RetrogeneDB ID:

retro_cpor_907

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_33:577728..580475(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCPOG00000004210
Aliases:None
Description:DNA ligase [Source:UniProtKB/TrEMBL;Acc:H0V2M3]


Retrocopy-Parental alignment summary:






>retro_cpor_907
CAGTGGAGTATCATGTCATTTTTCTACCCCACCAAAGAGGGTAAAGCAAAGAAGCCTGAGAAGGAAACCAACAGGAGCAG
CGGCAGAGAGACAGAGCCCCCTCCAAAGGTGGCACTGAGGGAGCGGAATGGAGTGGTGCCTGATAGTGACTCTCCAGTGA
AGAGGTCAGGGAGGAAGGCCGTGCGCGTCTTGAGCAGCGAAGCAGAGGAAAAAGATGAAGCCCTCAGCCCCACTGAAGAC
CAGAAGCCTGGGTCAGATTCCCCACAGGGGTCCCCGCCCAACCTCACCACGTGTCCCGGAAACAGCCCTCCCTTCTCGGA
CACTTCCCCTATGGTCGTCTCCCCATCAGGACTACCAAAGCGTCTCACAGCTTGGAAACAGCTCCCGAAACGGGTAATTC
AGGATGTGTTGGAGGATCAGAATGAGGACAAAGACAGAGAAGCTAAGAAGAGGAAGGAGGAAAAAGAAGCAGAGACTCCA
AGAGAAAGCCCAACAGAGACTGGAGCGGCAACAACGAAGGAAGAAGAGGAGGGGATCAGCCCTCGACACCCCCTGAGCCC
CCAGAACCCCAAAAGCAGAAGCCCCAGCAAAGACAGAAGGTGTTTCCACACCCAAGCTCCCCAGAAGCAGCAGCCACAGG
TAAAGAACCAGAGCAAGGCTGCCCCCAGAGTCTCCAGGACCCTCAGCAGTTTCTTCACAACCCGGAAGCCATCAGTCAAA
ACCCATGTGAAAGAAGAGCAGTCAGGTACCGCGGGAAAAGAGGGGGCCAAGGGATCCCTGGGCCCAGTGAGCTACAATCC
TGCTAAGAACAACTACCACCCCATGGAGTATGCCTGCTGGAGACAGGGCAGAAGGTTCCTTCCCTGGCTGTGGCACCGAC
GTTTGAGAAGATTGAGGAGGTTTCTGCTGGGCTCCGGATGGTGGAGACGCTGAGCAACTTGCTGCCCTCTGTGGTGGCCC
TGTCCCCTCCAGACCTGCTCCCTGTCCTCTACCTCACCCTTAACCGCCTTGGGCCTCCCCAGCAGGGCCTAGAGCTTGGC
GTTGGTGATGGTGTCCTTCTCAAGGCCGTGGCCCAGGCCACAGGCCACCATCTGGAATCTGTCCGGGCTGAGGCTGTTGA
GAGGGGAGACATTGGGCTGGTGGCTGAGAACAGCCGCAGTACTCAGAGACTGATGCTGCCACCACCTCCTCTTACCGCTT
CTGGGGTCTTCTCCAAGTTCCAGGACATTGCCCGGCTCACCGGCAATGCTTCCATGACCAAGAAGATGGCTATCATCAAA
GGCTGCTTTGTTGTCTGCCGCCACTCAGAAGCCCCGTTCATCGCCAGGGCCCTGAGTGGACGGCTGCGCCTCGGGTTGGC
CAAGCAGTCGGTGCTGGCTGCCCTTTCCCAGGCTGCGAGCCAAGAATTCCCAGGCCAAGAATTCCCTCTGGCCATGGTGG
ATGATGGGACAGGCAAGACCACAGAGGCCAGAAAGACATGGCTAGAGGAGCAAGGCATGATCTTGAAGCAGACATTCTGC
GAGGTGCCTGACCTGGACCGAATCATCCCTATGCTGCTGGAGCATGGCTTGGAGCGACTCCCAGAGCACTGCAGGCTGAG
CCCAGGGGTCCCTCTGAAACCTATGTTGGCCCATCCCACTCGGGGTGTCAGTGATGTCCTGAATCGCTTTGAGGAGGCAG
CCTTTACCTGCAAGTACAAATACGATGGGTAGAGGGCACAGATCCATCTTCTAGAAGGTGGGGAGGTGAAGATCTTCAGC
AGGAATCAGGAAGACAACATGGGGAAGTACCCCGACATCATCAGCCGCATCCCCAAGATTAAACTCCCCTCAGTCACATC
CTTTATCCTGGACATGAAGCTGTGGCTTGGGACCGGGAAAAAAAGCAGATCCAGCCATTACAAGTGCTAACCACTTGCAA
ACGGAAAGAAGTAGACACTGCAGAAATCCAGGTGCAGGTGTGTCCATGTGCCTTTGACCTCATCTACCTCAGTGGAGAGT
CTTTGGTCCCTGAGCCCCTGTCCCAACGCCGGCAGCTGCTCCGGGAGAACTTCGTAGAGACAGAAGGCGAGTTTGTCTTC
GCCACCTCTCTGGACACCAAGGACATGGAGCAGATTGCTGAGTTCTTGGAACAGTCAGTGAAAGACTCCTGCGAGGGGCT
GATGGTAAAGACCTTGGATGCTGATGCCACCTATGAGATTGCCAAGAGGTCACACAACTGGCTCAAGCTGAAGAAGGACT
ACCTCGATGGAATGGGTGACACCCTAGACCTCGTGGTGATAGGCACCTACCTGGGCCAGGGAAAGTGGACCAGCCACTAT
GGGGGCTTCCTGCTGGCTGCCTATGATGAGGAGAGCGAGGAGCTACAGGCCATATGCAACCTCGGAACGGGCTTCAGCAA
TGAGCAGCTGGAAGAGCATTACCAGAGCCTGGAGGCCCTGGTGCTTCCCACCCACGCCCCCACGTGCGGGCAGATGGTGC
CTTGGCGCCTGACCACTGGTTGGACCCCAATACTGTGTGGGAGGTGAAGTGTGCCATCTCTGTCTCTCCCCCATCTACCC
TGTTGCCCAGGGCCTGGTGGACAGTGAAAAGGGGCTCTCCCTCCACTTCCCTCGGTTTATTCGCGTACATGAGGACAAGA
AGCCAGAGGAGGCCACTACCAGTGCGTAGGCGGCCTGTCTGTACCACAAGCAAAGTCAGATTCAGAACCAAGGCATTGAC
TCAGACTCTGATGATGTAGAGTTCTAC

ORF - retro_cpor_907 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88. %
Parental protein coverage: 99.89 %
Number of stop codons detected: 2
Number of frameshifts detected 7


Retrocopy - Parental Gene Alignment:

ParentalQRSIMSFFYPTKEGKAKKPEKDTNKSSGRETEPPPKVALKERNGVVPDNDSPVKRSGRKAAQVLSSEGEE
Q.SIMSFFYPTKEGKAKKPEK.TN.SSGRETEPPPKVAL.ERNGVVPD.DSPVKRSGRKA..VLSSE.EE
RetrocopyQWSIMSFFYPTKEGKAKKPEKETNRSSGRETEPPPKVALRERNGVVPDSDSPVKRSGRKAVRVLSSEAEE
ParentalEDEALSPSEDQKPEPDSPQGSPPNLAKCPKNSPSFSDTSPMDISSSGIPKRITARKQLPKRVIQDVLEDQ
.DEALSP.EDQKP..DSPQGSPPNL..CP.NSP.FSDTSPM..S.SG.PKR.TA.KQLPKRVIQDVLEDQ
RetrocopyKDEALSPTEDQKPGSDSPQGSPPNLTTCPGNSPPFSDTSPMVVSPSGLPKRLTAWKQLPKRVIQDVLEDQ
ParentalNEDKDREAKKRKEEKEAETPRESLVETGAATVKEEEEG-HQPSTPPEPP-KAPKAEAPAKTEGVSTPKVP
NEDKDREAKKRKEEKEAETPRES..ETGAAT.KEEEEG..QPSTPPEPP...PKAEAPAKTEGVSTPK.P
RetrocopyNEDKDREAKKRKEEKEAETPRESPTETGAATTKEEEEG<DQPSTPPEPP<RTPKAEAPAKTEGVSTPKLP
Parental-QKQEPQEKNQSKAAPRVSRNLSSFFTPRKPSVKTDVKQEQSGTPGKEEAKRSLDPVSYNPAKNNYHPIE
.QKQ.PQ.KNQSKAAPRVSR.LSSFFT.RKPSVKT.VK.EQSGT.GKE.AK.SL.PVSYNPAKNNYHP.E
Retrocopy<QKQQPQVKNQSKAAPRVSRTLSSFFTTRKPSVKTHVKEEQSGTAGKEGAKGSLGPVSYNPAKNNYHPME
ParentalDACWRQG-QKVPYLAVARTFEKIEEVSARLRMVETLSNLLRSVVALSPPDLLPVLYLTLNRLGPPQQGLE
.ACWRQG.QKVP.LAVA.TFEKIEEVSA.LRMVETLSNLL.SVVALSPPDLLPVLYLTLNRLGPPQQGLE
RetrocopyYACWRQG<QKVPSLAVAPTFEKIEEVSAGLRMVETLSNLLPSVVALSPPDLLPVLYLTLNRLGPPQQGLE
ParentalLGVGDGVLLKAVAQATGRQLESVRAEAVEKGDIGLVAENSRSTQRLMLPPPPLTTSGVFSKFRDIARLTG
LGVGDGVLLKAVAQATG..LESVRAEAVE.GDIGLVAENSRSTQRLMLPPPPLT.SGVFSKF.DIARLTG
RetrocopyLGVGDGVLLKAVAQATGHHLESVRAEAVERGDIGLVAENSRSTQRLMLPPPPLTASGVFSKFQDIARLTG
ParentalNASMTKKMDIIKGLFVACRHSEARFIARALSGRLRLGLAEQSVLAALSQAVSLTPPGQEFPPAVVDAGKG
NASMTKKM.IIKG.FV.CRHSEA.FIARALSGRLRLGLA.QSVLAALSQA.S...PGQEFP.A.VD.G.G
RetrocopyNASMTKKMAIIKGCFVVCRHSEAPFIARALSGRLRLGLAKQSVLAALSQAASQEFPGQEFPLAMVDDGTG
ParentalKTTEARKTWLEEQGMILKQTFCEVPDLDRIIPVLLEHGLERLPEHCRLSPGVPLKPMLAHPTRGVSEVLK
KTTEARKTWLEEQGMILKQTFCEVPDLDRIIP.LLEHGLERLPEHCRLSPGVPLKPMLAHPTRGVS.VL.
RetrocopyKTTEARKTWLEEQGMILKQTFCEVPDLDRIIPMLLEHGLERLPEHCRLSPGVPLKPMLAHPTRGVSDVLN
ParentalRFEETAFTCEYKYDGQRAQIHLLEGGEVKIFSRNQEDNTGKYPDIISRIPKIKLPSVTSFILDT-EAVAW
RFEE.AFTC.YKYDG.RAQIHLLEGGEVKIFSRNQEDN.GKYPDIISRIPKIKLPSVTSFILD..EAVAW
RetrocopyRFEEAAFTCKYKYDG*RAQIHLLEGGEVKIFSRNQEDNMGKYPDIISRIPKIKLPSVTSFILDM<EAVAW
ParentalDREKKQIQPFQVLTTRKRKEVDAAEIQVQVCLYAFDLIYLNGESLVREPLSQRRQLLRENFVETEGEFVF
DREKKQIQP.QVLTT.KRKEVD.AEIQVQVC..AFDLIYL.GESLV.EPLSQRRQLLRENFVETEGEFVF
RetrocopyDREKKQIQPLQVLTTCKRKEVDTAEIQVQVCPCAFDLIYLSGESLVPEPLSQRRQLLRENFVETEGEFVF
ParentalATSLDTKDMEQIAEFLEQSVKDSCEGLMVKTLDVDATYEIAKRSHNWLKLKKDYLDGVGDTLDLVVIGAY
ATSLDTKDMEQIAEFLEQSVKDSCEGLMVKTLD.DATYEIAKRSHNWLKLKKDYLDG.GDTLDLVVIG.Y
RetrocopyATSLDTKDMEQIAEFLEQSVKDSCEGLMVKTLDADATYEIAKRSHNWLKLKKDYLDGMGDTLDLVVIGTY
ParentalLGRGKRAGRYGGFLLAAYDEESEELQAICKLGTGFSDEQLEEHYQSLQALVLPT-PRPYVRADGAVAPDH
LG.GK....YGGFLLAAYDEESEELQAIC.LGTGFS.EQLEEHYQSL.ALVLPT.PRP.VRADGA.APDH
RetrocopyLGQGKWTSHYGGFLLAAYDEESEELQAICNLGTGFSNEQLEEHYQSLEALVLPT<PRPHVRADGALAPDH
ParentalWLDPSAVWEVKCA-DLSLSPIYPAARGLVDSEKGISLRFPRFIRVREDKKPEEATTSAQVACLYRKQSQI
WLDP..VWEVKCA..L.LSPIYP.A.GLVDSEKG.SL.FPRFIRV.EDKKPEEATTSA..ACLY.KQSQI
RetrocopyWLDPNTVWEVKCA<HLCLSPIYPVAQGLVDSEKGLSLHFPRFIRVHEDKKPEEATTSA*AACLYHKQSQI
ParentalQNQGIDSDSDDEEFY
QNQGIDSDSDD.EFY
RetrocopyQNQGIDSDSDDVEFY

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 27 .09 RPM
SRP017611_kidney 0 .00 RPM 74 .33 RPM
SRP017611_liver 0 .00 RPM 32 .73 RPM
SRP040447_lung 0 .10 RPM 45 .83 RPM
SRP040447_skeletal_muscle 0 .00 RPM 24 .79 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_907 retrocopy.

TSS - click to see more details

Cavia porcellus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cpor_907 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 1 parental gene, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Cavia porcellus ENSCPOG00000004210 2 retrocopies
retro_cpor_907 , retro_cpor_914,


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