RetrogeneDB ID:

retro_ocun_3

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:16:1914069..1915245(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOCUG00000024093
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSOCUG00000007220
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ocun_3
ATGGTTGAAGCAGATCGCCCAGGAAAGCTCTTCATTGGTGGGCTTAATACAGAAACAAATGAGAAAGCCCTTGAAGCAGT
ATTTGGCAAATATGGACGAATAGTGGAGGTACTCTTGATGAAAGACCGTGAAACCAACAAATCAAGAGGTTTTGCTTTTG
TCACCTTTGAAAGCCCAGCAGATGCTAAGGATGCTGCCAGAGACATGAATGGAAAGTCCTTGGATGGGAAAGCCATCAAG
GTGGAACAGGCTACCAAGCCATCATTTGAAAGTGGTAGGCGTGGACCACCTCCACCTCCACGAAGCAGAGGCCCACCAAG
AGGTCTTCGGGGAGGAAGAGGAGGAAGTGGAGGAACTCGAGGACCTCCCTCACGTGGAGGGCACATGGATGATGGTGGCT
ATTCCATGAATTTTAACATGAGTTCTTCCAGGGGACCGCTTCCAGTAAAAAGAGGACCACCACCACGAAGTGGGGGTCCT
CCTCCTAAAAGATCAGCCCCTTCAGGACCAGTTCGCAGCAGCAGTGGAATGGGAGGAAGAGCCCCTGTATCACGTGGAAG
AGACAGTTACGGAGGCCCACCTCGGAGGGAGCCCCTGCCCTCTCGCAGAGATGTTTATTTGTCCCCAAGAGATGATGGAT
ACTCTACTAAAGACAGCTATTCAAGCAGAGATTACCCGAGTTCTCGTGATACAAGAGATTATGCACCACCACCAAGAGAC
TATACCTACCGTGATTATGGTCATTCCAGTTCACGTGATGACTATCCATCAAGAGGCTATAGTGATAGAGATGGATATGG
TCGTGATCGGGACTATTCAGATCATCCAAGTGGAGGTTCCTACCGAGATTCCTATGAGAGTTATGGTAACTCACGTAGTG
CTCCACCTACACGAGGGCCCCCGCCATCTTATGGTGGAAGCAGTCGCTATGATGATTACAGCAGCTCACGTGACGGATAT
GGTGGAAGTCGAGACAGTTACTCAAGCAGCCGAAGTGATCTCTACTCAAGTGGTCGCGATCGGGTTGGCAGACAAGAAAG
AGGGCTTCCTCCTTCTATGGAAAGGGGGTACCCTCCTCCACGTGATTCCTACAGCAGTTCAAGCCGCGGAGCACCAAGAG
GTGGTGGCCGTGGAGGAAACCGATCTGATAGAGGGGGAGGCAGAAGCAGATACTAG

ORF - retro_ocun_3 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 100.0 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMVEADRPGKLFIGGLNTETNEKALEAVFGKYGRIVEVLLMKDRETNKSRGFAFVTFESPADAKDAARDMN
MVEADRPGKLFIGGLNTETNEKALEAVFGKYGRIVEVLLMKDRETNKSRGFAFVTFESPADAKDAARDMN
RetrocopyMVEADRPGKLFIGGLNTETNEKALEAVFGKYGRIVEVLLMKDRETNKSRGFAFVTFESPADAKDAARDMN
ParentalGKSLDGKAIKVEQATKPSFESGRRGPPPPPRSRGPPRGLRGGRGGSGGTRGPPSRGGHMDDGGYSMNFNM
GKSLDGKAIKVEQATKPSFESGRRGPPPPPRSRGPPRGLRGGRGGSGGTRGPPSRGGHMDDGGYSMNFNM
RetrocopyGKSLDGKAIKVEQATKPSFESGRRGPPPPPRSRGPPRGLRGGRGGSGGTRGPPSRGGHMDDGGYSMNFNM
ParentalSSSRGPLPVKRGPPPRSGGPPPKRSAPSGPVRSSSGMGGRAPVSRGRDSYGGPPRREPLPSRRDVYLSPR
SSSRGPLPVKRGPPPRSGGPPPKRSAPSGPVRSSSGMGGRAPVSRGRDSYGGPPRREPLPSRRDVYLSPR
RetrocopySSSRGPLPVKRGPPPRSGGPPPKRSAPSGPVRSSSGMGGRAPVSRGRDSYGGPPRREPLPSRRDVYLSPR
ParentalDDGYSTKDSYSSRDYPSSRDTRDYAPPPRDYTYRDYGHSSSRDDYPSRGYSDRDGYGRDRDYSDHPSGGS
DDGYSTKDSYSSRDYPSSRDTRDYAPPPRDYTYRDYGHSSSRDDYPSRGYSDRDGYGRDRDYSDHPSGGS
RetrocopyDDGYSTKDSYSSRDYPSSRDTRDYAPPPRDYTYRDYGHSSSRDDYPSRGYSDRDGYGRDRDYSDHPSGGS
ParentalYRDSYESYGNSRSAPPTRGPPPSYGGSSRYDDYSSSRDGYGGSRDSYSSSRSDLYSSGRDRVGRQERGLP
YRDSYESYGNSRSAPPTRGPPPSYGGSSRYDDYSSSRDGYGGSRDSYSSSRSDLYSSGRDRVGRQERGLP
RetrocopyYRDSYESYGNSRSAPPTRGPPPSYGGSSRYDDYSSSRDGYGGSRDSYSSSRSDLYSSGRDRVGRQERGLP
ParentalPSMERGYPPPRDSYSSSSRGAPRGGGRGGNRSDRGGGRSRY
PSMERGYPPPRDSYSSSSRGAPRGGGRGGNRSDRGGGRSRY
RetrocopyPSMERGYPPPRDSYSSSSRGAPRGGGRGGNRSDRGGGRSRY

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 .17 RPM 38 .19 RPM
SRP017611_kidney 0 .30 RPM 35 .47 RPM
SRP017611_liver 0 .00 RPM 16 .34 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_3 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_3 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_3 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 26 parental genes, and 55 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000133081 retrocopy
retro_btau_36,
Canis familiaris ENSCAFG000000189624 retrocopies
retro_cfam_1106, retro_cfam_1244, retro_cfam_1649, retro_cfam_1914,
Choloepus hoffmanni ENSCHOG000000123693 retrocopies
retro_chof_1240, retro_chof_2596, retro_chof_880,
Cavia porcellus ENSCPOG000000121641 retrocopy
retro_cpor_778,
Dasypus novemcinctus ENSDNOG000000171993 retrocopies
retro_dnov_1436, retro_dnov_2205, retro_dnov_696,
Dipodomys ordii ENSDORG000000154811 retrocopy
retro_dord_793,
Echinops telfairi ENSETEG000000131781 retrocopy
retro_etel_1952,
Felis catus ENSFCAG000000047791 retrocopy
retro_fcat_1903,
Homo sapiens ENSG000001472747 retrocopies
retro_hsap_23, retro_hsap_3074, retro_hsap_3587, retro_hsap_4144, retro_hsap_4846, retro_hsap_800, retro_hsap_91,
Gorilla gorilla ENSGGOG000000069441 retrocopy
retro_ggor_657,
Loxodonta africana ENSLAFG000000055683 retrocopies
retro_lafr_1188, retro_lafr_276, retro_lafr_35,
Microcebus murinus ENSMICG000000068562 retrocopies
retro_mmur_1252, retro_mmur_661,
Myotis lucifugus ENSMLUG000000132095 retrocopies
retro_mluc_1630, retro_mluc_1746, retro_mluc_203, retro_mluc_2180, retro_mluc_80,
Monodelphis domestica ENSMODG000000140541 retrocopy
retro_mdom_1231,
Mustela putorius furoENSMPUG000000018552 retrocopies
retro_mputfur_1539, retro_mputfur_956,
Mus musculus ENSMUSG000000311342 retrocopies
retro_mmus_170, retro_mmus_187,
Oryctolagus cuniculus ENSOCUG00000007220 1 retrocopy
retro_ocun_3 ,
Otolemur garnettii ENSOGAG000000078395 retrocopies
retro_ogar_1057, retro_ogar_137, retro_ogar_1586, retro_ogar_2445, retro_ogar_2584,
Ochotona princeps ENSOPRG000000165931 retrocopy
retro_opri_372,
Pongo abelii ENSPPYG000000207713 retrocopies
retro_pabe_2548, retro_pabe_303, retro_pabe_766,
Rattus norvegicus ENSRNOG000000008661 retrocopy
retro_rnor_268,
Sorex araneus ENSSARG000000003971 retrocopy
retro_sara_169,
Ictidomys tridecemlineatus ENSSTOG000000062112 retrocopies
retro_itri_1205, retro_itri_1346,
Tupaia belangeri ENSTBEG000000011541 retrocopy
retro_tbel_1919,
Tarsius syrichta ENSTSYG000000095551 retrocopy
retro_tsyr_15,
Tursiops truncatus ENSTTRG000000073221 retrocopy
retro_ttru_1450,


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