RetrogeneDB ID:

retro_cpor_1246

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_6:17533273..17534474(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCPOG00000022840
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:QRICH1
Ensembl ID:ENSCPOG00000009958
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_1246
GTAGTGCAGACCCTTGCATACTCTCTCTTTCCAGCACAGTTTATGAATGGCAACATCCACATTCCAGTAGCTGTGCAGGC
TGTGGCAGGCACATACCAGAATACAGCTCCGACTGTCCATATACGGGGCACCCAGCAGCAGCCACAACAACAGACCCCCC
CCAAGAACAGACACCATCACCACCACAGCAGCAGCAGCAGCAGCTCCTGGTTATTTGTCCAGCTCAGACTGTCCAAGTTG
CTAAAGTTGAACCAAAGTCACAGCCACAGCCTTCCCCAGAACTTCTGCTTCCAAATTCTTTGAAACCAGAAGAAGGGCTT
GAAGTATGGAAAAACTGGGCCTAGACCAAGAATGGTGAACTGGAGAAGGATGCTCAGAACAGATTGGCTCCCATTGGGAG
GCACCAACTGCTTCGATTCCAAGATCTTATCTCCTCTGCTGTGGTTGAGTTGAATTATGGGCTGTGTCTAATGACATGGG
AAGCTTGAAATGGAGACTGTGAACCCTATGATCCTGATGTGCTGTACTATATTTTCCTGTGTATTCAAAAGTATCTTTTT
GAAAACGGAAGGGTGGATGACATTTTCTCTGATCTTTACTGTGTTTGATTCACGGAGTGGCTACATGAAATTCTGAAGGA
TGTTTAACCCCAGGTCACTCCACTTGGCTATGTCTTGCCCAGCCAGGTGACTGAGGAGATGCTGTGGGAGTGCAAGCAAC
TTGGGGCACACTTCCCCTCAACCCTACTGACCACCCTCATGTTCTTTAATCCCAAGTACTTCCTGTTGAAGACAGTGGCC
AGCACATGAAACTGGCCTTCTCTAAGGCCTTACGACAGACAAAGAAGAACCCCTCTAATCCCAAGGATAAAAACACGAGT
ATCTGGTACCTGAAGGCCCTTAGAATACATCAGACTGGCCAGAAAGTTTCAGATGACATGTATGCGGAGCAGACAGAAAA
TCCAGAGAATCCATTGAGGTGTCCCATCAAGCTCTATGATTTCTACCTCTTCAAATGTCCCCAGAGTGTGAAAGGCCAGA
ATGACACCTTTTACCTGACACCTGAGCCAGTAGTGGCCCCCAGCAGCCCAATCTGGTACTCAGTCCAGCCTATCACCCGA
GAGCAGATGGGACAAATGCTGACCCGAATCCTGGAGATACGAGAAATTCAGGAGGCCATTGCAGTGGCCAGCGCAAGCAC
A

ORF - retro_cpor_1246 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.88 %
Parental protein coverage: 51.54 %
Number of stop codons detected: 4
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalVVQTLANSLFPAQFMNGNIHIPVAVQAVAGTYQNTAQTVHIWDPQQQP-QQQTPQ-EQTPPPPQQQQQQL
VVQTLA.SLFPAQFMNGNIHIPVAVQAVAGTYQNTA.TVHI...QQQP.QQ.....EQTP.PP.......
RetrocopyVVQTLAYSLFPAQFMNGNIHIPVAVQAVAGTYQNTAPTVHIRGTQQQPQQQXXXK<EQTPSPPXXXXXXX
ParentalQVTCSAQTVQVAEVEPQSQPQPSPELLLPNSLKPEEGLEVWKNWAQTKNAELEKDAQNRLAPIGRRQLLR
.V.C.AQTVQVA.VEP.SQPQPSPELLLPNSLKPEEGLEVWKNWA.TKN.ELEKDAQNRLAPIGR.QLLR
RetrocopyLVICPAQTVQVAKVEPKSQPQPSPELLLPNSLKPEEGLEVWKNWA*TKNGELEKDAQNRLAPIGRHQLLR
ParentalFQEDLISSAVAELNYGLCLMTREARNGEGEPYDPDVLYYIFLCIQKYLFENGRVDDIFSDLYYVRFTEWL
FQ.DLISSAV.ELNYGLCLMT.EA.NG..EPYDPDVLYYIFLCIQKYLFENGRVDDIFSDLY.V.FTEWL
RetrocopyFQ-DLISSAVVELNYGLCLMTWEA*NGDCEPYDPDVLYYIFLCIQKYLFENGRVDDIFSDLYCV*FTEWL
ParentalHEVLKDVQPRVTPLGYVLPSHVTEEMLWECKQLGAHSPSTLLTTLMFFNTKYFLLKTV-DQHMKLAFSKV
HE.LKDV.P.VTPLGYVLPS.VTEEMLWECKQLGAH.PSTLLTTLMFFN.KYFLLKTV..QHMKLAFSK.
RetrocopyHEILKDV*PQVTPLGYVLPSQVTEEMLWECKQLGAHFPSTLLTTLMFFNPKYFLLKTV<GQHMKLAFSKA
ParentalLRQTKKNPSNPKDKSTSIRYLKALGIHQTGQKVTDDMYAEQTENPENPLRCPIKLYDFYLFKCPQSVKGR
LRQTKKNPSNPKDK.TSI.YLKAL.IHQTGQKV.DDMYAEQTENPENPLRCPIKLYDFYLFKCPQSVKG.
RetrocopyLRQTKKNPSNPKDKNTSIWYLKALRIHQTGQKVSDDMYAEQTENPENPLRCPIKLYDFYLFKCPQSVKGQ
ParentalNDTFYLTPEPVVAPNSPIWYSVQPISREQMGQMLTRILVIREIQETIAVASAST
NDTFYLTPEPVVAP.SPIWYSVQPI.REQMGQMLTRIL.IREIQE.IAVASAST
RetrocopyNDTFYLTPEPVVAPSSPIWYSVQPITREQMGQMLTRILEIREIQEAIAVASAST

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 47 .22 RPM
SRP017611_kidney 0 .00 RPM 40 .83 RPM
SRP017611_liver 0 .00 RPM 30 .03 RPM
SRP040447_lung 0 .00 RPM 54 .78 RPM
SRP040447_skeletal_muscle 0 .00 RPM 25 .32 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_1246 retrocopy.

TSS - click to see more details

Cavia porcellus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cpor_1246 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 1 retrocopy.

Species Parental gene accession Retrocopies number
Cavia porcellus ENSCPOG00000009958 1 retrocopy
retro_cpor_1246 ,


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