RetrogeneDB ID:

retro_fcat_1649

Retrocopy
location
Organism:Cat (Felis catus)
Coordinates:E1:19672974..19673537(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL13A
Ensembl ID:ENSFCAG00000009194
Aliases:None
Description:ribosomal protein L13a [Source:HGNC Symbol;Acc:10304]


Retrocopy-Parental alignment summary:






>retro_fcat_1649
GGCCGGGGCCATCTCCTTGGCCACCTGGAAGCCACTGTGTCTAAACAGGTGCTGCTGGGCTGGAAGGTTGTAGTGGTGCG
CTATGAGGGCATCAGCACTTCTGGCAATTTCTACAAAAACATTAAGTACCTGGCTTTCCTCCACAAGCCGCTGAGCCTCA
ACCCATCCCGTGGCCCATCCCCAGAGCCCAGCCGCATCTTCTGGAGGACAGTGTAAGGCCAGCTGCCCCACAGGACCATG
GGAGGCCAGGCTTCCCTGGACCGCCTCAATGTGTTTGATGGGATCTTGCCACCCTATGACAAGAAAAAGGGGATGGTGGT
TCCCGGTGCCCTCAAGGTTGTGGGTCTGAAGCCTACACGAACATTTCCTTACCTGAGCACCTGGCTCACGAGGTGGGCTG
GAAGTACCAGGCTGTAACAGCCACCCTGGAGGAGAAGAGGAAGAAGTCCAAGATCCATTATGGGAAGAAAAAGCATCTCA
TGAGGCTACAGAAACAGGCCAAAAACAATGTGAAGAAGAAGACCGACAAATACACAGAAGTCCTTGAGGCCCACAGACTC
CTG

ORF - retro_fcat_1649 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.32 %
Parental protein coverage: 96. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalGRGLQIGTFFSCLAVNLSTSRKVVVVRCEGINISGNFYRNKLKYLAFLRKRMNTNPSRGPYHFRAPSRIF
GRG...G..............KVVVVR.EGI..SGNFY.N..KYLAFL.K....NPSRGP.....PSRIF
RetrocopyGRGHLLGHLEATVSKQVLLGWKVVVVRYEGISTSGNFYKN-IKYLAFLHKPLSLNPSRGPSP--EPSRIF
ParentalWRTVRGMLPHKTKRGQAALDRLKVFDGIPPPYDKEKRMVVPAALKVVRLKPTRKFAYLG-RLAHEVGWKY
WRTV.G.LPH.T..GQA.LDRL.VFDGI.PPYDK.K.MVVP.ALKVV.LKPTR.F.YL...LAHEVGWKY
RetrocopyWRTV*GQLPHRTMGGQASLDRLNVFDGILPPYDKKKGMVVPGALKVVGLKPTRTFPYLS<HLAHEVGWKY
ParentalQAVTATLEEKRKEKAKIHYRKKKQLVRLRKQAEKNVEGKINKYTEVLKTHGLL
QAVTATLEEKRK.K.KIHY.KKK.L.RL.KQA..NV..K..KYTEVL..H.LL
RetrocopyQAVTATLEEKRK-KSKIHYGKKKHLMRLQKQAKNNVKKKTDKYTEVLEAHRLL

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 .11 RPM 53 .94 RPM
SRP017611_kidney 1 .44 RPM 214 .88 RPM
SRP017611_liver 0 .10 RPM 93 .20 RPM
Felis catus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_fcat_1649 retrocopy.
Felis catus was not studied using FANTOM5 data.
retro_fcat_1649 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 20 parental genes, and 120 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000052963 retrocopies
Canis familiaris ENSCAFG000000298923 retrocopies
Callithrix jacchus ENSCJAG0000000007216 retrocopies
Cavia porcellus ENSCPOG000000124172 retrocopies
Erinaceus europaeus ENSEEUG000000140716 retrocopies
Echinops telfairi ENSETEG000000170762 retrocopies
Felis catus ENSFCAG00000009194 4 retrocopies
Gorilla gorilla ENSGGOG0000000293211 retrocopies
Myotis lucifugus ENSMLUG0000000494510 retrocopies
Macaca mulatta ENSMMUG0000000755114 retrocopies
Mus musculus ENSMUSG000000741293 retrocopies
Oryctolagus cuniculus ENSOCUG000000252589 retrocopies
Otolemur garnettii ENSOGAG000000046257 retrocopies
Ochotona princeps ENSOPRG000000011943 retrocopies
Pongo abelii ENSPPYG000000102511 retrocopy
Pan troglodytes ENSPTRG000000112981 retrocopy
Rattus norvegicus ENSRNOG0000002061810 retrocopies
Sus scrofa ENSSSCG000000031664 retrocopies
Tarsius syrichta ENSTSYG000000087914 retrocopies
Tursiops truncatus ENSTTRG000000054857 retrocopies



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