RetrogeneDB ID:

retro_cpor_477

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_163:1844636..1847441(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCPOG00000023166
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:AP1B1
Ensembl ID:ENSCPOG00000005293
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_477
ATGACTGACTCCAAGTACTTCACAACCAATAAAAAGGGAGAAATCTTTGCATTAAAAGCTGAACTCAACAATGAAAAGAA
AGAAAAGAGGAAAGAGGCTGTGAAAAAAGTGATTGTTGCTACGACTGTGGGGAAGGATGTTAGCTCTCTCTTTCCGGATG
TAGTCAACTGTATGCAGACGGATAACCTGGAATTAAAGAAGCTCGTGTATCTGTACTTGACAAACTACGCCAAGAGTCAA
CCAGACATGGCCAGCATGGCTGTCAACAGTTTTGTGAAGGACTGTGAAGATCCCAATCCTTTGATTCGGGCCTTGGCAGT
CAGAACCATGGGGTGCATCCGGGTGGACAAGATTACAGAATATATTTGTGAGCCCCTTCGCAAGTGCTTGAAGGATGAAG
ATCCCTATGTTCGGAAAACAGCAGCAGTCTGTGTGGCAAAACTCCATGATATCAATGCCCAAATGGTGGAAGATCAGGGA
TTTCTCGATTCTCTGCGGGATCTCATAGCAGATTCAAATCCAATGGTGGTGGCTAATGCTGAAGCAGGATTGTCTGAAAT
TAGTGAGTCTCACCCAAACAGCAACTTTCTCAATTTGAACCCACAGAACATTAATAAGCTACTGACAGCTCTGAATGAGT
GCACCGAGTGGGGCCAGATTTTCATCTTGGACTGCTTGTCTAACTATAACCCTAAAGATGACTGGGAAGCTCAGAGCATC
TGTGAGTGGGTAACTCCCGGTTATCCCATGCCAACTCAGCAGTGGTATTCTCAGCAATAAAAGTCCTAATGAAATTTCTG
GAATTGTTACCCAAGGACTCCGACTACTACAATATGCTGCTGAAGAAGTTAGCTCCTCCACTTGTTACTTTGCTGTCTGG
GGAGCCAGAAGTGCAGTATGTTGCCTTGAGGAACATCAACTTAATTGTCCAGAAAAGGCCTGAAATCTTGAAGCAGGAAA
TCAAAGTCTTCTTTGTGAAGTACAATGATCCCATCTATGTTAAACTAGAGAAGTTGCACATCATGATTCGCCTGGTGTCC
CAAGCTAACATTGCTCAGGTTTTAGCAGAGCTGAAGGAATATGCCACTGAGGTGGATGCTGACTTCGTTCGCAAAGCTGT
GAGGGCCATTGGACGATGTGCCATCAAGGTGGAACAATCTGCAGAGCACTGTGTAAGCACATTGCTTGACTTAATCCAGA
CCAAAGTAAATTATGTGGTCCAAGAGGCAATTGTTGTCATCAGGGATATCTTCCGCAAATATCCCAACAAGTATAAAAGT
ATTATTGCCACTCTGTGTGAGAACTTAGACACCTTGGATGAGCCAGATGCACGAGCAGCCATGATTTGGATCATGGGAGA
ATATGCTGAAAGAATTGACAATGCAGATGAGTTACTAGAGAGTTTCTTGGAGGGTTTTCATGAAGAAAGTACCCAAGTCC
AGCTCATTCTGCTTACTGCCATAGTAAAGCTGTTTCTCAAGAAACCATCAGAAACACAAGAGCTCATCCAACAGGTCTTG
AGTTTGGCAACACAGGATTCCGATAATCCTGACCTCCGAGACCAGGGCTATATTTATTGGTGTCTTCTCTCAACTGACCC
CAGTGACAGCCAAAGAAGTAGTCTTGTCTGAGAAGCCACTAATCTCTGAGGAAACAGACCTTATTGAGCCAACTCTGCTG
GATGAACTGATATGTCACAATGGTTCCTTGGCCTCTGTGTATCATAAGCCTCCCAATGCTTTTGTGGGAGTCATGGGATT
CATCGCAAACACTTGCCAATTCATCATGGGAGCACTGATGCAGGTGACAGTCCTGTTGGCACCACCATTGCAAGCAACCT
GGAACAGCCTCAGGTTATCCCCTCTCAAGGTGACCTTCTTGGAGATCTTTTAAATCTTGACCTTGGTCCCCCCAGTCAAT
GTGCCACAGGTGTCCTCCATGCAGATGGGAGCAGTGGATCTCCTGGGAGGACTAGATAGTCTGGTCGGACAGTCCTTCAT
CCCATCATCACTGCCTGCAACCTTTGCTCCCTCACCGACTCCTGCCATAGTCAGCAGTGTTCTTAATGACCTGTTTGAAC
TCTCCATGGGGATAGGCATGGCGCCTGGTGGATACGTGGCTCCTAAGGCTGTCTGGCTACTTGGAGTAAAGGCCAAAGGC
TTGGAGATTTCAGGAACATTTACTCACCGCCAGGGGCACATCTATATGGAAATGAACTTCACCAACAAAGCTCTGCAGCA
TATGACAGACTTTGCAATCCAGCTTAACAAGAACAGCTTTGGTGTCATCCCAAGCACTCCTCTGGCCATCCATACACCAC
TGATGCCAAACCAAAGCATTGACGTCTCCCTGCCTCTCAACACCTTGGGCCCAGTCATGAAGATGGAACCTCTAAATAAC
TTGCAGGTGGCTGTTAGAAACAATATTGATGTCTTCTACTTTAGCTGCCTCATCCCACTCAATGTGCTTTTTGTAGAAGA
TGGCAAAATGGAGCGCCAAGTCTTCCTGGCAACATGGAAGGACATTCCCAATGAAAATGAACTCCAGTTTCAGATTAAGG
AATGTCATTTAAATGCTGACACTGTTTCCAGCAAATTGCAAAACAACAATGTTTATACTATTGCCAAGAGAAACGTGGAA
GGGCAGGACATGCTGTACCAGTCCCTAAAGCTCGCTAATGGCATTTGGATTTTGGCTGAGCTACGTATCCAGCCAGGAAA
CCCTAATTATACGCTGTCACTGAAATGTAGAGCTCCTGAAGTGTCTCAATACATCTATCAGGTCTACGATAGCATTTTGA
AAAAC

ORF - retro_cpor_477 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.87 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMTDSKYFTTTKKGEIFELKAELNSDKKEKKKEAVKKVIASMTVGKDVSALFPDVVNCMQTDNLELKKLVY
MTDSKYFTT.KKGEIF.LKAELN..KKEK.KEAVKKVI...TVGKDVS.LFPDVVNCMQTDNLELKKLVY
RetrocopyMTDSKYFTTNKKGEIFALKAELNNEKKEKRKEAVKKVIVATTVGKDVSSLFPDVVNCMQTDNLELKKLVY
ParentalLYLMNYAKSQPDMAIMAVNTFVKDCEDPNPLIRALAVRTMGCIRVDKITEYLCEPLRKCLKDEDPYVRKT
LYL.NYAKSQPDMA.MAVN.FVKDCEDPNPLIRALAVRTMGCIRVDKITEY.CEPLRKCLKDEDPYVRKT
RetrocopyLYLTNYAKSQPDMASMAVNSFVKDCEDPNPLIRALAVRTMGCIRVDKITEYICEPLRKCLKDEDPYVRKT
ParentalAAVCVAKLHDINAQLVEDQGFLDTLKDLISDSNPMVVANAVAALSEIAESHPSSNLLDLNPQSINKLLTA
AAVCVAKLHDINAQ.VEDQGFLD.L.DLI.DSNPMVVANA.A.LSEI.ESHP.SN.L.LNPQ.INKLLTA
RetrocopyAAVCVAKLHDINAQMVEDQGFLDSLRDLIADSNPMVVANAEAGLSEISESHPNSNFLNLNPQNINKLLTA
ParentalLNECTEWGQIFILDCLANYTPKDDREAQSICERVTP-RLSHANSAVVLSAVKVLMKFMEMLSKDLDYYGT
LNECTEWGQIFILDCL.NY.PKDD.EAQSICE.VTP.RLSHANSAVV.SA.KVLMKF.E.L.KD.DYY..
RetrocopyLNECTEWGQIFILDCLSNYNPKDDWEAQSICEWVTP<RLSHANSAVVFSAIKVLMKFLELLPKDSDYYNM
ParentalLLKKLAPPLVTLLSAEPELQYVALRNINLIVQKRPEILKHEMKVFFVKYNDPIYVKLEKLDIMIRLASQA
LLKKLAPPLVTLLS.EPE.QYVALRNINLIVQKRPEILK.E.KVFFVKYNDPIYVKLEKL.IMIRL.SQA
RetrocopyLLKKLAPPLVTLLSGEPEVQYVALRNINLIVQKRPEILKQEIKVFFVKYNDPIYVKLEKLHIMIRLVSQA
ParentalNIAQVLAELKEYATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIKDIFR
NIAQVLAELKEYATEVD.DFVRKAVRAIGRCAIKVEQSAE.CVSTLLDLIQTKVNYVVQEAIVVI.DIFR
RetrocopyNIAQVLAELKEYATEVDADFVRKAVRAIGRCAIKVEQSAEHCVSTLLDLIQTKVNYVVQEAIVVIRDIFR
ParentalKYPNKYESVIATLCENLDSLDEPEARAAMIWIVGEYAERIDNADELLESFLEGFHDESTQVQLQLLTAIV
KYPNKY.S.IATLCENLD.LDEP.ARAAMIWI.GEYAERIDNADELLESFLEGFH.ESTQVQL.LLTAIV
RetrocopyKYPNKYKSIIATLCENLDTLDEPDARAAMIWIMGEYAERIDNADELLESFLEGFHEESTQVQLILLTAIV
ParentalKLFLKKPTETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTD-PVAAKEVVLAEKPLISEETDLIEPT
KLFLKKP.ETQEL.QQVLSLATQDSDNPDLRD.GYIYW.LLSTD.PV.AKEVVL.EKPLISEETDLIEPT
RetrocopyKLFLKKPSETQELIQQVLSLATQDSDNPDLRDQGYIYWCLLSTD>PVTAKEVVLSEKPLISEETDLIEPT
ParentalLLDELICYIGTLASVYHKPPSAFVEGGRGVV-HKSLPPRTASNESTESPETAPAGAPTAEQPDVIPTQGD
LLDELIC..G.LASVYHKPP.AFV.G..G....K.LP....S.....SP......A...EQP.VIP.QGD
RetrocopyLLDELICHNGSLASVYHKPPNAFV-GVMGFI<RKHLPIHHGSTDAGDSP-VGTTIASNLEQPQVIPSQGD
ParentalLLGDLLNLDLG-PPVSGPPLTTSSVQMGAVDLLGGGLDSLIGDTNFGAPPPA--APARLGAPIGSGLSDL
LLGDLLNLDLG.PPV..P.....S.QMGAVDLL.GGLDSL.G........PA..AP....A...S.L.DL
RetrocopyLLGDLLNLDLG>PPVNVPQVS--SMQMGAVDLL-GGLDSLVGQSFIPSSLPATFAPSPTPAIVSSVLNDL
ParentalFDLTSGVGTLSGSYVPPKAVWLPAMKAKGLEISGTFMRQVGSISMDLQLTNKALQVMTDFAIQFNRNSFG
F.L..G.G...G.YV.PKAVWL...KAKGLEISGTF....G.I.M....TNKALQ.MTDFAIQ.N.NSFG
RetrocopyFELSMGIGMAPGGYVAPKAVWLLGVKAKGLEISGTFTHRQGHIYMEMNFTNKALQHMTDFAIQLNKNSFG
ParentalLAPAAPLQVHAPLSPNQTVEISLPLNTVGSVMKMDPLNNLQVAVKNNIDIFYFSTLYPLHILFVEDGKMD
..P..PL..H.PL.PNQ....SLPLNT.G.VMKM.PLNNLQVAV.NNID.FYFS.L.PL..LFVEDGKM.
RetrocopyVIPSTPLAIHTPLMPNQSIDVSLPLNTLGPVMKMEPLNNLQVAVRNNIDVFYFSCLIPLNVLFVEDGKME
ParentalRQMFLATWKDIPNENEAQFQIRDCSLNAEAVSTKLQNSNIFTIAKRNVEGQDMLYQSLKLTNGIWVLAEL
RQ.FLATWKDIPNENE.QFQI..C.LNA..VS.KLQN.N..TIAKRNVEGQDMLYQSLKL.NGIW.LAEL
RetrocopyRQVFLATWKDIPNENELQFQIKECHLNADTVSSKLQNNNVYTIAKRNVEGQDMLYQSLKLANGIWILAEL
ParentalRIQPGSPSFTLSLKCRAPEVSQHVYQAYETILKN
RIQPG.P..TLSLKCRAPEVSQ..YQ.Y..ILKN
RetrocopyRIQPGNPNYTLSLKCRAPEVSQYIYQVYDSILKN

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 .15 RPM 94 .50 RPM
SRP017611_kidney 1 .57 RPM 85 .63 RPM
SRP017611_liver 0 .44 RPM 85 .92 RPM
SRP040447_lung 0 .30 RPM 103 .30 RPM
SRP040447_skeletal_muscle 0 .04 RPM 74 .47 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_477 retrocopy.

TSS - click to see more details

Cavia porcellus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cpor_477 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 3 parental genes, and 3 retrocopies.

Species Parental gene accession Retrocopies number
Cavia porcellus ENSCPOG00000005293 1 retrocopy
retro_cpor_477 ,
Macropus eugenii ENSMEUG000000084381 retrocopy
retro_meug_1205,
Macaca mulatta ENSMMUG000000213801 retrocopy
retro_mmul_2615,




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