RetrogeneDB ID:

retro_cpor_150

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_0:21729331..21730024(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCPOG00000026078
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TPM3
Ensembl ID:ENSCPOG00000007279
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_150
CAGCAGCAAGCCAGTGACCCAGAGAAGGGGGCCGAGTGCCTCCAGAGGGAAGTAGAGGGAGAAAGCCGGGCTTGGGAACA
GGCTGAGGCAGAAGTGGCCTCCTTAAACGGCAGGATCCAGCTCATTGAAGAGAAGCTGGACCATGCACAGGAGCGCCTGG
CCCCTGCCCTGCAAAAGCTGGAGGAAGCTGAGAAAGCCTCCGAGGAGAGTGAGAGGGGAACGATCGTTAGTGAAAACCCA
ACTGTAAAAGATAAAGAAAAGATGGAACTCCAGGAATCTGACTTCAGTGGGTTAAACACACTGCAGAAGAGACAGACAGG
AAATGTGAGGAGTTGGTTAGTAAGTTGACATTTATTGAAGTTGATTTGGAACACACAGAGGACAGCGCTGAGCTGGCAGA
GTCCCATTGCCAGGAGAAGGATGAGCGGATCAGACTGATGGACCAGAACCTGCAGGATCTGCGCGCTGCTGAAGATAAGC
ACTCTCAAAAAGAAAACAAATATAAGGAAGAGATAAAGATGCTTACTGATAAACTCAAGGAGGCGGAGACCCACGCTGAG
CTTGCTGAGAGATCAGTTGCCAACCTGGAAAAGACAACCGATGGACTTGGAAGAGAAGCTGAAATGCACCACAGAGGAGC
AGCTCTGTGTGCGAAGGATGCTGGGCCAGGCCCTGCCCTATCTGCAGGAGATG

ORF - retro_cpor_150 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.1 %
Parental protein coverage: 93.15 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalQQQADDAEERAERLQREVEGERRAREQAEAEVASLNRRIQLVEEELDRAQERLATALQKLEEAEKAADES
QQQA.D.E..AE.LQREVEGE.RA.EQAEAEVASLN.RIQL.EE.LD.AQERLA.ALQKLEEAEKA..ES
RetrocopyQQQASDPEKGAECLQREVEGESRAWEQAEAEVASLNGRIQLIEEKLDHAQERLAPALQKLEEAEKASEES
ParentalERGMKVIENRALKDEEKMELQE-IQLKEAKHIAEEADRKYEEVARKLVIIEGDLERTEERAELAESRCRE
ERG..V.EN...KD.EKMELQE.I.L...KH.AEE.DRK.EE...KL..IE.DLE.TE..AELAES.C.E
RetrocopyERGTIVSENPTVKDKEKMELQE<I*LQWVKHTAEETDRKCEELVSKLTFIEVDLEHTEDSAELAESHCQE
ParentalMDEQIRLMDQNLKCLSAAEEKYSQKEDKYEEEIKILTDKLKEAETRAEFAERSVAKLEKTID-DLEDKLK
.DE.IRLMDQNL..L.AAE.K.SQKE.KY.EEIK.LTDKLKEAET.AE.AERSVA.LEKT.D.DLE.KLK
RetrocopyKDERIRLMDQNLQDLRAAEDKHSQKENKYKEEIKMLTDKLKEAETHAELAERSVANLEKTTD>DLEEKLK
ParentalCTKEEHLCTQRMLDQTLLDLNEM
CT.EE.LC..RML.Q.L..L.EM
RetrocopyCTTEEQLCVRRMLGQALPYLQEM

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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 71 .38 RPM
SRP017611_kidney 0 .00 RPM 37 .06 RPM
SRP017611_liver 0 .00 RPM 28 .86 RPM
SRP040447_lung 0 .00 RPM 112 .31 RPM
SRP040447_skeletal_muscle 0 .00 RPM 2466 .71 RPM
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_150 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_150 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 13 parental genes, and 43 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000118772 retrocopies
Bos taurus ENSBTAG000000332173 retrocopies
Canis familiaris ENSCAFG000000173114 retrocopies
Cavia porcellus ENSCPOG00000007279 1 retrocopy
retro_cpor_150 ,
Dasypus novemcinctus ENSDNOG000000191567 retrocopies
Equus caballus ENSECAG000000109421 retrocopy
Felis catus ENSFCAG000000125961 retrocopy
Homo sapiens ENSG000001435499 retrocopies
Myotis lucifugus ENSMLUG000000133311 retrocopy
Macaca mulatta ENSMMUG0000001080510 retrocopies
Mustela putorius furoENSMPUG000000078751 retrocopy
Mus musculus ENSMUSG000000279401 retrocopy
Oryctolagus cuniculus ENSOCUG000000118212 retrocopies



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