RetrogeneDB ID:

retro_fcat_1094

Retrocopy
location
Organism:Cat (Felis catus)
Coordinates:C1:70118773..70119356(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PRR3
Ensembl ID:ENSFCAG00000025918
Aliases:None
Description:proline rich 3 [Source:HGNC Symbol;Acc:21149]


Retrocopy-Parental alignment summary:






>retro_fcat_1094
GCAGCCATTGCCGCAACCATGATGTTGAAACAAAAGAAGCAGAATTAGCAGCAGCAGCCACCACTGCAGCAGCCTCTGCT
GCCAGAGCGGAAAGAGACTGGAGACGAGGAGCATGGAAGTCCCATCGGACCACCCAGCATTCTGGGCCTTACTCCCGTGG
CCACTGGAAAGCCTGGTAACTCTAAGTCAGCTCTTCACAGAGGTCTTCCAGGGTCAAGGGGATGAATGATTCAACCACTG
CTGAGTCTCCCACCTCCTTCCTGGGGCAGAGGCCCAGTCTGGGGAGGCCTAGGCCCCAGGTGTGGCCCATGTGGTTGTGG
TTGGTGGAGGGCCAATACTGAACCTTTTTCCTGGACCAAGCCATGGAGGTCCTTTCAGAGGAGGCTTTCACAAAGAGCAG
AGAAGTCCTCGAAGGCTCAAAAGTTGGTCTCTTATCAAAAATACCTACCCACCCAAGTATGGCCCCTAAGTTATGGAAGA
CAAATCCTACCACCCTGTCTGCTGACATTTTGCCAAAAAGGGCCACTGTCGATATGAGGACCTCTGTGCCTTCTGCCATC
CAGGTGTCAATGGACCTCCTCTG

ORF - retro_fcat_1094 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.04 %
Parental protein coverage: 90.19 %
Number of stop codons detected: 4
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalAAIAATTMPKRKKQSQQQQPPLQQPPLPEREETGDEEDGSPIGPPSLLGPPPMANGKPGDPKSALHRGPP
AAIAAT.M.K.KKQ..QQQPPLQQP.LPER.ETGDEE.GSPIGPPS.LG..P.A.GKPG..KSALHRG.P
RetrocopyAAIAATMMLKQKKQN*QQQPPLQQPLLPERKETGDEEHGSPIGPPSILGLTPVATGKPGNSKSALHRGLP
ParentalGSRGPMIPPLLSLPPPPRGRGPIRGGVGPRCGPYGRGWWGANTEPPF-PGPGHGGP-RGGFHKEQRNPRR
GSRG.MI.PLLSLPPP..GRGP..GG.GPRCGP.G.G.W......PF.PGP.HGGP.RGGFHKEQR.PRR
RetrocopyGSRG*MIQPLLSLPPPSWGRGPVWGGLGPRCGPCGCG-WWRANTEPF>PGPSHGGPFRGGFHKEQRSPRR
ParentalLKSWSLI-NACPPKDGPQVMEDKSNRPVCRHFAKKGHCRYEDLCAFYHPGVNGPPL
LKSWSLI.N..PPK.GP.VMEDKS..PVC.HFAKKGHCRYEDLCAF.HPGVNGPPL
RetrocopyLKSWSLIKNTYPPKYGP*VMEDKSYHPVC*HFAKKGHCRYEDLCAFCHPGVNGPPL

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 .11 RPM 10 .10 RPM
SRP017611_kidney 0 .00 RPM 6 .08 RPM
SRP017611_liver 0 .00 RPM 3 .74 RPM

ChIP-Seq - click to see more details

Felis catus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_fcat_1094 retrocopy.

TSS - click to see more details

Felis catus was not studied using FANTOM5 data.

Lab - click to see more details

retro_fcat_1094 was not experimentally validated.

Retrocopy orthology:
Felis catus 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 12 parental genes, and 16 retrocopies.

Species Parental gene accession Retrocopies number
Cavia porcellus ENSCPOG000000227701 retrocopy
retro_cpor_775,
Felis catus ENSFCAG00000025918 2 retrocopies
retro_fcat_1094 , retro_fcat_1698,
Gorilla gorilla ENSGGOG000000146041 retrocopy
retro_ggor_1915,
Myotis lucifugus ENSMLUG000000087581 retrocopy
retro_mluc_1567,
Macaca mulatta ENSMMUG000000138931 retrocopy
retro_mmul_1431,
Nomascus leucogenys ENSNLEG000000051041 retrocopy
retro_nleu_1548,
Otolemur garnettii ENSOGAG000000044302 retrocopies
retro_ogar_1030, retro_ogar_1324,
Pongo abelii ENSPPYG000000164091 retrocopy
retro_pabe_2279,
Pan troglodytes ENSPTRG000000179291 retrocopy
retro_ptro_1861,
Sorex araneus ENSSARG000000027472 retrocopies
retro_sara_143, retro_sara_9,
Ictidomys tridecemlineatus ENSSTOG000000118291 retrocopy
retro_itri_126,
Tarsius syrichta ENSTSYG000000001662 retrocopies
retro_tsyr_308, retro_tsyr_841,


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