGNGDGGSTSETPQPPRKKRARVDPTVENEETFMNRVEVKVKIPEELKPWLVDDWDLITRQ
KT.KNKQKTPGNGDGGSTSE.PQPPRKKRAR.DPTVE.E..F.NR.EVKVKIPEELKPWLV.DWDL.TRQ
RetrocopyKTRKNKQKTPGNGDGGSTSEAPQPPRKKRARADPTVESEDAFKNRMEVKVKIPEELKPWLVEDWDLVTRQ
ParentalKQLFYLPAKKNVDSILEDYANYKKSRGNTDNKEYAVNEVVAGIKEYFNVMLGTQLLYKFERPQYAEILAD
KQLF.LPAKKNVD.ILE.YAN.KKS.GN.DNKEYAVNEVV.GIKEYFNVMLGTQLLYKFERPQYAEIL..
RetrocopyKQLFQLPAKKNVDAILEEYANCKKSQGNIDNKEYAVNEVVGGIKEYFNVMLGTQLLYKFERPQYAEILLA
ParentalHPDAPMSQVYGAPHLLRLFVRIGAMLAYTPLDEKSLALLLNYLHDFLKYLAKNSATLFSASDYEVAPPEY
HPDAPMSQVYGAPHLLRLFVRIGAMLAYTPLDEKSLALLL.YLHDFLKYLAKNSA.LF.ASDY.VA..EY
RetrocopyHPDAPMSQVYGAPHLLRLFVRIGAMLAYTPLDEKSLALLLGYLHDFLKYLAKNSASLFTASDYKVASAEY
ParentalHRKAV
HRKA.
RetrocopyHRKAL

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 139 .24 RPM 123 .62 RPM
SRP017611_kidney 68 .72 RPM 81 .69 RPM
SRP017611_liver 48 .33 RPM 32 .14 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_21 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_21 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_21 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 28 parental genes, and 72 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000123441 retrocopy
retro_amel_124,
Bos taurus ENSBTAG000000109881 retrocopy
retro_btau_137,
Canis familiaris ENSCAFG000000141131 retrocopy
retro_cfam_20,
Callithrix jacchus ENSCJAG000000022145 retrocopies
retro_cjac_2113, retro_cjac_2280, retro_cjac_2574, retro_cjac_3026, retro_cjac_3179,
Cavia porcellus ENSCPOG000000037783 retrocopies
retro_cpor_114, retro_cpor_1409, retro_cpor_915,
Equus caballus ENSECAG000000080911 retrocopy
retro_ecab_62,
Felis catus ENSFCAG000000121971 retrocopy
retro_fcat_75,
Homo sapiens ENSG000001857873 retrocopies
retro_hsap_309, retro_hsap_3125, retro_hsap_850,
Gorilla gorilla ENSGGOG000000168263 retrocopies
retro_ggor_125, retro_ggor_2141, retro_ggor_694,
Loxodonta africana ENSLAFG000000098511 retrocopy
retro_lafr_62,
Myotis lucifugus ENSMLUG000000017561 retrocopy
retro_mluc_324,
Macaca mulatta ENSMMUG000000229261 retrocopy
retro_mmul_1064,
Monodelphis domestica ENSMODG000000115172 retrocopies
retro_mdom_150, retro_mdom_158,
Mustela putorius furoENSMPUG000000154291 retrocopy
retro_mputfur_180,
Mus musculus ENSMUSG000000622709 retrocopies
retro_mmus_1454, retro_mmus_1697, retro_mmus_176, retro_mmus_1771, retro_mmus_1825, retro_mmus_1833, retro_mmus_2500, retro_mmus_2612, retro_mmus_289,
Nomascus leucogenys ENSNLEG000000086783 retrocopies
retro_nleu_417, retro_nleu_445, retro_nleu_51,
Oryctolagus cuniculus ENSOCUG00000015117 2 retrocopies
retro_ocun_108, retro_ocun_21 ,
Otolemur garnettii ENSOGAG000000060474 retrocopies
retro_ogar_1594, retro_ogar_2616, retro_ogar_2896, retro_ogar_50,
Pongo abelii ENSPPYG000000067034 retrocopies
retro_pabe_1046, retro_pabe_201, retro_pabe_2581, retro_pabe_695,
Pan troglodytes ENSPTRG000000073513 retrocopies
retro_ptro_2114, retro_ptro_47, retro_ptro_591,
Rattus norvegicus ENSRNOG000000144106 retrocopies
retro_rnor_1076, retro_rnor_2270, retro_rnor_2357, retro_rnor_374, retro_rnor_793, retro_rnor_980,
Sorex araneus ENSSARG000000045191 retrocopy
retro_sara_15,
Sarcophilus harrisii ENSSHAG000000184021 retrocopy
retro_shar_393,
Sus scrofa ENSSSCG000000017691 retrocopy
retro_sscr_93,
Ictidomys tridecemlineatus ENSSTOG000000132943 retrocopies
retro_itri_111, retro_itri_1545, retro_itri_1608,
Tupaia belangeri ENSTBEG000000018978 retrocopies
retro_tbel_1694, retro_tbel_1704, retro_tbel_4638, retro_tbel_518, retro_tbel_550, retro_tbel_69, retro_tbel_753, retro_tbel_76,
Tursiops truncatus ENSTTRG000000166061 retrocopy
retro_ttru_472,
Vicugna pacos ENSVPAG000000088471 retrocopy
retro_vpac_229,


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