RetrogeneDB ID:

retro_cpor_227

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_101:4741287..4743057(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:DCP1A
Ensembl ID:ENSCPOG00000000073
Aliases:None
Description:decapping mRNA 1A [Source:HGNC Symbol;Acc:18714]


Retrocopy-Parental alignment summary:






>retro_cpor_227
AGGGGCTCAGCTTCGAGATTCAAGATGGAGTCGTTGAGTCGAGCGGGGCAGGAGATGAGTCTGGCGGCTTTGAAGCAACA
CGACCCCTACATCACCAGCATCGCAGACCTCACGGGCCAGGTCGCTCTGTACACCTTCTGCCCCAAGGCCAACCAGTGGG
AGAAGACAGATATAGAAGGGACCTTATTTGTATATCGACGGTCAGCCTCACCCTACCATGGTTTTACCATTGTAAATCGA
CTGAATATGCACAATCTAGTTGAACCAGTGAATAAAGATTTGGAATTTCAACTCCATGAACCATTTCTTCTGTATAGAAA
TGCAAGCTTATCAATATACAGTATCTGGTTTTATGACAAGAACGACTGTCACCGCATAGCAAAACTCATGGCAGATGTGG
TAGAAGAGGAGACACGGTGATCCCAGCAAGCTGCTCGAGATAAACAGAGTCCCAGCCAGGCCAATGGCTGCAGTGACCAT
AGGCCTATTGACATCCTGGAAATGCTGAGTAGAGCCAAGGATGAGTACGAGAGGGCTCAGATGGGCGACTTAAATATCTC
CAGCCCTGGGTTACAGCCAAGCACTCAGCTTTTCAATCTAGGAAGCACTGAAACTCTAGAAGAGACATCCTCTGGATCAC
AAGATAAGTCTGCTCCATCTGGACATAAACATCTGACAGTGGAAGAATTGTTTGGAACTTCTTTGCCAAAAGAACAACCA
GCAGTTATGGGTCTGGATTCAGAAGAAGTAGAGAAGCTCGCAGGAGATGCCACCCAGAAAGAGCCCAGCTCGTTCCTACC
ATTTCCCTTTGAGCATTCTGGAGAAGCCGCTCAGTTGGAAAACCTAAGTGTCCATTCAGCTGCTCACCACACAGTCCAAC
CTGAAGTCTCCACTCCGGTGCTCATCACTCCAGCTTCAATCACACAGTCTAGTGAAAGGCATGCTCCAAGCTACACGAGC
CCATTGAGCCCCGTTCTCAGTCCCACTCTGCCACCTGAAGCTGCTACTACACAGGTTGCCCCTGCATTACCTCGAAATAG
CACTATGATGCCTGCAATGAAAACCACACCTAGGCAGAGGTCTCCACTGTTGAACCAGCCAATCCAGGAGCTAAGCCACA
GCAGTCTAATTGCCAGCCAGAGCCCCTTCAGGGCCCCACTGAGTATGACAAACACAGCTGGCACACCCCTCCCAAGTGTT
GATCTTCTGCAGAAACTCAGGTTGACTTCACAGCATGACCAAATACAGACACAGCCACTTGGGAAAGGTGCTGTAGCACC
CAGCTTTCCTCCAGCAGCTGGCCAGCTGGCCACACCCGAGAGCTTCATAGAGCCTCCCCCGAAGACAGCAGCCGCCAGAA
CAGTGGCCTCTGCCTCCCTGAGCAACATGGTGCTTGCTCCCCTTCAGTCTATGCAGCAAAACCAGGACCCTGAAGTATTT
GCCCAGCCTAAGATGCTATCCAGTGCCATCTCGGTTGCAGGCCCTCCATTGGTTACTGCGACAACCACAGCAGTATCTTC
AGTCCTGCTATCGCCAAGTGTTTTTCAGCAGACTGTTCCAAGGTCTGCCGACCTTGAGAGAAAAGCAAATTCTCCTTCTC
CCCTCACCATTGGCACACCAGAAAATCAGAGAAAGTCTTCCCTTATTCTCAGCAAGTCTCAGCTCCAGGATACATTGATA
CATCTGATTAAGAATGATTCCAGCTTCCTCAGTACACTTCATGAAGTTTACCTGCAGGTTCTGACCAAGAGCAAAGACAA
CCACAACCTA

ORF - retro_cpor_227 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 99.49 %
Parental protein coverage: 98.33 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalRGSASRFKMESLSRAGQEMSLAALKQHDPYITSIADLTGQVALYTFCPKANQWEKTDIEGTLFVYRRSAS
RGSASRFKMESLSRAGQEMSLAALKQHDPYITSIADLTGQVALYTFCPKANQWEKTDIEGTLFVYRRSAS
RetrocopyRGSASRFKMESLSRAGQEMSLAALKQHDPYITSIADLTGQVALYTFCPKANQWEKTDIEGTLFVYRRSAS
ParentalPYHGFTIVNRLNMHNLVEPVNKDLEFQLHEPFLLYRNASLSIYSIWFYDKNDCHRIAKLMADVVEEETRR
PYHGFTIVNRLNMHNLVEPVNKDLEFQLHEPFLLYRNASLSIYSIWFYDKNDCHRIAKLMADVVEEETR.
RetrocopyPYHGFTIVNRLNMHNLVEPVNKDLEFQLHEPFLLYRNASLSIYSIWFYDKNDCHRIAKLMADVVEEETR*
ParentalSQQAARDKQSPSQANGCSDHRPIDILEMLSRAKDEYERAQMGDSNISSPGLQPSTQLFNLGSTETLEETS
SQQAARDKQSPSQANGCSDHRPIDILEMLSRAKDEYERAQMGD.NISSPGLQPSTQLFNLGSTETLEETS
RetrocopySQQAARDKQSPSQANGCSDHRPIDILEMLSRAKDEYERAQMGDLNISSPGLQPSTQLFNLGSTETLEETS
ParentalSGSQDKSAPSGHKHLTVEELFGTSLPKEQPAVMGLDSEEVEKLAGDATQKEPSSFLPFPFEHSGEAAQLE
SGSQDKSAPSGHKHLTVEELFGTSLPKEQPAVMGLDSEEVEKLAGDATQKEPSSFLPFPFEHSGEAAQLE
RetrocopySGSQDKSAPSGHKHLTVEELFGTSLPKEQPAVMGLDSEEVEKLAGDATQKEPSSFLPFPFEHSGEAAQLE
ParentalNLSVHSAAHHTVQPEVSTPVLITPASITQSSERHAPSYTSPLSPVLSPTLPPEAATTQVAPALPRNSTMM
NLSVHSAAHHTVQPEVSTPVLITPASITQSSERHAPSYTSPLSPVLSPTLPPEAATTQVAPALPRNSTMM
RetrocopyNLSVHSAAHHTVQPEVSTPVLITPASITQSSERHAPSYTSPLSPVLSPTLPPEAATTQVAPALPRNSTMM
ParentalPAMKTTPRQRSPLLNQPIQELSHSSLIASQSPFRAPLSMTNTAGTPLPSVDLLQKLRLTSQHDQIQTQPL
PAMKTTPRQRSPLLNQPIQELSHSSLIASQSPFRAPLSMTNTAGTPLPSVDLLQKLRLTSQHDQIQTQPL
RetrocopyPAMKTTPRQRSPLLNQPIQELSHSSLIASQSPFRAPLSMTNTAGTPLPSVDLLQKLRLTSQHDQIQTQPL
ParentalGKGAVAPSFPPAAGQLATPESFIEPPPKTAAARTVASASLSNMVLAPLQSMQQNQDPEVFAQPKMLSSAI
GKGAVAPSFPPAAGQLATPESFIEPPPKTAAARTVASASLSNMVLAPLQSMQQNQDPEVFAQPKMLSSAI
RetrocopyGKGAVAPSFPPAAGQLATPESFIEPPPKTAAARTVASASLSNMVLAPLQSMQQNQDPEVFAQPKMLSSAI
ParentalSVAGPPLVTATTTAVSSVLLSPSVFQQTVPRSADLERKANSPSPLTIGTPENQRKSSLILSKSQLQDTLI
SVAGPPLVTATTTAVSSVLLSPSVFQQTVPRSADLERKANSPSPLTIGTPENQRKSSLILSKSQLQDTLI
RetrocopySVAGPPLVTATTTAVSSVLLSPSVFQQTVPRSADLERKANSPSPLTIGTPENQRKSSLILSKSQLQDTLI
ParentalHLIKNDSSFLSTLHEVYLQVLTKSKDNYNL
HLIKNDSSFLSTLHEVYLQVLTKSKDN.NL
RetrocopyHLIKNDSSFLSTLHEVYLQVLTKSKDNHNL

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 3 .91 RPM
SRP017611_kidney 0 .31 RPM 2 .93 RPM
SRP017611_liver 0 .00 RPM 2 .09 RPM
SRP040447_lung 0 .03 RPM 7 .69 RPM
SRP040447_skeletal_muscle 0 .08 RPM 4 .33 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_227 retrocopy.

TSS - click to see more details

Cavia porcellus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cpor_227 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 2 parental genes, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000064361 retrocopy
retro_chof_288,
Cavia porcellus ENSCPOG00000000073 1 retrocopy
retro_cpor_227 ,


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