RetrogeneDB ID:

retro_ocun_153

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:X:83297815..83298964(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOCUG00000010919
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:PABPC4
Ensembl ID:ENSOCUG00000000562
Aliases:None
Description:poly(A) binding protein, cytoplasmic 4 (inducible form) [Source:HGNC Symbol;Acc:8557]


Retrocopy-Parental alignment summary:






>retro_ocun_153
ATGGGGAGCGGGGAGCCGAATCCTGCTGGCAAGAAAAAGAAATACCTCAAGGCCGCCCTGTATGTAGGTGACTTGGACCC
AGATGTCACCGAGGACATGCTGTATAAGAAGTTCAGGCCTGCTGGCCCTCTGCGCTTCACCCGCATCTGCCGTGACCCGG
TGACCCGCAGCCCCCTGGGCTATGGCTATGTTAACTTCCGCTTTCCGGCGGATGCCGAGTGGGCCTTGAACACCATGAAT
TTTGATTTGATTAACGGCAAACCCTTCCGCCTCATGTGGTCACAGCCAGATGACCGCTTAAGGAAGTCTGGAGTTGGAAA
TATATTCATCAAAAACCTGGACAAATCCATAGACAATAGGGCCCTGTTTTACTTATTTTCTGCTTTTGGGAACATTCTCT
CCTGCAAAGTGGTAAGCGATGACCACGGCTCTAAGGGCTATGCCTATGTGCATTTTGACAGCCTGGCTGCTGCCAACAGG
GCCATCTGGCACATGAATGGAGTGCGGCTCAACAACCGCCAGGTGTATGTTGGCAGATTCAAATTCCCGGAAGAGCGGGC
AGCTGAAGTCAGAACCAGGGATAGAGCAACTTTCACGAATGTTTTCGTTAAAAACTTTGGCGATGACATGGATGACGAAA
AACTGAAGGAACTGTTCAGCGAATACGGGCCAACCGAAAGTGTCAAGGTAATCAGAGATGCCAGTGGGAAATCGAAAGGC
TTTGGATTTGTGAGATATGAGACACATGAGGCTGCCCAAAAGGCTGTGCTAGACCTGCATGGAAAGTCCATCGATGGGAA
AGTCCTATACGTAGGGCGAGCGCAGAAGAAAATCGAACGCCTGGCTGAGTTAAGGCGGAGATTTGAGAGGCTAAGATTAA
AAGAAAAAAGCCGCCCTCCAGGGGTGCCTATCTATATTAAGAACCTCGATGAGAGCATCAGTGATGAGAAACTGAAGGAG
GAATTTTCTTCCTTTGGATCAATTAGCCGGGCCAAAGTGATGATGGAAGTGGGGCATGGCAAAGGGTTTGGTGTTGTGTG
CTTCTCCTCTTTTGAAGAGGCAACCAAAGCAGTGGATGAGATGAATGGTCGCATAGTGGGTTCCAAGCCCTTGCATGTCA
CCCTGGGCCAGGCCAGACGCAGGTGGTGA

ORF - retro_ocun_153 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.58 %
Parental protein coverage: 50.91 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalYPMASLYVGDLHSDVTEAMLYEKFSPAGPVLSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVI
Y..A.LYVGDL..DVTE.MLY.KF.PAGP....R.CRD..TR..LGY.YVNF..PADAE.AL.TMNFD.I
RetrocopyYLKAALYVGDLDPDVTEDMLYKKFRPAGPLRFTRICRDPVTRSPLGYGYVNFRFPADAEWALNTMNFDLI
ParentalKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYAFVHFET
.GKP.R.MWSQ.D..LRKSGVGN.FIKNLDKSIDN.AL...FSAFGNILSCKVV.D..GSKGYA.VHF..
RetrocopyNGKPFRLMWSQPDDRLRKSGVGNIFIKNLDKSIDNRALFYLFSAFGNILSCKVVSDDHGSKGYAYVHFDS
ParentalQEAADKAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAKE-FTNVYIKNFGEEVDDESLKDLFSQFGK
..AA..AI..MNG..LN.R.V.VGRFK...ER.AE........FTNV..KNFG...DDE.LK.LFS..G.
RetrocopyLAAANRAIWHMNGVRLNNRQVYVGRFKFPEERAAEVRTRDRATFTNVFVKNFGDDMDDEKLKELFSEYGP
ParentalTLSVKVMRDPSGKSKGFGFVSYEKHEDANKAVEEMNGKEIGGKVIFVGRAQKKVERQAELKRKFEQLKQE
T.SVKV.RD.SGKSKGFGFV.YE.HE.A.KAV....GK.I.GKV..VGRAQKK.ER.AEL.R.FE.L...
RetrocopyTESVKVIRDASGKSKGFGFVRYETHEAAQKAVLDLHGKSIDGKVLYVGRAQKKIERLAELRRRFERLRLK
ParentalRISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLEDGRSKGFGFVCFSSPEEATKAVTEMNGR
..SR..GV..YIKNLD..I.DEKL..EFS.FGSI..AKVM.E.G..KGFG.VCFSS.EEATKAV.EMNGR
RetrocopyEKSRPPGVPIYIKNLDESISDEKLKEEFSSFGSISRAKVMMEVGHGKGFGVVCFSSFEEATKAVDEMNGR
ParentalIVGSKPLYVALAQRK
IVGSKPL.V.L.Q..
RetrocopyIVGSKPLHVTLGQAR

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 2 .32 RPM 36 .48 RPM
SRP017611_kidney 0 .20 RPM 69 .33 RPM
SRP017611_liver 0 .00 RPM 53 .49 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_153 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_153 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_153 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 20 parental genes, and 42 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000115352 retrocopies
retro_amel_107, retro_amel_676,
Callithrix jacchus ENSCJAG000000025123 retrocopies
retro_cjac_214, retro_cjac_2722, retro_cjac_284,
Cavia porcellus ENSCPOG000000095522 retrocopies
retro_cpor_1330, retro_cpor_77,
Felis catus ENSFCAG000000152542 retrocopies
retro_fcat_116, retro_fcat_545,
Homo sapiens ENSG000000906212 retrocopies
retro_hsap_109, retro_hsap_74,
Gorilla gorilla ENSGGOG000000040023 retrocopies
retro_ggor_2127, retro_ggor_87, retro_ggor_916,
Microcebus murinus ENSMICG000000166331 retrocopy
retro_mmur_675,
Macaca mulatta ENSMMUG000000074971 retrocopy
retro_mmul_178,
Monodelphis domestica ENSMODG000000176572 retrocopies
retro_mdom_1090, retro_mdom_1805,
Mustela putorius furoENSMPUG000000144142 retrocopies
retro_mputfur_152, retro_mputfur_546,
Mus musculus ENSMUSG000000112577 retrocopies
retro_mmus_2006, retro_mmus_2326, retro_mmus_2327, retro_mmus_798, retro_mmus_801, retro_mmus_803, retro_mmus_805,
Nomascus leucogenys ENSNLEG000000119282 retrocopies
retro_nleu_1517, retro_nleu_62,
Oryctolagus cuniculus ENSOCUG00000000562 2 retrocopies
retro_ocun_153 , retro_ocun_792,
Oryctolagus cuniculus ENSOCUG000000043541 retrocopy
retro_ocun_13,
Otolemur garnettii ENSOGAG000000040671 retrocopy
retro_ogar_71,
Ochotona princeps ENSOPRG000000119841 retrocopy
retro_opri_1133,
Pongo abelii ENSPPYG000000015062 retrocopies
retro_pabe_190, retro_pabe_2563,
Pan troglodytes ENSPTRG000000005733 retrocopies
retro_ptro_101, retro_ptro_2093, retro_ptro_8,
Rattus norvegicus ENSRNOG000000156422 retrocopies
retro_rnor_175, retro_rnor_92,
Sarcophilus harrisii ENSSHAG000000181391 retrocopy
retro_shar_823,


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