RetrogeneDB ID:

retro_cpor_315

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_120:617403..618186(-)
Located in intron of:ENSCPOG00000005845
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PCNA
Ensembl ID:ENSCPOG00000009242
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_315
ATGTTCGAGGCGCGCCTGGTCCAAGGCTCCATCCTGAAGAAGGTGCTGGAGGCTCTCAAGGACCTCATCAACGAGGCCTG
CTGGGATATCAGCTCGGGCGGCGTGAACCTACAGAGCATGGACTCGTCCCACGTCTCCCTGGTGCAGCTCACGCTGCGCT
CTGAGGGCTTCGACACGTACCGCTGTGACCGCAACTTGGCCATGGGTGTGAATCTCACCAGCATGTCCAAAATACTGAAA
TGCGCTGGCAATGAAGACATCATTACCCTAAGAGCTGAAGATAATGCAGACACTCTGGCACTAGTATTCGAAGCACCAAA
TCAGGAGAAAGTATCCGATTATGAAATGAAGTTAATGGATTTGGATGTTGAACAACTTGGAATTCCAGAGCAAGAATACA
GTTGTGTGGTAAAGATGCCTTCTGGTGAGTTCGCACGTATATGCCGAGACCTCAGTCACATCGGAGATGCTGTGGTGATA
TCATGTGCAAAAGATGGAGTGAAATTTTCTGCAAGTGGAGAACTTGGAAATGGAAACATTAAGTTGTCACAAACCAGCAA
CGTTGACAAAGAGGAAAAAGCTGTTACCATAGAGATGAATGAGCCTGTTCAGCTAACTTTTGCACTGAGGTATCTAAACT
TCTTTACAAAAGCAACTCCACTCTCTCCTACAGTAACACTCAGCATGTCTGCAGATGTACCCCTTGTTGTAGAGTATAAA
ATTTCTGATATGGGACATTTGAAGTACTATTTGGCTCCCAAGATTGAGGATGAAGAAGGATCT

ORF - retro_cpor_315 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 99.62 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMFEARLVQGSILKKVLEALKDLINEACWDISSGGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGV
MFEARLVQGSILKKVLEALKDLINEACWDISSGGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGV
RetrocopyMFEARLVQGSILKKVLEALKDLINEACWDISSGGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGV
ParentalNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMP
NLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMP
RetrocopyNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMP
ParentalSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSNVDKEEEAVTIEMNEPVQLTFALR
SGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSNVDKEE.AVTIEMNEPVQLTFALR
RetrocopySGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSNVDKEEKAVTIEMNEPVQLTFALR
ParentalYLNFFTKATPLSPTVTLSMSADVPLVVEYKISDMGHLKYYLAPKIEDEEGS
YLNFFTKATPLSPTVTLSMSADVPLVVEYKISDMGHLKYYLAPKIEDEEGS
RetrocopyYLNFFTKATPLSPTVTLSMSADVPLVVEYKISDMGHLKYYLAPKIEDEEGS

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 .23 RPM 12 .25 RPM
SRP017611_kidney 0 .42 RPM 29 .52 RPM
SRP017611_liver 0 .87 RPM 28 .64 RPM
SRP040447_lung 1 .34 RPM 52 .41 RPM
SRP040447_skeletal_muscle 0 .30 RPM 16 .76 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_315 retrocopy.

TSS - click to see more details

Cavia porcellus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cpor_315 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 24 parental genes, and 43 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000090891 retrocopy
retro_amel_1719,
Canis familiaris ENSCAFG000000060302 retrocopies
retro_cfam_1626, retro_cfam_946,
Callithrix jacchus ENSCJAG000000212783 retrocopies
retro_cjac_2159, retro_cjac_2175, retro_cjac_930,
Cavia porcellus ENSCPOG00000009242 1 retrocopy
retro_cpor_315 ,
Erinaceus europaeus ENSEEUG000000030691 retrocopy
retro_eeur_358,
Echinops telfairi ENSETEG000000065773 retrocopies
retro_etel_1152, retro_etel_1539, retro_etel_2217,
Felis catus ENSFCAG000000090682 retrocopies
retro_fcat_1363, retro_fcat_1729,
Homo sapiens ENSG000001326463 retrocopies
retro_hsap_3067, retro_hsap_4817, retro_hsap_857,
Gorilla gorilla ENSGGOG000000016952 retrocopies
retro_ggor_2107, retro_ggor_700,
Myotis lucifugus ENSMLUG000000016931 retrocopy
retro_mluc_1658,
Macaca mulatta ENSMMUG000000132593 retrocopies
retro_mmul_1059, retro_mmul_1960, retro_mmul_2570,
Monodelphis domestica ENSMODG000000116491 retrocopy
retro_mdom_933,
Mustela putorius furoENSMPUG000000061952 retrocopies
retro_mputfur_330, retro_mputfur_629,
Mus musculus ENSMUSG000000273421 retrocopy
retro_mmus_114,
Nomascus leucogenys ENSNLEG000000077262 retrocopies
retro_nleu_2192, retro_nleu_424,
Otolemur garnettii ENSOGAG000000331612 retrocopies
retro_ogar_1258, retro_ogar_2960,
Procavia capensis ENSPCAG000000105001 retrocopy
retro_pcap_130,
Pongo abelii ENSPPYG000000107953 retrocopies
retro_pabe_2542, retro_pabe_3745, retro_pabe_690,
Pan troglodytes ENSPTRG000000132223 retrocopies
retro_ptro_2068, retro_ptro_3206, retro_ptro_595,
Pteropus vampyrus ENSPVAG000000028651 retrocopy
retro_pvam_193,
Rattus norvegicus ENSRNOG000000212641 retrocopy
retro_rnor_1035,
Sorex araneus ENSSARG000000040701 retrocopy
retro_sara_640,
Sus scrofa ENSSSCG000000306421 retrocopy
retro_sscr_113,
Tursiops truncatus ENSTTRG000000153682 retrocopies
retro_ttru_1868, retro_ttru_440,


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