RetrogeneDB ID:

retro_cpor_20

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_13:13986688..13988350(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCPOG00000006681
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:GYK
Ensembl ID:ENSCPOG00000003261
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_20
ATGGCAGCCGCAGAGAAAGCAGTTGTGGACCCTTTGGTCGGGGCAGTGGACCAGGGTACTAGCTCGACACGCTTTTTAGT
TTTCAATTCAAAAACAGCTGAACTGCTTAGTTATCATCAAGTGGAAATAAAGCAGCTGTTCCCCAGAGAAGGGTGGGCAG
AACAAGACCCTAAGGAAATTCTGCAGTCTGTCCACGACTGCATAGAGAAAACCTGTGAAAAACTCGGACAGCTCAATATT
GACATTTCCAACATAAAGGCTATTGGTGTCAGCAACCAGAGGGAAACCACCGTCATCTGGGACAAGTTAACCGGTGAGCC
TCTCTACAATGCTGTCCTGTGGCTTGATCTAAGAACCCAGGCAACCGTGGAGAAACTGAGTAAACTAATTCCAGAAAATA
AAAACTTTCTCAAGACCAAGACGGGCCTTCCGCTTAGCACTTACTTCAGCGCAGTGAAACTTCGCTGGCTCTTTGACAAC
GTAAGCCAAGTTCAGAAGGCTGTTGAGGGACACAGAGCTCTTTTTGGGACTATTGATTCGTGGCTTATTTGGTGTTTGAC
AGGAGGAGTCAACGGAGGGGTCCACTGTACCGATGTAACAAATGCCAGCAGGACAATGCTTTTCAACATTCATTCTTTGG
AATGGGATGAAGAGCTCTGCGACTTCTTTGGAATCCCAATGGAAATTCTTCCCAATGCCCGGAGTTCTTCTGAGATCTAT
GGCCTGATGAAATCTGGGTCCTTAGAAGGGGTGCCAATATCGGGGTGTTTGGGTGATCAATCTGCTGCTTTGGTTGGACA
AATGTGCTTCCAAGATGGACAAGCCAAAAATACATATGGAACAGGATGCTTCTTACTGTGTAACACAGGCCGTAAGTGTG
TATTTTCTGAACATGGCCTTCTGACCACCGTGGCTTACAAACTTGGAAGAGACCAACCAGTATGTTATGCCTTGGAAGGG
TCCATAGCTATAGCTGGTGCTGTTATTCGCTGGCTAAGAGACAACCTTGGAATTATTAAGACCTCAGAGGAAATTGAAAA
GCTTGCTAAAGAAGCAGGTACTTCGTATGACTGCTACTTTGTTCCAGCATTTTCAGGGCTGTATGCACCTTATTGGAAAC
CCAGTGCCAGAGGGATAATCTGTGGTCTCACTCAGTTCACCAACAAATGTCATATCGGTTTTGCTGCCTTAGAAGCTGTT
TGTTTCCAAACCCGAGAAATTTTGGATGCCATGAATCATGACTGTGGAATTCCCCTCAGTCATTTGCAGGTAGATGGAGG
AATGACCAACAACAAAATTCTTATGCAGTTACAGGCAGACATTTTGTGTATTCCAGTAATGAAGCCCACCATGCCAGAAA
CAACTGCCCTGGGTGCTGCCATGGCAGCAGGAGCCGCAGAAGGAGTCAGTGTTTGGAGTCTCAAACCAGAGGATTTGTCA
GTTGTCACAATGGAGCGGTTTGAACCTCATGTCAATCATGAAGAAAGTGAAATTCGTTACGCTACATGGAAGAAAGCCGT
GATGAGGTCAATGGACTGGGTTACAACAGAGTCTCCGGAAAGTGAAGACTCTGGTGTCTTCTGTAGTCTGAGTTTGGGCT
TTTTTATAGTAAGTAGCATGGTAATGTTAATCGGAGCAAGGTACCTCTCAACTAGCCCATAA

ORF - retro_cpor_20 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.02 %
Parental protein coverage: 99.82 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMASTKKADLGPLVGAVDQGTSSTRFLVFNSKTAELLSHHQVEIKQEFPREGWVEQDPKEILQSVYECIEK
MA...KA...PLVGAVDQGTSSTRFLVFNSKTAELLS.HQVEIKQ.FPREGW.EQDPKEILQSV..CIEK
RetrocopyMAAAEKAVVDPLVGAVDQGTSSTRFLVFNSKTAELLSYHQVEIKQLFPREGWAEQDPKEILQSVHDCIEK
ParentalTCEKLGQLNIDISNIKAIGVSNQRETTVVWDKLTGEPLYNAVVWLDLRTQSTVENLSKRIPGNNNFVKSK
TCEKLGQLNIDISNIKAIGVSNQRETTV.WDKLTGEPLYNAV.WLDLRTQ.TVE.LSK.IP.N.NF.K.K
RetrocopyTCEKLGQLNIDISNIKAIGVSNQRETTVIWDKLTGEPLYNAVLWLDLRTQATVEKLSKLIPENKNFLKTK
ParentalTGLPLSTYFSAVKLRWLLDNVRKVQKAVEENRALFGTIDSWLIWSLTGGVNGGVHCTDVTNASRTMLFNI
TGLPLSTYFSAVKLRWL.DNV..VQKAVE..RALFGTIDSWLIW.LTGGVNGGVHCTDVTNASRTMLFNI
RetrocopyTGLPLSTYFSAVKLRWLFDNVSQVQKAVEGHRALFGTIDSWLIWCLTGGVNGGVHCTDVTNASRTMLFNI
ParentalHSLEWDKELCEFFGIPMEILPNVRSSSEIYGLMKAGALEGVPISGCLGDQSAALVGQMCFQDGQAKNTYG
HSLEWD.ELC.FFGIPMEILPN.RSSSEIYGLMK.G.LEGVPISGCLGDQSAALVGQMCFQDGQAKNTYG
RetrocopyHSLEWDEELCDFFGIPMEILPNARSSSEIYGLMKSGSLEGVPISGCLGDQSAALVGQMCFQDGQAKNTYG
ParentalTGCFLLCNTGHKCVFSEHGLLTTVAYKLGRDKPVYYALEGSVAIAGAVIRWLRDNLGIIKTSEEIEKLAK
TGCFLLCNTG.KCVFSEHGLLTTVAYKLGRD.PV.YALEGS.AIAGAVIRWLRDNLGIIKTSEEIEKLAK
RetrocopyTGCFLLCNTGRKCVFSEHGLLTTVAYKLGRDQPVCYALEGSIAIAGAVIRWLRDNLGIIKTSEEIEKLAK
ParentalEVGTSYGCYFVPAFSGLYAPYWETKCIGIIICGLTQFTNKCHIAFAALEAVCFQTREILDAMNRDCGIPL
E.GTSY.CYFVPAFSGLYAPYW.....G.IICGLTQFTNKCHI.FAALEAVCFQTREILDAMN.DCGIPL
RetrocopyEAGTSYDCYFVPAFSGLYAPYWKPSARG-IICGLTQFTNKCHIGFAALEAVCFQTREILDAMNHDCGIPL
ParentalSHLQVDGGMTSNKILMQLQADILYIPVVKPSMPETTALGAAMAAGAAEGVGVWSLEPEDLSAVTMERFEP
SHLQVDGGMT.NKILMQLQADIL.IPV.KP.MPETTALGAAMAAGAAEGV.VWSL.PEDLS.VTMERFEP
RetrocopySHLQVDGGMTNNKILMQLQADILCIPVMKPTMPETTALGAAMAAGAAEGVSVWSLKPEDLSVVTMERFEP
ParentalQINAEESEIRYSTWKKAVMKSMGWVTTQSPESGDPSIFCSLPLGFFIVSSMVMFIGARYIS
..N.EESEIRY.TWKKAVM.SM.WVTT.SPES.D...FCSL.LGFFIVSSMVM.IGARY.S
RetrocopyHVNHEESEIRYATWKKAVMRSMDWVTTESPESEDSGVFCSLSLGFFIVSSMVMLIGARYLS

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 .06 RPM 10 .53 RPM
SRP017611_kidney 0 .00 RPM 27 .64 RPM
SRP017611_liver 0 .00 RPM 57 .80 RPM
SRP040447_lung 0 .03 RPM 42 .02 RPM
SRP040447_skeletal_muscle 0 .00 RPM 4 .64 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_20 retrocopy.

TSS - click to see more details

Cavia porcellus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cpor_20 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 34 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000091611 retrocopy
retro_amel_45,
Canis familiaris ENSCAFG000000137131 retrocopy
retro_cfam_19,
Callithrix jacchus ENSCJAG000000076333 retrocopies
retro_cjac_125, retro_cjac_3161, retro_cjac_4035,
Cavia porcellus ENSCPOG00000003261 2 retrocopies
retro_cpor_11, retro_cpor_20 ,
Equus caballus ENSECAG000000035991 retrocopy
retro_ecab_9,
Echinops telfairi ENSETEG000000082792 retrocopies
retro_etel_2000, retro_etel_247,
Felis catus ENSFCAG000000042641 retrocopy
retro_fcat_140,
Homo sapiens ENSG000001988144 retrocopies
retro_hsap_3087, retro_hsap_3120, retro_hsap_4885, retro_hsap_70,
Loxodonta africana ENSLAFG000000076321 retrocopy
retro_lafr_30,
Myotis lucifugus ENSMLUG000000010462 retrocopies
retro_mluc_151, retro_mluc_853,
Monodelphis domestica ENSMODG000000024171 retrocopy
retro_mdom_234,
Mus musculus ENSMUSG000000250592 retrocopies
retro_mmus_119, retro_mmus_97,
Nomascus leucogenys ENSNLEG000000101022 retrocopies
retro_nleu_1650, retro_nleu_771,
Oryctolagus cuniculus ENSOCUG000000130232 retrocopies
retro_ocun_2, retro_ocun_81,
Otolemur garnettii ENSOGAG000000169521 retrocopy
retro_ogar_261,
Pteropus vampyrus ENSPVAG000000124601 retrocopy
retro_pvam_1417,
Rattus norvegicus ENSRNOG000000341162 retrocopies
retro_rnor_114, retro_rnor_34,
Sarcophilus harrisii ENSSHAG000000064701 retrocopy
retro_shar_35,
Sus scrofa ENSSSCG000000122022 retrocopies
retro_sscr_479, retro_sscr_59,
Ictidomys tridecemlineatus ENSSTOG000000087321 retrocopy
retro_itri_1436,
Tarsius syrichta ENSTSYG000000082491 retrocopy
retro_tsyr_29,




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