RetrogeneDB ID:

retro_ocun_54

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:1:94385897..94386791(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOCUG00000010504
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL5
Ensembl ID:ENSOCUG00000010089
Aliases:None
Description:ribosomal protein L5 (RPL5), mRNA [Source:RefSeq mRNA;Acc:NM_001195679]


Retrocopy-Parental alignment summary:






>retro_ocun_54
ATGGGGTTTGTTAAAGTTGTCAAGAACAAGGCCTACTTTAAGAGATACCAAGTGAAGTTTCGAAGACGGCGAGAGGGTAA
AACTGATTACTATGCTCGGAAACGCTTGGTGATCCAGGATAAAAATAAGTACAACACACCCAAATACAGGATGATAGTTC
GTGTAACTAATAGAGATATCATTTGTCAGATTGCTTATGCCCGTATAGAAGGGGATATGATAGTCTGTGCAGCTTATGCA
CACGAACTGCCAAAATACGGTGTGAAAGTTGGCCTGACCAATTATGCTGCAGCATATTGTACTGGCCTGCTGCTGGCTCG
CAGGCTTCTCAATAGGTTTGGCATGGACAAGATCTATGAAGGCCAAGTGGAGGTGACTGGAGATGAATACAATGTGGAAA
GCATTGATGGTCAACCTGGTGCCTTCACCTGCTATTTAGATGCAGGCCTTGCCAGAACTACTACTGGCAATAAAGTTTTT
GGAGCCCTGAAGGGAGCTGTGGATGGAGGCTTGTCCATCCCTCATGGTACCAAACGATTCCCTGGTTACGATTCTGAAAG
CAAGGAGTTTAATGCAGAAGTACATCGGAAGCACATTATGGGGCAGAATGTTGCAGATTACATGCGTTACCTAATGGAAG
AAGATGAAGATGCTTACAAGAAGCAATTCTCTCAGTACATAAAGAACAATGTGACTCCAGACATGATGGAGGAGATGTAC
AAGAAAGCCCACGCGGCTATACAAGAGAATCCAGTGTATGAGAAGAAGCCCAAGAGAGAAGTTAAAAAGAAGAGGTGGAA
CCGTCCCAAAATGTCCCTTGCCCAGAAGAAAGATCGGGTAGCTCAAAAGAAAGCAAGCTTCCTCAGAGCTCAGGAGCGGG
CTGCTGAGAGCTAA

ORF - retro_ocun_54 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 99.32 %
Parental protein coverage: 99.66 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalGFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDIICQIAYARIEG
GFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDIICQIAYARIEG
RetrocopyGFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDIICQIAYARIEG
ParentalDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGQPGA
DMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGQPGA
RetrocopyDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGQPGA
ParentalFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMGQNVADYMRYL
FTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPH.TKRFPGYDSESKEFNAEVHRKHIMGQNVADYMRYL
RetrocopyFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHGTKRFPGYDSESKEFNAEVHRKHIMGQNVADYMRYL
ParentalMEEDEDAYKKQFSQYIKNNVTPDMMEEMYKKAHAAIRENPVYEKKPKREVKKKRWNRPKMSLAQKKDRVA
MEEDEDAYKKQFSQYIKNNVTPDMMEEMYKKAHAAI.ENPVYEKKPKREVKKKRWNRPKMSLAQKKDRVA
RetrocopyMEEDEDAYKKQFSQYIKNNVTPDMMEEMYKKAHAAIQENPVYEKKPKREVKKKRWNRPKMSLAQKKDRVA
ParentalQKKASFLRAQERAAES
QKKASFLRAQERAAES
RetrocopyQKKASFLRAQERAAES

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 .11 RPM 39 .29 RPM
SRP017611_kidney 0 .30 RPM 72 .47 RPM
SRP017611_liver 0 .00 RPM 22 .58 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_54 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_54 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_54 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 18 parental genes, and 66 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000098785 retrocopies
retro_amel_1200, retro_amel_137, retro_amel_139, retro_amel_1439, retro_amel_1669,
Bos taurus ENSBTAG000000020262 retrocopies
retro_btau_120, retro_btau_67,
Cavia porcellus ENSCPOG000000006988 retrocopies
retro_cpor_1047, retro_cpor_1097, retro_cpor_1141, retro_cpor_1259, retro_cpor_1354, retro_cpor_1387, retro_cpor_428, retro_cpor_737,
Dipodomys ordii ENSDORG000000056742 retrocopies
retro_dord_226, retro_dord_670,
Equus caballus ENSECAG000000210651 retrocopy
retro_ecab_654,
Macropus eugenii ENSMEUG000000063613 retrocopies
retro_meug_1168, retro_meug_1537, retro_meug_2146,
Monodelphis domestica ENSMODG000000116351 retrocopy
retro_mdom_748,
Mustela putorius furoENSMPUG000000041506 retrocopies
retro_mputfur_213, retro_mputfur_449, retro_mputfur_451, retro_mputfur_597, retro_mputfur_721, retro_mputfur_833,
Mus musculus ENSMUSG0000005855811 retrocopies
retro_mmus_1000, retro_mmus_1185, retro_mmus_1338, retro_mmus_1789, retro_mmus_1991, retro_mmus_2577, retro_mmus_2846, retro_mmus_297, retro_mmus_3076, retro_mmus_504, retro_mmus_911,
Ornithorhynchus anatinus ENSOANG000000046691 retrocopy
retro_oana_97,
Oryctolagus cuniculus ENSOCUG00000010089 2 retrocopies
retro_ocun_265, retro_ocun_54 ,
Petromyzon marinus ENSPMAG000000020401 retrocopy
retro_pmar_23,
Pteropus vampyrus ENSPVAG000000151174 retrocopies
retro_pvam_1427, retro_pvam_355, retro_pvam_505, retro_pvam_527,
Rattus norvegicus ENSRNOG000000235296 retrocopies
retro_rnor_113, retro_rnor_2246, retro_rnor_2418, retro_rnor_2498, retro_rnor_2802, retro_rnor_2922,
Sarcophilus harrisii ENSSHAG000000064171 retrocopy
retro_shar_202,
Sus scrofa ENSSSCG000000068992 retrocopies
retro_sscr_149, retro_sscr_219,
Tupaia belangeri ENSTBEG000000105605 retrocopies
retro_tbel_101, retro_tbel_1054, retro_tbel_1518, retro_tbel_3006, retro_tbel_3530,
Tursiops truncatus ENSTTRG000000130975 retrocopies
retro_ttru_1446, retro_ttru_1548, retro_ttru_1796, retro_ttru_645, retro_ttru_979,


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