RetrogeneDB ID:

retro_cfam_683

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:15:30478706..30480317(-)
Located in intron of:ENSCAFG00000006105
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GALNT12
Ensembl ID:ENSCAFG00000002494
Aliases:None
Description:UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 12 (GalNAc-T12) [Source:HGNC Symbol;Acc:19877]


Retrocopy-Parental alignment summary:






>retro_cfam_683
CGGGAGCGGGGCCCCAGACAGCTCGCAGACCCCCGGCGAGAGGCAGAGGACTTGTCCCGGCCGCTGTACAAGAAGCCGCC
GGCAGACTCCCACGCGCTCGGGGAGTGGGGAAAGGCCAGCAAACTGCAGCTCGGCGAGGGTGAACTGAAGCAGCAAGAAG
AACTTATTGAGAGATATGCCATTAACATTTATCTCAGTGACAGGATTTCCCTGCACCGCCACATAGAGGATAAGCGAATG
TACGAGTGCAGAGCCAAGACGTTTGACTATCGCAGCCTCCCCACCACCTCCGTTATCATCGCCTTCTATAATGAAGCCTG
GTCGACCCTGCTCCGCACCATCCACAGTGTCCTGGAGACCTCCCCTGCAGTCCTTTTGAAGGAGATCGTCCTGGTGGATG
ACTTGAGCGACCGAGCTTATTTGAAGACGCAGCTGGAAACGTACATCAGCGACCTCGACAGAGTCCGCTTGATCAGAACG
AGTAAGCGCGAGGGGCTGGTGAGAGCCCGCCTCATCGGGGCCACTTTCGCCACTGGGGACGTCCTCACTTTCCTGGATTG
TCACTGCGAGTGCAACTCGGGCTGGTTAGAACCGCTCTTGGAAAGAATTAGTGAAGACGAAACAGCAATCGTTTGTCCCG
TTATAGACACCATCGATTGGAATACTTTTGAATTTTATATGCAGACCGGGGAGCCCATGATTGGTGGGTTTGACTGGCGC
CTAACCTTCCAATGGCATTCCGTCCCCAAACATGAGAGGGACAGACGGAAATCGAGAATTGACCCCATCAGATCGCCCAC
CATGGCTGGAGGACTGTTTGCGGTCAGCAAGAAATATTTTCAGTACCTTGGAACATACGACACCGGAATGGAAGTGTGGG
GAGGTGAAAACCTTGAGCTGTCTTTTAGGGTGTGGCAGTGTGGCGGGAAATTGGAGATCCACCCGTGTTCCCATGTGGGC
CATGTGTTCCCCAAGCGGGCACCATATGCTCGGCCCAATTTCCTCCAGAACACTGCTCGGGCAGCGGAAGTGTGGATGGA
TGAGTACAAAGAGCATTTCTACAACCGAAACCCCCCAGCGAGGAAAGAAGCTTATGGTGATATTTCTGAAAGGAAATTAC
TACGAGATCGGCTGAAGTGCAAGAGCTTTGACTGGTATTTGAAAAACGTATTTTCTAATTTACACGTTCCAGAGGATAGG
CCAGGCTGGCATGGAGCTATTCGCAGTATGGGAATCTCTTCTGAGTGTTTAGATTATAATTCTCCCGACAACAACCCGAC
AGGTGCCAACCTTTCACTGTTTGGATGCCACGGTCAAGGAGGCAATCAATTCTTTGAATATACTTCAAACAAAGAGATAA
GGTTTAACTCTGTGACAGAGTTATGTGCAGAGGTTCCTGAGCAAAAAAAACACGTAGGGATGCAAAATTGTCCAAAAGAC
GGGTTCCCTGTTCCAGCAAACATCGTTTGGCATTTTAGAGAAGACGGGACCATTTTTCATCCACACTCGGGGCTGTGTCT
TAGTGCCTTCCGGACACCTGAGGGTCGATCTGATGTTCAGATGAGAACTTGTGATGCTCTAGATAAAAATCAAATCTGGA
AGTTTGAGAAA

ORF - retro_cfam_683 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 56.96 %
Parental protein coverage: 92.73 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalRGAGAAEPGPPRAPRPGRRAPVLPRPPVPSDALGARGEAVRLQLQGEELRLQEESVRLHQINIYLSDRIS
R..G......PR........P....PP..S.ALG..G.A..LQL...EL..QEE......INIYLSDRIS
RetrocopyRERGPRQLADPRREAEDLSRPLYKKPPADSHALGEWGKASKLQLGEGELKQQEELIERYAINIYLSDRIS
ParentalLHRRLPERWNPLCKEKKYDYENLPTTSVVIAFYNEAWSTLLRTVYSVLETSPDILLEEVILVDDYSDREH
LHR.........C..K..DY..LPTTSV.IAFYNEAWSTLLRT..SVLETSP..LL.E..LVDD.SDR..
RetrocopyLHRHIEDKRMYECRAKTFDYRSLPTTSVIIAFYNEAWSTLLRTIHSVLETSPAVLLKEIVLVDDLSDRAY
ParentalLKERLANELSGLPKVRLIRANKREGLVRARLLGASAAKGEVLTFLDCHCECHEGWLEPLLQRIHEEESAV
LK..L....S.L..VRLIR..KREGLVRARL.GA..A.G.VLTFLDCHCEC..GWLEPLL.RI.E.E.A.
RetrocopyLKTQLETYISDLDRVRLIRTSKREGLVRARLIGATFATGDVLTFLDCHCECNSGWLEPLLERISEDETAI
ParentalVCPVIDVIDWNTFEYLGNPREPQIGGFDWRLVFTWHVVPERERMRMRSPIDVIRSPTMAGGLFAVSKKYF
VCPVID.IDWNTFE......EP.IGGFDWRL.F.WH.VP..ER.R..S.ID.IRSPTMAGGLFAVSKKYF
RetrocopyVCPVIDTIDWNTFEFYMQTGEPMIGGFDWRLTFQWHSVPKHERDRRKSRIDPIRSPTMAGGLFAVSKKYF
ParentalEYLGSYDTGMEVWGGENLEFSFRIWQCGGTLETHPCSHVGHVFPKQAPYSRNKALANSVRAAEVWMDDFK
.YLG.YDTGMEVWGGENLE.SFR.WQCGG.LE.HPCSHVGHVFPK.APY.R...L.N..RAAEVWMD..K
RetrocopyQYLGTYDTGMEVWGGENLELSFRVWQCGGKLEIHPCSHVGHVFPKRAPYARPNFLQNTARAAEVWMDEYK
ParentalELYYHRNPHARLEPFGDVTERKQLRAKLQCKDFRWFLENVYPELHVPEDRPGFFGMLQNKGLKDYCFDYN
E..Y.RNP.AR.E..GD..ERK.LR..L.CK.F.W.L.NV...LHVPEDRPG..G.....G....C.DYN
RetrocopyEHFYNRNPPARKEAYGDISERKLLRDRLKCKSFDWYLKNVFSNLHVPEDRPGWHGAIRSMGISSECLDYN
ParentalPPNENQVVGYQVLLYICHGMGQNQFFEYTSQNEIRYNTHQPEACIAVDAGTDVLVMHLCQE---ITPENQ
.P..N...G....L..CHG.G.NQFFEYTS..EIR.N....E.C..V........M..C.......P.N.
RetrocopySP-DNNPTGANLSLFGCHGQGGNQFFEYTSNKEIRFNS-VTELCAEVPEXXXHVGMQNCPKDGFPVPANI
ParentalKFILQEDGSLFHVQSKKCVQAERKALSDSFVPLLRDCIDSEHQKWLFKE
.....EDG..FH..S..C..A.R.....S.V...........Q.W.F..
RetrocopyVWHFREDGTIFHPHSGLCLSAFRTPEGRSDVQMRTCDALDKNQIWKFEK

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 2 .44 RPM 4 .24 RPM
SRP017611_brain 1 .43 RPM 7 .30 RPM
SRP017611_kidney 3 .37 RPM 11 .89 RPM
SRP017611_liver 2 .68 RPM 1 .38 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_683 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_683 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_683 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Sus scrofa retro_sscr_32
Parental genes homology:
Parental genes homology involve 34 parental genes, and 38 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000023021 retrocopy
retro_acar_54,
Ailuropoda melanoleuca ENSAMEG000000045201 retrocopy
retro_amel_93,
Anas platyrhynchos ENSAPLG000000121971 retrocopy
retro_apla_8,
Bos taurus ENSBTAG000000090371 retrocopy
retro_btau_1410,
Canis familiaris ENSCAFG00000002494 1 retrocopy
retro_cfam_683 ,
Canis familiaris ENSCAFG000000078401 retrocopy
retro_cfam_220,
Cavia porcellus ENSCPOG000000124181 retrocopy
retro_cpor_1467,
Equus caballus ENSECAG000000165461 retrocopy
retro_ecab_52,
Ficedula albicollis ENSFALG000000051881 retrocopy
retro_falb_8,
Felis catus ENSFCAG000000088311 retrocopy
retro_fcat_126,
Gorilla gorilla ENSGGOG000000057921 retrocopy
retro_ggor_890,
Loxodonta africana ENSLAFG000000220111 retrocopy
retro_lafr_536,
Meleagris gallopavo ENSMGAG000000072441 retrocopy
retro_mgal_1,
Microcebus murinus ENSMICG000000110751 retrocopy
retro_mmur_282,
Myotis lucifugus ENSMLUG000000026301 retrocopy
retro_mluc_804,
Macaca mulatta ENSMMUG000000195611 retrocopy
retro_mmul_888,
Mustela putorius furoENSMPUG000000065021 retrocopy
retro_mputfur_569,
Mus musculus ENSMUSG000000397741 retrocopy
retro_mmus_183,
Nomascus leucogenys ENSNLEG000000170191 retrocopy
retro_nleu_940,
Oryctolagus cuniculus ENSOCUG000000162211 retrocopy
retro_ocun_1260,
Otolemur garnettii ENSOGAG000000014082 retrocopies
retro_ogar_3253, retro_ogar_717,
Ochotona princeps ENSOPRG000000060292 retrocopies
retro_opri_121, retro_opri_515,
Procavia capensis ENSPCAG000000050681 retrocopy
retro_pcap_63,
Pongo abelii ENSPPYG000000194371 retrocopy
retro_pabe_949,
Pelodiscus sinensis ENSPSIG000000172461 retrocopy
retro_psin_1,
Pan troglodytes ENSPTRG000000211801 retrocopy
retro_ptro_777,
Pteropus vampyrus ENSPVAG000000087741 retrocopy
retro_pvam_1347,
Rattus norvegicus ENSRNOG000000080993 retrocopies
retro_rnor_1084, retro_rnor_1085, retro_rnor_2453,
Sarcophilus harrisii ENSSHAG000000174741 retrocopy
retro_shar_44,
Sus scrofa ENSSSCG000000053791 retrocopy
retro_sscr_32,
Ictidomys tridecemlineatus ENSSTOG000000213061 retrocopy
retro_itri_41,
Tupaia belangeri ENSTBEG000000036271 retrocopy
retro_tbel_2065,
Tarsius syrichta ENSTSYG000000049751 retrocopy
retro_tsyr_386,
Tursiops truncatus ENSTTRG000000108481 retrocopy
retro_ttru_212,




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