RetrogeneDB ID:

retro_fcat_1895

Retrocopy
location
Organism:Cat (Felis catus)
Coordinates:X:15059357..15060069(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSFCAG00000006395
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SNRPN
Ensembl ID:ENSFCAG00000022298
Aliases:None
Description:small nuclear ribonucleoprotein polypeptide N [Source:HGNC Symbol;Acc:11164]


Retrocopy-Parental alignment summary:






>retro_fcat_1895
ACTGTGGGAAAGAGCAGCAAGATGCCACGGCACACGGACTATAGACCCACGCGTATCCTGCAAGATGACCGAACATTCAT
TGGCACCTCTAAGGCTTTTGACAAACGTAGGAACGTGATCCTCCGGAATTATGATGAATCCAGCAAGATCTGGCCAAAGA
ATGCGAAGCGCCCAGAGCGTGAAGAAAAGCGGGTTGGGGGTCTGGTGTTGCTACGTAGGGAGAACTTGGGTTTCCATGCC
TGTCAAGGACCACCCCCCAGAGACCCTGGCATTGCTCGGGGTACCACTTGCTGGAGCGGCAGGAGGTCCTGGGGTCGGCA
GGGCAGCGGGCAGAGGAGTGCCAGCCGGTGTTCCAATCCCCCCGGCTCCTGCTGGATCTGCAGGCCCCGTGCGAGGGGTT
GGGGGACCATCCCAACAGGAAATGGCTCCACAGGGAAGAGGTACTGTAGCCGCTGCCGCAGTTGCTGCTATTGCCATAAT
TGCTGCAGCCCCCACCCGGTGCCCACCGGGACGGGGGACCCCACCCACTCCCGTGGGCGGAGCTACACCACCTCCAGGCA
TCAGGGCTCCTCCACGTGGTATGAGACCACCCATGGGCCCACCAATTGGGCTTCCCCCTGCCGGAGGGACGCCAATAGGC
ATTCCCCCTCCAGGAATGAGACCCCCTCCGCCAGGTATTAGAGGTCCCCCTCCCCCAGGAGTGTGTCCACCA

ORF - retro_fcat_1895 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.25 %
Parental protein coverage: 97.11 %
Number of stop codons detected: 0
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDK--HXILCDCDEFRKIKPKNAKQPEREEKRVLGLVL
TVGKSSKM..H.DYR...ILQD.R.FIGT.KAFDK....IL...DE..KI.PKNAK.PEREEKRV.GLVL
RetrocopyTVGKSSKMPRHTDYRPTRILQDDRTFIGTSKAFDKRRNVILRNYDESSKIWPKNAKRPEREEKRVGGLVL
ParentalLRGENLVSMTVEGPPPKDTGIAR-VPLAGAAGGPGVGRAAGRGVPAGVPIPQAPAGLAGPVRGVGGPSQQ
LR.ENL......GPPP.D.GIAR.VPLAGAAGGPGVGRAAGRGVPAGVPIP.APAG.AGPVRGVGGPSQQ
RetrocopyLRRENLGFHACQGPPPRDPGIAR>VPLAGAAGGPGVGRAAGRGVPAGVPIPPAPAGSAGPVRGVGGPSQQ
ParentalVMTPQGRGTVAAAAVAATASIAGAPTQYPPGRGTPPTPVGRATPPPGIMAPPPGMRPPMGPPIGLPPARG
.M.PQGRGTVAAAAVAA.A.IA.APT..PPGRGTPPTPVG.ATPPPGI.APP.GMRPPMGPPIGLPPA.G
RetrocopyEMAPQGRGTVAAAAVAAIAIIAAAPTRCPPGRGTPPTPVGGATPPPGIRAPPRGMRPPMGPPIGLPPAGG
ParentalTPIGMPPPGMRPPPPGIRGPPPPGMRPP
TPIG.PPPGMRPPPPGIRGPPPPG..PP
RetrocopyTPIGIPPPGMRPPPPGIRGPPPPGVCPP

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 159 .19 RPM
SRP017611_kidney 0 .00 RPM 19 .58 RPM
SRP017611_liver 0 .00 RPM 11 .83 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_1895 retrocopy.

TSS - click to see more details

Felis catus was not studied using FANTOM5 data.

Lab - click to see more details

retro_fcat_1895 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 22 parental genes, and 53 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000070343 retrocopies
retro_amel_1048, retro_amel_714, retro_amel_839,
Bos taurus ENSBTAG000000082511 retrocopy
retro_btau_620,
Canis familiaris ENSCAFG000000101276 retrocopies
retro_cfam_1753, retro_cfam_1874, retro_cfam_2039, retro_cfam_627, retro_cfam_682, retro_cfam_752,
Choloepus hoffmanni ENSCHOG000000018462 retrocopies
retro_chof_2275, retro_chof_385,
Cavia porcellus ENSCPOG000000202701 retrocopy
retro_cpor_878,
Felis catus ENSFCAG000000144472 retrocopies
retro_fcat_1788, retro_fcat_1960,
Felis catus ENSFCAG00000022298 2 retrocopies
retro_fcat_1390, retro_fcat_1895 ,
Homo sapiens ENSG000001287391 retrocopy
retro_hsap_2580,
Gorilla gorilla ENSGGOG000000039881 retrocopy
retro_ggor_1615,
Loxodonta africana ENSLAFG000000094581 retrocopy
retro_lafr_1012,
Myotis lucifugus ENSMLUG000000233613 retrocopies
retro_mluc_1192, retro_mluc_1816, retro_mluc_2156,
Macaca mulatta ENSMMUG000000231391 retrocopy
retro_mmul_644,
Mustela putorius furoENSMPUG000000146381 retrocopy
retro_mputfur_1080,
Mus musculus ENSMUSG000000009483 retrocopies
retro_mmus_1285, retro_mmus_1733, retro_mmus_665,
Oryctolagus cuniculus ENSOCUG000000035324 retrocopies
retro_ocun_1291, retro_ocun_488, retro_ocun_689, retro_ocun_846,
Otolemur garnettii ENSOGAG000000073925 retrocopies
retro_ogar_1179, retro_ogar_3042, retro_ogar_3060, retro_ogar_475, retro_ogar_722,
Pongo abelii ENSPPYG000000062691 retrocopy
retro_pabe_1900,
Pan troglodytes ENSPTRG000000068261 retrocopy
retro_ptro_1507,
Rattus norvegicus ENSRNOG000000159766 retrocopies
retro_rnor_1122, retro_rnor_1314, retro_rnor_1485, retro_rnor_2161, retro_rnor_2462, retro_rnor_2517,
Sus scrofa ENSSSCG000000281242 retrocopies
retro_sscr_350, retro_sscr_405,
Ictidomys tridecemlineatus ENSSTOG000000013391 retrocopy
retro_itri_44,
Tursiops truncatus ENSTTRG000000109665 retrocopies
retro_ttru_1005, retro_ttru_1051, retro_ttru_1473, retro_ttru_580, retro_ttru_600,


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