RetrogeneDB ID:

retro_ocun_792

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:15:30659821..30660925(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOCUG00000028226
Aliases:None
Status:KNOWN_PSEUDOGENE
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_792
ATGAATGTGGCAGCCAAGTACCGCATGGCCTCCCTCTATGTGGGCGACCTCCATTCCGATGTCACCGAGGACCTGCTGTT
CAAGAAGTTCAGCAGGGTGGGGCCCGTGTTGTCCATCCGCATCTGCAGGGACCTGGTGACCCGCCGCTCTCTGGGCTATG
CCTACGTCAACTTCCTGCAGCTGGCCGATGCCCAGAAGGCCCTGGACACAATGAACTTTGATGTGGTGAAAGGCAAGGCC
ATCCGACTCATGTGGTCCCAACGGGACGCCTACTTGAGGAAATCTGGAATCGGGAACGTCTTCATCAAGAATCTGGACAA
GTCCATAGACAACAAAAGCCTTTATGAATGTTTTTCAGCTTTTGGAAAGATCCTTTCTTCCAAGGTGATGAGTGATGACC
GGGGCTCCAAGGGTTATGCGTTCGTGCACTTCCAGAGCCAGAGCGCCGCAGACAGGGCCATCGAGGAGATGAACGGGAAG
TTCCTCAAGGACTGCAAGGTGTTTGTGGGCAGATTCAAAAGCCGCAAAGATCGGGAAGCCGAGCTCAGAAACAAAGCCAG
TGAATTCACCAATGTCTACATCAAAAACTTCGGGGACGACATGGATGATGAGAGGCTGCGGGAAGTCTTCAGTACCTACG
GCAGAATTCTCAGTGTTAAGGTGATGACCAACTCCTGTGGGAAATCCAGAGGCTTTGGCTTTGTGAGTTTTGACAGCCAC
GAGGCCGCCAGAAAGGCCGTGGAAGAAATGAACGGCAAGGAAGTAAACGGGCAGCCCATTTTTGTAGGTCGGGCACAGAA
GAAGGTAGAGCGGCAGGCTGAGTTAAAGCAAATGTTTGAACAGTTGAAAAAGGAAAGAATCCGCGGGTGCCAGGGGGCGA
AACTCTACATTAAGAACCTTGATGAGAACATTGATGATGAAAAACTCCGAAAGGAGTTTTCTTCCTTTGGGTCCATTAGC
AGAGTTAAGGTGATGCAGGAAGAAGGACAAAGCAAAGGTTTCGGCTTGATCTGCTTCTCCTCTTCTGAGGATGCCGCTAG
AGCAATGACTGTGATGAATGGTCGCATCTTGGGCTCCAAACCTCTCAACATCGCTTTGGCCCAG

ORF - retro_ocun_792 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.44 %
Parental protein coverage: 51.61 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMNAAASSYPMASLYVGDLHSDVTEAMLYEKFSPAGPVLSIRVCRDMITRRSLGYAYVNFQQPADAERALD
MN.AA..Y.MASLYVGDLHSDVTE..L..KFS..GPVLSIR.CRD..TRRSLGYAYVNF.Q.ADA..ALD
RetrocopyMNVAAK-YRMASLYVGDLHSDVTEDLLFKKFSRVGPVLSIRICRDLVTRRSLGYAYVNFLQLADAQKALD
ParentalTMNFDVIKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY
TMNFDV.KGK.IR.MWSQRD..LRKSG.GNVFIKNLDKSIDNK.LY..FSAFG.ILS.KV..D..GSKGY
RetrocopyTMNFDVVKGKAIRLMWSQRDAYLRKSGIGNVFIKNLDKSIDNKSLYECFSAFGKILSSKVMSDDRGSKGY
ParentalAFVHFETQEAADKAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVYIKNFGEEVDDESLKDL
AFVHF..Q.AAD.AIE.MNG..L.D.KVFVGRFKSRK.REAEL..KA.EFTNVYIKNFG...DDE.L...
RetrocopyAFVHFQSQSAADRAIEEMNGKFLKDCKVFVGRFKSRKDREAELRNKASEFTNVYIKNFGDDMDDERLREV
ParentalFSQFGKTLSVKVMRDPSGKSKGFGFVSYEKHEDANKAVEEMNGKEIGGKVIFVGRAQKKVERQAELKRKF
FS..G..LSVKVM....GKS.GFGFVS...HE.A.KAVEEMNGKE..G..IFVGRAQKKVERQAELK..F
RetrocopyFSTYGRILSVKVMTNSCGKSRGFGFVSFDSHEAARKAVEEMNGKEVNGQPIFVGRAQKKVERQAELKQMF
ParentalEQLKQERISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLEDGRSKGFGFVCFSSPEEATKAV
EQLK.ERI...QG..LYIKNLD..IDDEKLRKEFS.FGSI...KVM.E.G.SKGFG..CFSS.E.A..A.
RetrocopyEQLKKERIRGCQGAKLYIKNLDENIDDEKLRKEFSSFGSISRVKVMQEEGQSKGFGLICFSSSEDAARAM
ParentalTEMNGRIVGSKPLYVALAQ
T.MNGRI.GSKPL..ALAQ
RetrocopyTVMNGRILGSKPLNIALAQ

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 36 .48 RPM
SRP017611_kidney 0 .51 RPM 69 .33 RPM
SRP017611_liver 0 .08 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_792 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_792 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_792 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Bos taurus retro_btau_656
Equus caballus retro_ecab_502
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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