RetrogeneDB ID:

retro_fcat_1984

Retrocopy
location
Organism:Cat (Felis catus)
Coordinates:X:47631632..47632823(-)
Located in intron of:ENSFCAG00000012644
Retrocopy
information
Ensembl ID:ENSFCAG00000031959
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSFCAG00000008729
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_fcat_1984
ATGGTGAAAGAAACTACTTACTATGATGTTTTGGGGGTCAAACCCAATGCCACCCAGGAAGAATTGAAAAAGGCTTACAG
GAAATTGGCTTTGAAGTACCACCCTGACAAGAATCCAAATGAAGGAGAGAAGTTCAAACAGATTTCTCAAGCTTATGAAG
TGCTCTCTGATGCGAAGAAAAGGGAATTATATGACAAAGGAGGAGAACAGGCAATTAAAGAAGGTGGAGCAGGTGGTGGT
TTTGGCTCCCCCATGGACATCTTTGATATGTTTTTTGGAGGAGGAGGAAGGATGCAGAGAGAGAGGAGAGGTAAAAATGT
TGTGCATCAGCTCTCTGTAACCTTAGAAGATTTATATAATGGCGCAACAAGAAAACTAGCTCTGCAAAAGAATGTGATTT
GCGACAAATGTGAAGGCCGAAGTGGTAAGAAAGGAGCGGTAGAACGTTGTCCCAATTGCCGAGGTACTGGAATGCAAATA
AGAATTCATCAGATAGGACCTGGAATGGTTCAGCAAATTCAATCTGTGTGCATGGAGTGCCAGGGCCATGGGGAACGAAT
CAGTCCTAAAGATAGATGTAAAAGCTGCAACGGAAGGAAGATAGTTCAAGAAAAGAAGATTCTAGAAGTTCATATTGACA
AAGGCATGAAAGATGGCCAGAAGATAACATTCCATGGTGAAGGAGACCAAGAACCTGGACTGGAACCAGGAGATATTATC
ATTGTTTTAGATCAGAAGGACCATGCTGTTTTTACTAGGTGAGGAGAGGATCTTTTCATGTGTATGGACATACAGCTGGT
TGAAGCACTGTGCGGCTTTCAAAAGCCAATATCTACTCTAGACAACAGAACCATTGTCATTACCTCTCATCCAGGTCAGA
TTGTCAAGCATGGAGATATCAAGTGTGTGCTGAATGAAGGCATGCCAATTTATCGTAGACCATACGAAAAGGGTCGCCTA
ATCATCGAATTTAAGGTAAACTTCCCTGAGAATGGCTTTCTCTCTCCTGATAAACTGTCTTTGCTGGAAAAGCTCCTACC
TGAGAGGAAGAAAGTAGAAGAGACTGATGAAATGGACCAGGTAGAACTGGTGGACTTTGATCCAAATCAGGAAAGAAGGC
GCCATTACAATGGAGAAGCGTATGAGGATGATGAACATCACCCTAGGGGAGGTGTTCAGTGTCAGACCTCT

ORF - retro_fcat_1984 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.72 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMVKETTYYDVLGVKPNATQEELKKAYRKLALKYHPDKNPNEGEKFKQISQAYEVLSDAKKRELYDKGGEQ
MVKETTYYDVLGVKPNATQEELKKAYRKLALKYHPDKNPNEGEKFKQISQAYEVLSDAKKRELYDKGGEQ
RetrocopyMVKETTYYDVLGVKPNATQEELKKAYRKLALKYHPDKNPNEGEKFKQISQAYEVLSDAKKRELYDKGGEQ
ParentalAIKEGGAGGGFGSPMDIFDMFFGGGGRMQRERRGKNVVHQLSVTLEDLYNGATRKLALQKNVICDKCEGR
AIKEGGAGGGFGSPMDIFDMFF............KNVVHQLSVTLEDLYNGATRKLALQKNVICDKCEGR
RetrocopyAIKEGGAGGGFGSPMDIFDMFFXXXXXXXXXXXXKNVVHQLSVTLEDLYNGATRKLALQKNVICDKCEGR
ParentalGGKKGAVECCPNCRGTGMQIRIHQIGPGMVQQIQSVCMECQGHGERISPKDRCKSCNGRKIVREKKILEV
.GKKGAVE.CPNCRGTGMQIRIHQIGPGMVQQIQSVCMECQGHGERISPKDRCKSCNGRKIV.EKKILEV
RetrocopySGKKGAVERCPNCRGTGMQIRIHQIGPGMVQQIQSVCMECQGHGERISPKDRCKSCNGRKIVQEKKILEV
ParentalHIDKGMKDGQKITFHGEGDQEPGLEPGDIIIVLDQKDHAVFTRRGEDLFMCMDIQLVEALCGFQKPISTL
HIDKGMKDGQKITFHGEGDQEPGLEPGDIIIVLDQKDHAVFTR.GEDLFMCMDIQLVEALCGFQKPISTL
RetrocopyHIDKGMKDGQKITFHGEGDQEPGLEPGDIIIVLDQKDHAVFTR*GEDLFMCMDIQLVEALCGFQKPISTL
ParentalDNRTIVITSHPGQIVKHGDIKCVLNEGMPIYRRPYEKGRLIIEFKVNFPENGFLSPDKLSLLEKLLPERK
DNRTIVITSHPGQIVKHGDIKCVLNEGMPIYRRPYEKGRLIIEFKVNFPENGFLSPDKLSLLEKLLPERK
RetrocopyDNRTIVITSHPGQIVKHGDIKCVLNEGMPIYRRPYEKGRLIIEFKVNFPENGFLSPDKLSLLEKLLPERK
ParentalEVEETDEMDQVELVDFDPNQERRRHYNGEAYEDDEHHPRGGVQCQTS
.VEETDEMDQVELVDFDPNQERRRHYNGEAYEDDEHHPRGGVQCQTS
RetrocopyKVEETDEMDQVELVDFDPNQERRRHYNGEAYEDDEHHPRGGVQCQTS

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 .80 RPM 104 .44 RPM
SRP017611_kidney 0 .10 RPM 45 .04 RPM
SRP017611_liver 0 .10 RPM 55 .80 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_1984 retrocopy.

TSS - click to see more details

Felis catus was not studied using FANTOM5 data.

Lab - click to see more details

retro_fcat_1984 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 18 parental genes, and 114 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000075894 retrocopies
retro_amel_1509, retro_amel_455, retro_amel_756, retro_amel_946,
Bos taurus ENSBTAG000000162656 retrocopies
retro_btau_1440, retro_btau_1599, retro_btau_1800, retro_btau_1826, retro_btau_574, retro_btau_828,
Canis familiaris ENSCAFG0000000181823 retrocopies
retro_cfam_1111, retro_cfam_1153, retro_cfam_1218, retro_cfam_1229, retro_cfam_1315, retro_cfam_1352, retro_cfam_1420, retro_cfam_1457, retro_cfam_1520, retro_cfam_1668, retro_cfam_1833, retro_cfam_1941, retro_cfam_1949, retro_cfam_1994, retro_cfam_2004, retro_cfam_2162, retro_cfam_352, retro_cfam_391, retro_cfam_419, retro_cfam_749, retro_cfam_751, retro_cfam_923, retro_cfam_993,
Choloepus hoffmanni ENSCHOG000000006319 retrocopies
retro_chof_1760, retro_chof_186, retro_chof_2020, retro_chof_2541, retro_chof_2694, retro_chof_287, retro_chof_417, retro_chof_498, retro_chof_946,
Dasypus novemcinctus ENSDNOG000000183423 retrocopies
retro_dnov_1139, retro_dnov_640, retro_dnov_884,
Felis catus ENSFCAG00000008729 5 retrocopies
retro_fcat_1241, retro_fcat_1407, retro_fcat_1502, retro_fcat_1984 , retro_fcat_811,
Homo sapiens ENSG000000860614 retrocopies
retro_hsap_2331, retro_hsap_2569, retro_hsap_3647, retro_hsap_4889,
Gorilla gorilla ENSGGOG000000070303 retrocopies
retro_ggor_1603, retro_ggor_2463, retro_ggor_418,
Macaca mulatta ENSMMUG000000077406 retrocopies
retro_mmul_1313, retro_mmul_1802, retro_mmul_2477, retro_mmul_2482, retro_mmul_2625, retro_mmul_400,
Monodelphis domestica ENSMODG000000033847 retrocopies
retro_mdom_1140, retro_mdom_1253, retro_mdom_1451, retro_mdom_1627, retro_mdom_1824, retro_mdom_742, retro_mdom_874,
Nomascus leucogenys ENSNLEG000000052684 retrocopies
retro_nleu_1255, retro_nleu_2550, retro_nleu_2793, retro_nleu_509,
Oryctolagus cuniculus ENSOCUG000000048332 retrocopies
retro_ocun_516, retro_ocun_70,
Pongo abelii ENSPPYG000000191414 retrocopies
retro_pabe_1892, retro_pabe_2111, retro_pabe_2559, retro_pabe_2994,
Pan troglodytes ENSPTRG000000208524 retrocopies
retro_ptro_1499, retro_ptro_1705, retro_ptro_177, retro_ptro_2472,
Sarcophilus harrisii ENSSHAG000000123661 retrocopy
retro_shar_762,
Sus scrofa ENSSSCG000000110002 retrocopies
retro_sscr_134, retro_sscr_984,
Tupaia belangeri ENSTBEG0000000059623 retrocopies
retro_tbel_1281, retro_tbel_134, retro_tbel_1529, retro_tbel_1542, retro_tbel_2260, retro_tbel_2293, retro_tbel_2316, retro_tbel_2428, retro_tbel_2445, retro_tbel_2917, retro_tbel_2965, retro_tbel_2972, retro_tbel_329, retro_tbel_3345, retro_tbel_3353, retro_tbel_3692, retro_tbel_4014, retro_tbel_4223, retro_tbel_432, retro_tbel_591, retro_tbel_617, retro_tbel_634, retro_tbel_842,
Tursiops truncatus ENSTTRG000000073874 retrocopies
retro_ttru_1181, retro_ttru_1551, retro_ttru_567, retro_ttru_783,


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