RetrogeneDB ID:

retro_cpor_77

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_26:11568055..11569204(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCPOG00000002555
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:PABPC4
Ensembl ID:ENSCPOG00000009552
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_77
ATGGGGAGTGGGGAGCCTAATCCTGCAGGCAAGAAAAAGAAGTACCTCAAAGCAGCCCTATATGTGGGTGACTTGGATCC
AGAAGTCACTGAGGACATGCTCTATAAGAAGTTCAGGCCTGCTGGCCCTCTGCGCTTCACCAGAATCTGCCGTGACCCAG
TGACTCACAGTCCTCTGGGCTATGGCTATGTTAACTTCCGTTTTCCTGCGGATGCTGAGTGGGCCCTGAACACCATGAAT
TTTGACTTGATTAATGGCAAACCATTCCGCCTCATGTGGTCACAGCCAGATGACCGTTTAAGAAAGTCTGGAGTTGGAAA
TATATTCATCAAAAACCTGGACAAATCCATAGATAATAGGAGTCTCTTTTATTTGTTTTCTGCTTTTGGGAACATTCTTT
CCTGTAAAGTCGTTTGTGATGACAATGGTTCTAAGGGTTATGCATATGTACATTTTGACAGTCTGGCTGCTGCCAATAGG
GCTATCTGGCACATGAATGGAGTGCAGCTCAACAACCGCCAAGTGTATGTTGGCAGATTCAAATTCCCCGAAGAACGAGC
AGCTGAAGTCAGAACCAGGGATAAAGCAACTTTCACCAATGTTTTTGTTAAAAACCTTGGAGATGACATGGATGATGAAA
AACTGAAGACACTTTTCAGTGAATATGGGCAAACTGAGAGCGTTAAGTTAGTAAGAGATGCTAGTGGGAAATCTAAAGGT
TTTGGATTTGTGAGATATGAGACACATGACGCTGCTCAAAAGGCTGTGTTAGACCTTCATGGAAAATCAGTGGATGGGAA
AGTTCTATATGTAGGACGAGCACAGAAGAAAATTGAACGTTTGGCTGAATTAAGGCGGAGGTTTGAAAGGCTGAGATTAA
AAGAAAAAAGTCGGCCTCCAGGCGTGCCTATTTATATTAAGAACCTGGATGAGACCATAGATGAGGAAAAACTGAAAGAA
GAATTTTCTGCATTTGGATCTATTAGCCGAGCTAAGGTGATGATGGAAGTGGGACAAGGGAAAGGGTTTGGTGTCATCTG
CTTCTCTTCCTTTGAAGAGGCCACCAAAGCAGTGGAAGAGATGAATGGTCGCTTAGTGGGCTCCAAACCCTTGCATGTCA
CACTGGGCCAGGTTAGGCGCAGGTGGTGA

ORF - retro_cpor_77 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.29 %
Parental protein coverage: 54.85 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalYPMASLYVGDLHSDVTEAMLYEKFSPAGPVLSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVI
Y..A.LYVGDL...VTE.MLY.KF.PAGP....R.CRD..T...LGY.YVNF..PADAE.AL.TMNFD.I
RetrocopyYLKAALYVGDLDPEVTEDMLYKKFRPAGPLRFTRICRDPVTHSPLGYGYVNFRFPADAEWALNTMNFDLI
ParentalKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYAFVHFET
.GKP.R.MWSQ.D..LRKSGVGN.FIKNLDKSIDN..L...FSAFGNILSCKVVCD.NGSKGYA.VHF..
RetrocopyNGKPFRLMWSQPDDRLRKSGVGNIFIKNLDKSIDNRSLFYLFSAFGNILSCKVVCDDNGSKGYAYVHFDS
ParentalQEAADKAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAK-EFTNVYIKNFGEEVDDENLKELFSQFGK
..AA..AI..MNG..LN.R.V.VGRFK...ER.AE.....K..FTNV..KN.G...DDE.LK.LFS..G.
RetrocopyLAAANRAIWHMNGVQLNNRQVYVGRFKFPEERAAEVRTRDKATFTNVFVKNLGDDMDDEKLKTLFSEYGQ
ParentalTLSVKVMRDPSGKSKGFGFVSYEKHEDANKAVEEMNGKEINGKIIFVGRAQKKVERQAELKRKFEQLKQE
T.SVK..RD.SGKSKGFGFV.YE.H..A.KAV....GK...GK...VGRAQKK.ER.AEL.R.FE.L...
RetrocopyTESVKLVRDASGKSKGFGFVRYETHDAAQKAVLDLHGKSVDGKVLYVGRAQKKIERLAELRRRFERLRLK
ParentalRISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLEDGRSKGFGFVCFSSPEEATKAVTEMNGR
..SR..GV..YIKNLD.TID.EKL..EFS.FGSI..AKVM.E.G..KGFG..CFSS.EEATKAV.EMNGR
RetrocopyEKSRPPGVPIYIKNLDETIDEEKLKEEFSAFGSISRAKVMMEVGQGKGFGVICFSSFEEATKAVEEMNGR
ParentalIVGSKPLYVALAQ
.VGSKPL.V.L.Q
RetrocopyLVGSKPLHVTLGQ

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 1 .44 RPM 35 .03 RPM
SRP017611_kidney 0 .84 RPM 66 .48 RPM
SRP017611_liver 0 .04 RPM 33 .04 RPM
SRP040447_lung 0 .55 RPM 77 .38 RPM
SRP040447_skeletal_muscle 0 .62 RPM 440 .71 RPM

ChIP-Seq - click to see more details

Cavia porcellus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cpor_77 retrocopy.

TSS - click to see more details

Cavia porcellus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cpor_77 was not experimentally validated.

Retrocopy orthology:
Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
Parental genes homology:
Parental genes homology involve 21 parental genes, and 43 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 ENSCPOG000000020441 retrocopy
retro_cpor_1379,
Cavia porcellus ENSCPOG00000009552 2 retrocopies
retro_cpor_1330, retro_cpor_77 ,
Cavia porcellus ENSCPOG000000129171 retrocopy
retro_cpor_1324,
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 ENSOCUG000000005622 retrocopies
retro_ocun_153, retro_ocun_792,
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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