RetrogeneDB ID:

retro_cfam_1862

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:7:73519008..73520319(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCAFG00000024483
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCAFG00000015834
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cfam_1862
ATGGCGGCCGGGACCCTGTACACATATCCTGAAAACTGGAGGGCCTTCAAGGCTCTCATTGCTGCTCAGTACAGCGGGGC
TCAGGTGCGCGTGCTCTCCGCACCACCCCACTTCCACTTTGGCCAAACCAACCGCACCCCTGAATTTCTCCGTAAATTTC
CTGCCGGCAAGGTTCCAGCATTTGAGGGTGATGATGGATTCTGTGTGTTTGAGAGCAGTGCCATTGCCTACTATGTGAAC
AATGAGGAGCTGCGGGGAAATACTCCAGAGGCAGCAGCCCAGGTGGTGCAGTGGGTGAGCTTTGCTGATAGCGACATAGT
GCCCCCAGCCAGTACCTGGGTGTTTCCTACCTTGGGCATCATGCACCACAACAAGCAGGCCACAGAGAATGCAAAGGAGG
AAGTGAGGCGAATTCTGGGGCTCCTGGATACTCATTTGAAGACCAGGACTTTTCTAGTGGGCAAACGTGTGACACTGGCT
GACATCACAGTTGTCTGCACCCTGTTGTGGCTCTATAAACAGGTCCTGGAGCCTTCTTTCCGCCAGGCCTTTCCCAATAC
CAACCGCTGGTTCCTTACCTGCATTAACCAGCCCCAGTTCCGGGCTGTCTTGGGGGAGGTGAAACTCTGTGAGAAGATGG
CCCAGTTTGATGCTAAAAAGTTTGCAGAGAGCCAACCTAAAAAAGACACCCCACGGAAAGAGAAGGATTCTCGGGAAGAG
AAGCAGAAGCTCCAGGCTGAGTGGAAAGAGGAGAAGAAGGCTGCTGCCCCTGCTCCTGAGGAGGAAATGGATGAATGTGA
GCAGGCACTGGCTGCTGAGCCAAAGGCCAAAGACCCCTTTGCTCACCTGCCCAAGAGTACCTTTGTGCTAGACGAATTTA
AGCGCAAGTACTCCAATGAGGACACTCTCCCTGTGGCACTGCCCTATTTCTGGGAGCACTTCGATAAGGATGGCTGGTCC
CTGTGGTACGCTGAGTACCGCTTCCCTGAGGAGCTCACTCAGACCTTTATGAGTTGTAACCTCATCACTGGAATGTTCCA
ACGGTTGGACAAGCTGAGGAAGAATGCCTTTGCCAGTGTCATCCTCTTTGGAACCAACAACAGCAGCTCCATTTCTGGAG
TCTGGGTCTTCCGAGGCCAGGAGCTTGCCTTTCCGCTGAGTCCAGATTGGCAGGTGGACTATGAGTCCTATACGTGGCGG
AAACTGGATCCTGGCAGCGAGGAGACCCAGACGCTGGTTCGAGAGGACTTTTCCTGGGAGGGGGCCTTCCAGCATGTGGG
CAAAACCTTCAATCAGGGCAAGATCTTCAAG

ORF - retro_cfam_1862 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 98.17 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMAAGTLYTYPENWRAFKALIAAQYSGAQVRVLSAPPHFHFGQTNRTPEFLRKFPAGKVPAFEGDDGFCVF
MAAGTLYTYPENWRAFKALIAAQYSGAQVRVLSAPPHFHFGQTNRTPEFLRKFPAGKVPAFEGDDGFCVF
RetrocopyMAAGTLYTYPENWRAFKALIAAQYSGAQVRVLSAPPHFHFGQTNRTPEFLRKFPAGKVPAFEGDDGFCVF
ParentalESNAIAYYVSNEELRGNTPEAAAQVVQWVSFADSDIVPPASTWVFPTLGIMHHNKQATENAKEEVRRILG
ES.AIAYYV.NEELRGNTPEAAAQVVQWVSFADSDIVPPASTWVFPTLGIMHHNKQATENAKEEVRRILG
RetrocopyESSAIAYYVNNEELRGNTPEAAAQVVQWVSFADSDIVPPASTWVFPTLGIMHHNKQATENAKEEVRRILG
ParentalLLDTHLKTRTFLVGERVTLADITVVCTLLWLYKQVLEPSFRQAFPNTNRWFLTCINQPQFRAVLGEVKLC
LLDTHLKTRTFLVG.RVTLADITVVCTLLWLYKQVLEPSFRQAFPNTNRWFLTCINQPQFRAVLGEVKLC
RetrocopyLLDTHLKTRTFLVGKRVTLADITVVCTLLWLYKQVLEPSFRQAFPNTNRWFLTCINQPQFRAVLGEVKLC
ParentalEKMAQFDAKKFAESQPKKDTPRKEKGSREEKQKPQAERKEEKKAAAPAPEEEMDECEQALAAEPKAKDPF
EKMAQFDAKKFAESQPKKDTPRKEK.SREEKQK.QAE.KEEKKAAAPAPEEEMDECEQALAAEPKAKDPF
RetrocopyEKMAQFDAKKFAESQPKKDTPRKEKDSREEKQKLQAEWKEEKKAAAPAPEEEMDECEQALAAEPKAKDPF
ParentalAHLPKSTFVLDEFKRKYSNEDTLTVALPYFWEHFDKDGWSLWYAEYRFPEELTQTFMSCNLITGMFQRLD
AHLPKSTFVLDEFKRKYSNEDTL.VALPYFWEHFDKDGWSLWYAEYRFPEELTQTFMSCNLITGMFQRLD
RetrocopyAHLPKSTFVLDEFKRKYSNEDTLPVALPYFWEHFDKDGWSLWYAEYRFPEELTQTFMSCNLITGMFQRLD
ParentalKLRKNAFASVILFGTNNSSSISGVWVFRGQELAFPLSPDWQVDYESYTWRKLDPGSEETQTLVREYFSWE
KLRKNAFASVILFGTNNSSSISGVWVFRGQELAFPLSPDWQVDYESYTWRKLDPGSEETQTLVRE.FSWE
RetrocopyKLRKNAFASVILFGTNNSSSISGVWVFRGQELAFPLSPDWQVDYESYTWRKLDPGSEETQTLVREDFSWE
ParentalGAFQHVGKTFNQGKIFK
GAFQHVGKTFNQGKIFK
RetrocopyGAFQHVGKTFNQGKIFK

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
SRP012049_cerebellum 0 .04 RPM 70 .47 RPM
SRP017611_brain 0 .00 RPM 32 .95 RPM
SRP017611_kidney 0 .26 RPM 245 .66 RPM
SRP017611_liver 0 .00 RPM 68 .74 RPM

ChIP-Seq - click to see more details

Canis familiaris was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cfam_1862 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_1862 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_1862 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 27 parental genes, and 81 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000067451 retrocopy
retro_amel_772,
Bos taurus ENSBTAG000000118431 retrocopy
retro_btau_1600,
Canis familiaris ENSCAFG00000015834 6 retrocopies
retro_cfam_1241, retro_cfam_1398, retro_cfam_1862 , retro_cfam_478, retro_cfam_638, retro_cfam_653,
Callithrix jacchus ENSCJAG000000189496 retrocopies
retro_cjac_1464, retro_cjac_1770, retro_cjac_1942, retro_cjac_3147, retro_cjac_841, retro_cjac_874,
Equus caballus ENSECAG000000143341 retrocopy
retro_ecab_419,
Erinaceus europaeus ENSEEUG000000012311 retrocopy
retro_eeur_575,
Homo sapiens ENSG000002547724 retrocopies
retro_hsap_2778, retro_hsap_2982, retro_hsap_3906, retro_hsap_4744,
Gorilla gorilla ENSGGOG0000001355712 retrocopies
retro_ggor_1935, retro_ggor_1936, retro_ggor_1991, retro_ggor_1992, retro_ggor_2064, retro_ggor_2065, retro_ggor_2214, retro_ggor_243, retro_ggor_2542, retro_ggor_2633, retro_ggor_2946, retro_ggor_2947,
Latimeria chalumnae ENSLACG000000147001 retrocopy
retro_lcha_82,
Loxodonta africana ENSLAFG000000033391 retrocopy
retro_lafr_381,
Myotis lucifugus ENSMLUG000000003421 retrocopy
retro_mluc_1110,
Macaca mulatta ENSMMUG000000065985 retrocopies
retro_mmul_1447, retro_mmul_1905, retro_mmul_2528, retro_mmul_736, retro_mmul_802,
Monodelphis domestica ENSMODG000000076911 retrocopy
retro_mdom_68,
Mustela putorius furoENSMPUG000000139422 retrocopies
retro_mputfur_427, retro_mputfur_944,
Mus musculus ENSMUSG000000716447 retrocopies
retro_mmus_1447, retro_mmus_1839, retro_mmus_2350, retro_mmus_2765, retro_mmus_3080, retro_mmus_425, retro_mmus_989,
Nomascus leucogenys ENSNLEG000000035282 retrocopies
retro_nleu_1510, retro_nleu_681,
Oryctolagus cuniculus ENSOCUG000000209593 retrocopies
retro_ocun_1693, retro_ocun_369, retro_ocun_693,
Otolemur garnettii ENSOGAG000000008271 retrocopy
retro_ogar_1344,
Ochotona princeps ENSOPRG000000145631 retrocopy
retro_opri_814,
Pongo abelii ENSPPYG000000294345 retrocopies
retro_pabe_2237, retro_pabe_2378, retro_pabe_2409, retro_pabe_2473, retro_pabe_3690,
Pan troglodytes ENSPTRG000000037683 retrocopies
retro_ptro_1879, retro_ptro_2017, retro_ptro_3159,
Pteropus vampyrus ENSPVAG000000034401 retrocopy
retro_pvam_1239,
Rattus norvegicus ENSRNOG000000200758 retrocopies
retro_rnor_1312, retro_rnor_2126, retro_rnor_2235, retro_rnor_2269, retro_rnor_2468, retro_rnor_2617, retro_rnor_2928, retro_rnor_979,
Sorex araneus ENSSARG000000112321 retrocopy
retro_sara_718,
Sus scrofa ENSSSCG000000130641 retrocopy
retro_sscr_164,
Ictidomys tridecemlineatus ENSSTOG000000028512 retrocopies
retro_itri_852, retro_itri_886,
Tursiops truncatus ENSTTRG000000024593 retrocopies
retro_ttru_1082, retro_ttru_1544, retro_ttru_1603,


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