RetrogeneDB ID:

retro_cpor_11

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_5:3432237..3433899(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCPOG00000007741
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_11
ATGGCTGCTGAGAAGAAGGCAGCGGTGGGATCCTTAGTTGGGACGGTAGTACAGAGCACCAGCACCACTAGTTTTCTGGT
TTTCAAGGCAAAAACAGCAGAACTACTCAGTCAGCATCAAGTGGAATTAACCCAAGAGTTCCCAAAAGACGGATGGGTAG
AACAGGACCCAAAGGAAATTCTACAGTCTGTCTATGAGTGTATAGCCAGAACATGTGAGAAACTCGACCAAGAGAATATT
GATATATCCAACATAAAAGCTATAGGTATCAGCAACCAGAGGGAAACCACCGTCATCTGGGACAAGTTAACTGGAGAGCC
ACTTTACAATGCGGTGGTTTGGCTTGACCTTAGAACCCAGTCTACCGTTGAAATTCTTAGTAAAAAAATTCCTGGAAATA
ATAACTTCGTCAAGTCCAAGACTGGCCTTCCGCTTAGCACCTACTTCAGTGCCGTGAAACTTCGTTGGATGTTTGACAAT
GTAAGACAAATCCAGAAAGCTGTGGAAGAAGGTCGAGCTCTGTTTGGTACAATTGATTCTTGGCTTATCTGGAGTATGAC
AGGGGGAGTCAATGGAGGTGTCCATGGGACAGATGTAACAAATGCAAGTAGGACAATGCTTTTCAACATCCATTCTTTGG
AATGGGATAAAGAGCTGTGTAAGTTTTTTGAAATTCCCATGAACATACTTCCAAATGTCTGGAGTTGTTCTGAGATCTAC
GGCCTTATGAAAGGTGGCATTTTGGAAGGTATCCCAATATCTGGGTGTTTGGGAGATCAGTCTGCTGCATTAGTAGGACA
AATGTGCTTCCAGGAAGGACAAGCCAAAAACACATACGGGACAGGTTGTTTCTTACTATGCAATACAGGTCAAAAGTGTA
TATTTTCTGAACATGGTCTTCTGACCACAATAGCTTACAAACTAGGCAAAGATAAACCAGTGTATTATGCATTGGAAGGT
TCTGTTGCTATAGCTGGTGCTGCTGTTCGATGGCTGAAAGACAACCTTGGTATTATAAAGACCTCAGAAGAAATTGAAAC
CCTTGCTAAAGAAGCAGGTACTTCTTTTGGCTGCTACTTTGTCCCAGCCTTTTCAGGGTTGTATGCACCTTATTGGGAGC
CCAGTGCAAGAGGAATAATCTGTGGTCTCACTCAGTTTACCAATAAGTGTCATATTGCTTATGCTGCATTAGAAGCTATT
TGTTTCCAAACTCGAGAGATTTTGGATGCCATGAACCATGATTGTGGAATTCCACTCCATCATTTACAGGTAGATGGGAA
CATGACTAAAAACAAAATTCTTATGCAACTACAAGCAGATATTCTGCATATTCCAGTAATAAAGTCTTCTATGTCTAATA
TAATAGCACTGGGAGCCGCTATGGCTGCAGGGGCTGCAGAAGGAGTAGATGTTTGGAGTTTAAAATCCAAGAATTTGTCA
GCAGTCACAGTGGAGCAAATTGAACCACAGATCCAGGCCACAGAAAGTGAAAGCCGTTATTCTACATGGAAAAAAGCTGT
GAAGAAGACGATGGGTTGGGTTTCACCTCAGACTGCTGAAAATGGTGAATTTACTACCTTCTCTAGTATGCCTTTGGGCT
TTTTTATAGTGAGTAGCATGATAATATTCATTGGCGCAAGATACATCTCAGGCATACCCTAA

ORF - retro_cpor_11 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.79 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMASTKKADLGPLVGAVDQGTSSTRFLVFNSKTAELLSHHQVEIKQEFPREGWVEQDPKEILQSVYECIEK
MA..KKA..G.LVG.V.Q.TS.T.FLVF..KTAELLS.HQVE..QEFP..GWVEQDPKEILQSVYECI..
RetrocopyMAAEKKAAVGSLVGTVVQSTSTTSFLVFKAKTAELLSQHQVELTQEFPKDGWVEQDPKEILQSVYECIAR
ParentalTCEKLGQLNIDISNIKAIGVSNQRETTVVWDKLTGEPLYNAVVWLDLRTQSTVENLSKRIPGNNNFVKSK
TCEKL.Q.NIDISNIKAIG.SNQRETTV.WDKLTGEPLYNAVVWLDLRTQSTVE.LSK.IPGNNNFVKSK
RetrocopyTCEKLDQENIDISNIKAIGISNQRETTVIWDKLTGEPLYNAVVWLDLRTQSTVEILSKKIPGNNNFVKSK
ParentalTGLPLSTYFSAVKLRWLLDNVRKVQKAVEENRALFGTIDSWLIWSLTGGVNGGVHCTDVTNASRTMLFNI
TGLPLSTYFSAVKLRW..DNVR..QKAVEE.RALFGTIDSWLIWS.TGGVNGGVH.TDVTNASRTMLFNI
RetrocopyTGLPLSTYFSAVKLRWMFDNVRQIQKAVEEGRALFGTIDSWLIWSMTGGVNGGVHGTDVTNASRTMLFNI
ParentalHSLEWDKELCEFFGIPMEILPNVRSSSEIYGLMKAGALEGVPISGCLGDQSAALVGQMCFQDGQAKNTYG
HSLEWDKELC.FF.IPM.ILPNV.S.SEIYGLMK.G.LEG.PISGCLGDQSAALVGQMCFQ.GQAKNTYG
RetrocopyHSLEWDKELCKFFEIPMNILPNVWSCSEIYGLMKGGILEGIPISGCLGDQSAALVGQMCFQEGQAKNTYG
ParentalTGCFLLCNTGHKCVFSEHGLLTTVAYKLGRDKPVYYALEGSVAIAGAVIRWLRDNLGIIKTSEEIEKLAK
TGCFLLCNTG.KC.FSEHGLLTT.AYKLG.DKPVYYALEGSVAIAGA..RWL.DNLGIIKTSEEIE.LAK
RetrocopyTGCFLLCNTGQKCIFSEHGLLTTIAYKLGKDKPVYYALEGSVAIAGAAVRWLKDNLGIIKTSEEIETLAK
ParentalEVGTSYGCYFVPAFSGLYAPYWETKCIGIIICGLTQFTNKCHIAFAALEAVCFQTREILDAMNRDCGIPL
E.GTS.GCYFVPAFSGLYAPYWE....G.IICGLTQFTNKCHIA.AALEA.CFQTREILDAMN.DCGIPL
RetrocopyEAGTSFGCYFVPAFSGLYAPYWEPSARG-IICGLTQFTNKCHIAYAALEAICFQTREILDAMNHDCGIPL
ParentalSHLQVDGGMTSNKILMQLQADILYIPVVKPSMPETTALGAAMAAGAAEGVGVWSLEPEDLSAVTMERFEP
.HLQVDG.MT.NKILMQLQADIL.IPV.K.SM....ALGAAMAAGAAEGV.VWSL....LSAVT.E..EP
RetrocopyHHLQVDGNMTKNKILMQLQADILHIPVIKSSMSNIIALGAAMAAGAAEGVDVWSLKSKNLSAVTVEQIEP
ParentalQINAEESEIRYSTWKKAVMKSMGWVTTQSPESGDPSIFCSLPLGFFIVSSMVMFIGARYISG
QI.A.ESE.RYSTWKKAV.K.MGWV..Q..E.G....F.S.PLGFFIVSSM..FIGARYISG
RetrocopyQIQATESESRYSTWKKAVKKTMGWVSPQTAENGEFTTFSSMPLGFFIVSSMIIFIGARYISG

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 .00 RPM 10 .53 RPM
SRP017611_kidney 0 .00 RPM 27 .64 RPM
SRP017611_liver 0 .00 RPM 57 .80 RPM
SRP040447_lung 0 .00 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_11 retrocopy.

TSS - click to see more details

Cavia porcellus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cpor_11 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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