RetrogeneDB ID:

retro_ocun_242

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:13:84561672..84563622(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOCUG00000027270
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSOCUG00000004432
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ocun_242
ATGGTGTCCACGGATTACAGTACCTACAGCCAAGCTGCAGCCCAGCAGGGCTACAGTGCTTACACCGCCCAGCCAACTCA
AGGATATGCACAGACCAGCCAGGCATATGGGCAACAAAGCTATGGAACCTATGGACAGCCCACTGATGTCAGCTATAGCC
AGGCTCAGACCACTGCGACCTATGGGCAGACAGCCTATGCAACTTCCTACGGACAGCCTCCCACTGGTTATACTACTCCA
ACTGCCCCCCAGGCATACAGCCAGCCTGTCCAGGGGTATGGCACTGGTGCTTATGATACCACCACTGCTACAGTCACCAC
CACCCAGGCCTCCTATGCAGCTCAGTCTGCATATGGCACTCAGCCTGCTTACCCAGCCTATGGGCAGCAGCCCACAGCCA
CTGCACCTGCAAGACCACAGGATGGTAACAAGCCAGCAGAGACTAGTCAACCCCAGTCTAGCACTGGGGGTTACAACCAG
CCCAGCCTAGGATATGGACAGAGTAACTACAGTTATCCCCAGGTACCTGGGAGCTACCCCATGCAGCCAGTCACCGCACC
ACCATCCTATCCTCCCACCAGCTACTCCTCTTCCCAGCCGACTAGTTACGATCAGAGCAGTTACTCTCAGCAGAACACCT
ACGGGCAGCCGAGCAGCTATGGACAGCAGAGTAGCTATGGTCAACAAAGCAGCTATGGGCAGCAGCCTCCCACTAGTTAC
CCCCCCCCCCAAACTGGATCCTACAGCCAGGCTCCAAGTCAATATAGCCAACAGAGCAGCAGCTACGGGCAGCAGAGTTC
ATTCCGACAGGACCACCCCAGTAGCATGGGTGTTTATGGGCAGGAGTCTGGAGGATTTTCCGGACCAGGAGAGAACCGGA
GCATGAGTGGCCCTGATAACCGGGGCAGGGGAAGAGGGGGATTTGATCGTGGAGGCATGAGCAGAGGTGGGCGGGGAGGA
GGACGCGGTGGAATGGGCGCTGGAGAGCGAGGTGGCTTCAATAAGCCTGGTGGACCCATGGATGAAGGACCAGATCTTGA
TCTAGGCCCACCTGTAGATCTGGATGAAGACTCTGACAACAGTGCAATTTATGTGCAAGGATTAAATGATAATGTGACTG
TGGATGATCTGGCAGACTTCTTTAAGCAGTGTGGGGTTGTTAAGATGAACAAGAGAACTGGGCAACCCATGATCCATGTA
TACCTGGACAAGGAGACAGGAAAGCCCAAAGGTGATGCCACAGTGTCCTATGAAGACCCACCAACCGCCAAGGCTGCTGT
GGAATGGTTTGATGGGAAAGATTTTCAAGGGAGCAAACTGAAAGTGTCTCTGGCCCGGAAGAAGCCTCCAATGAACAGCA
TGCGGGGTGGCATGCCGCCCCGGGAGGGCCTAGGGATGCCGCCGCCCCTCCGCGGAGGTCCTGGTGGGCCCATGGGTCGC
ATGGGAGGCCGTGGAGGAATCCGAGGCGGCTTCCCCCCGAGAGGGCCCCGGGGTTCCCGAGGGAACCCTTCTGGAGGAGG
GAACGTCCAGCACCGAGCTGGAGACTGGCAATGTCCCAACCCGGGCTGTGGAAACCAGAACTTTGCCTGGAGAACAGAAT
GCAACCAGTGTAAGGCCCCGAAGCCCGAGGGCTTCCTGCCACCACCCTTCCCGCCCCCGGGTGGCGATCGTGGCAGAGGC
GGCCCTGGTGGCATGAGGGGTGGAAGAGGTGGCCTCATGGACCGCAGTGGGCCCGGTGGAATGTTCAGAGGGGGCCGTGG
TGGAGACAGAGGTGGCTTCCGTGGTGGCCGGGGCATGGACCGAGGTGGCTTTGGAGGAGGAAGACGAGGTGGCCCAGGGG
GTCCACCTGGACCTTTGATGGAACAGATGGGAGGAAGAAGAGGTGGCCGTGGAGGACCTGGAAAAATGGATAAAGGGGAG
CACCGCCAGGAGCGCAGAGACCGCCCCTAC

ORF - retro_ocun_242 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.95 %
Parental protein coverage: 86.95 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalDYSTYSQAAAQQGYSAYTAQPTQGYAQTSQQAYGQQSYGTYGQPTDVSYSQAQTTATYGQTAYATSYGQP
DYSTYSQAAAQQGYSAYTAQPTQGYAQTS.QAYGQQSYGTYGQPTDVSYSQAQTTATYGQTAYATSYGQP
RetrocopyDYSTYSQAAAQQGYSAYTAQPTQGYAQTS-QAYGQQSYGTYGQPTDVSYSQAQTTATYGQTAYATSYGQP
ParentalPTGYTTPTAPQAYSQPVQGYGTGAYDTTTATVTTTQASYAAQSAYGTQPAYPAYGQQPTATAPARPQDGN
PTGYTTPTAPQAYSQPVQGYGTGAYDTTTATVTTTQASYAAQSAYGTQPAYPAYGQQPTATAPARPQDGN
RetrocopyPTGYTTPTAPQAYSQPVQGYGTGAYDTTTATVTTTQASYAAQSAYGTQPAYPAYGQQPTATAPARPQDGN
ParentalKPAETSQPQSSTGGYNQPSLGYGQSNYSYPQVPGSYPMQPVTAPPSYPPTSYSSSQPTSYDQSSYSQQNT
KPAETSQPQSSTGGYNQPSLGYGQSNYSYPQVPGSYPMQPVTAPPSYPPTSYSSSQPTSYDQSSYSQQNT
RetrocopyKPAETSQPQSSTGGYNQPSLGYGQSNYSYPQVPGSYPMQPVTAPPSYPPTSYSSSQPTSYDQSSYSQQNT
ParentalYGQPSSYGQQSSYGQQSSYGQQPPTSYPP-QTGSYSQAPSQYSQQSSSYGQQSSFRQDHPSSMGVYGQES
YGQPSSYGQQSSYGQQSSYGQQPPTSYPP.QTGSYSQAPSQYSQQSSSYGQQSSFRQDHPSSMGVYGQES
RetrocopyYGQPSSYGQQSSYGQQSSYGQQPPTSYPPPQTGSYSQAPSQYSQQSSSYGQQSSFRQDHPSSMGVYGQES
ParentalGGFSGPGENRSMSGPDNRGRGRGGFDRGGMSRGGRGGGRGGMGSAGERGGFNKPGGPMDEGPDLDLEGPP
GGFSGPGENRSMSGPDNRGRGRGGFDRGGMSRGGRGGGRGGMG.AGERGGFNKPGGPMDEGPDLDL.GPP
RetrocopyGGFSGPGENRSMSGPDNRGRGRGGFDRGGMSRGGRGGGRGGMG-AGERGGFNKPGGPMDEGPDLDL-GPP
ParentalVDLDEDSDNSAIYVQGLNDNVTVDDLADFFKQCGVVKMNKRTGQPMIHVYLDKETGKPKGDATVSYEDPP
VDLDEDSDNSAIYVQGLNDNVTVDDLADFFKQCGVVKMNKRTGQPMIHVYLDKETGKPKGDATVSYEDPP
RetrocopyVDLDEDSDNSAIYVQGLNDNVTVDDLADFFKQCGVVKMNKRTGQPMIHVYLDKETGKPKGDATVSYEDPP
ParentalTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSMRGGMPPREGRGMPPPLRGGPGGPGGPGGPMGRMGGRG
TAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSMRGGMPPREG.GMPPPLRGGPGGP.G..G..GR.G.RG
RetrocopyTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSMRGGMPPREGLGMPPPLRGGPGGPMGRMG--GRGGIRG
ParentalGDRGGFPPRGPRGSRGNPSGGGNVQHRAGDWQCPNPGCGNQNFAWRTECNQCKAPKPEGFLPPPFPPPGG
G....FPPRGPRGSRGNPSGGGNVQHRAGDWQCPNPGCGNQNFAWRTECNQCKAPKPEGFLPPPFPPPGG
RetrocopyG----FPPRGPRGSRGNPSGGGNVQHRAGDWQCPNPGCGNQNFAWRTECNQCKAPKPEGFLPPPFPPPGG
ParentalDRGRGGPGGMRGGRGGLMDRGGPGGMFRGGRGGDRGGFRGGRGMDRGGFGGGRRGGPGGPPGP-MDQMGV
DRGRGGPGGMRGGRGGLMDR.GPGGMFRGGRGGDRGGFRGGRGMDRGGFGGGRRGGPGGPPGP.M.QMG.
RetrocopyDRGRGGPGGMRGGRGGLMDRSGPGGMFRGGRGGDRGGFRGGRGMDRGGFGGGRRGGPGGPPGPLMEQMGG
ParentalRRGGRGGPGKMDKGEHRQERRDRPY
RRGGRGGPGKMDKGEHRQERRDRPY
RetrocopyRRGGRGGPGKMDKGEHRQERRDRPY

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 12 .53 RPM 71 .25 RPM
SRP017611_kidney 12 .77 RPM 59 .60 RPM
SRP017611_liver 5 .63 RPM 34 .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_242 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_242 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_242 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 17 parental genes, and 30 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000082982 retrocopies
retro_amel_191, retro_amel_959,
Canis familiaris ENSCAFG000000121608 retrocopies
retro_cfam_1142, retro_cfam_1183, retro_cfam_1225, retro_cfam_133, retro_cfam_1397, retro_cfam_1736, retro_cfam_1889, retro_cfam_560,
Callithrix jacchus ENSCJAG000000199874 retrocopies
retro_cjac_1716, retro_cjac_2022, retro_cjac_2813, retro_cjac_2911,
Cavia porcellus ENSCPOG000000095021 retrocopy
retro_cpor_1353,
Felis catus ENSFCAG000000042431 retrocopy
retro_fcat_519,
Homo sapiens ENSG000001829441 retrocopy
retro_hsap_463,
Gorilla gorilla ENSGGOG000000122121 retrocopy
retro_ggor_444,
Macropus eugenii ENSMEUG000000087031 retrocopy
retro_meug_1424,
Myotis lucifugus ENSMLUG000000120581 retrocopy
retro_mluc_328,
Monodelphis domestica ENSMODG000000086791 retrocopy
retro_mdom_279,
Mustela putorius furoENSMPUG000000134322 retrocopies
retro_mputfur_56, retro_mputfur_572,
Mus musculus ENSMUSG000000090791 retrocopy
retro_mmus_1379,
Oryctolagus cuniculus ENSOCUG00000004432 2 retrocopies
retro_ocun_1346, retro_ocun_242 ,
Pongo abelii ENSPPYG000000116841 retrocopy
retro_pabe_1769,
Pan troglodytes ENSPTRG000000142181 retrocopy
retro_ptro_350,
Ictidomys tridecemlineatus ENSSTOG000000231771 retrocopy
retro_itri_1892,
Tursiops truncatus ENSTTRG000000118811 retrocopy
retro_ttru_1366,


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