RetrogeneDB ID:

retro_cpor_943

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_36:834971..835498(+)
Located in intron of:ENSCPOG00000002669
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCPOG00000019337
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_943
CCTGTGAAAATGGTTTGCTACTCTCTTGACCCAGAAAATCCCACAAAATCATGCAAATCAACAAGGTCAAATCTTTGTGC
TCACTTTAAGAACTCTTATGATGCTGCCCAGGCCAATAAGGGTATGCATATTTAAAAGTCCTCCAAGTGTCTGAAGCATG
TCATATTAAAGAAGCAATCCATGACACTGCGGTGTTAAAACAGTGGAGTTGGTAGGTCTGTCCAAGCCAACAGTGGGGCT
GGACACAGGGTTGGTGGCCCAAAAAGAGTGCTTCATTTTTGCTGTACATGCTTAAAAATGCAGAGTAATTCTGAACTTAA
GGATTTAGAAGTAGATTCTCTAGTCATTGAACATATCCAAGTGAATAAAGCTCCCAACACTTATGGAGCTCAGATTCAGA
TTGACCCATATTTGTATTCCCCTGCCATAGTGAAATGATCATTATTGAAAACAAATAAACCATTTCTAGATCAGAAGAGG
AAGTTGCACAGAAAGAAAAAATATCCCAGGAGAAACTGAAGAACCAA

ORF - retro_cpor_943 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.22 %
Parental protein coverage: 96.79 %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalPVKMVRYSLDPENPTKSCKSRGSNLRVHFKNTRETAQAIKGMHIRKATKYLKDVTLKKQCVPFRRYNGGV
PVKMV.YSLDPENPTKSCKS..SNL..HFKN....AQA.KGMHI.K..K.LK.V.LKKQ....R..N.GV
RetrocopyPVKMVCYSLDPENPTKSCKSTRSNLCAHFKNSYDAAQANKGMHI*KSSKCLKHVILKKQSMTLRC*NSGV
ParentalGRCAQA-KQWGWTQGRWPKKSAEFLLHM-LKNAESNAELKGLDVDSLVIEHIQVNKAPKMRRRTYRAHGR
GR..QA..QWGWTQG.WPKKSA.FLL.M.LK...SN.ELK.L.VDSLVIEHIQVNKAP.....TY.A...
RetrocopyGRSVQA<QQWGWTQGWWPKKSASFLLYM>LK-MQSNSELKDLEVDSLVIEHIQVNKAPN----TYGAQIQ
ParentalINPYMSSP-CHIEMILTEKEQIVPKPEEEVAQKKKISQKKLKKQ
I.PY..SP.CH.EMI..E........EEEVAQK.KISQ.KLK.Q
RetrocopyIDPYLYSP<CHSEMIIIENK*TISRSEEEVAQKEKISQEKLKNQ

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 100 .83 RPM
SRP017611_kidney 0 .10 RPM 156 .51 RPM
SRP017611_liver 0 .00 RPM 112 .95 RPM
SRP040447_lung 0 .00 RPM 221 .34 RPM
SRP040447_skeletal_muscle 0 .00 RPM 227 .83 RPM
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_943 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_943 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 20 parental genes, and 501 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG0000000787250 retrocopies
Cavia porcellus ENSCPOG00000019337 31 retrocopies
Equus caballus ENSECAG000000115479 retrocopies
Echinops telfairi ENSETEG0000001132210 retrocopies
Homo sapiens ENSG000002154721 retrocopy
Latimeria chalumnae ENSLACG000000088351 retrocopy
Macropus eugenii ENSMEUG0000001670926 retrocopies
Microcebus murinus ENSMICG0000001710214 retrocopies
Myotis lucifugus ENSMLUG0000002555422 retrocopies
Myotis lucifugus ENSMLUG0000002926436 retrocopies
Macaca mulatta ENSMMUG0000001883726 retrocopies
Mus musculus ENSMUSG0000006232880 retrocopies
Oryctolagus cuniculus ENSOCUG000000124852 retrocopies
Procavia capensis ENSPCAG000000031038 retrocopies
Pongo abelii ENSPPYG0000000915143 retrocopies
Pteropus vampyrus ENSPVAG0000000196976 retrocopies
Sarcophilus harrisii ENSSHAG0000000306014 retrocopies
Tarsius syrichta ENSTSYG0000000740220 retrocopies
Tursiops truncatus ENSTTRG0000000579731 retrocopies
Vicugna pacos ENSVPAG000000095681 retrocopy



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