RetrogeneDB ID:

retro_cfam_253

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:1:32514684..32515940(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCAFG00000000289
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCAFG00000003953
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cfam_253
AGGTATTTCATGCACGGGGTTTGTAAAGACGGAGATAATTGTCGCTACTCGCATGACCTCTCTGACAGTCCTTATGGTGT
AGTGTGCAAGTATTTTCAGCGAGGCTACTGTATTTACGGAGACCGCTGCAGATATGAACATAGCAAGCTATTGAAACATG
AAGAAGTGACTGCTGCAGATCTAACTGCAAAATCATCTCTTGCTGCTTCCTCAAGTCTCTCATCGGGAGTTGGACCAGTT
GTTGAAATGAATACGGGTGAAGCAGAGTCCAGAAATTCAAACTTTGCTACTGTCGGCGCAGGTTCAGAAGACTGGGTGAA
TGCCATTGAGTTTGTTCCCGGGCAGCCCTACTGTGGCCGTACTGCCCCTTCCTGCACTGAAGCGCCCCCACAGGGCTCTG
TGACCAAGGAAGAATCAGAGAAAGAACAGACAGCAGTGGAAACCAAGAAGCAGCTTTGCCCCTATGCTGCAGTGGGAGAG
TGCCGGTATGGGGAGAACTGTGTGTATCTCCACGGAGACTCGTGTGACATGTGTGGGCTGCAGGTCCTCCATCCAATGCA
TGCCGCCCAGAGATCACAACATATAAAATCTTGCATTGAGGCCCATGAGAAGGACATGGAGCTCTCATTTGCTGTCCAGC
ACAGTAAGGACATGGTGTGTGGGATCTGCATGGTCTATGAGAAAGCCAACCCCAGTGAGCGTCGCTTTGGGATTCTCTCC
AACTGCAACCACACTTACTGTCTCAAGTGTATTCGCAAGTGGAGGAGTGTGAAGCAATTTGAGAGCAAGATCATAAAGTC
CTGCCCCGAATGCCGGATCACATCTAACTTTGTCATTCCAAGTGAGTACTGGGTGGAGGAGAAAGAAGAGAAGCAGAAAC
TCATTCAGAAATACAAGGAGGCAATGAGCAACAAGGCGTGCAGGTATTTTGATGAAGGACGTGGGAGCTGCCCATTTGGA
GGGAACTGTTTTTACAAGCATGGTACCCTGATGGCCGTAGAGAGGAGCCACAGAGACAGAAAGTGGGAACATCAAGCAGA
TACCGGGCCCAACGAAGGAACCACTTCTGGGAGCTCATTGAGGAAAGAGAGAACAGCAACCCCTTTGACAACGAAGTAGA
GGAGGTTGTCACCTTTGAGCTGGGTGAGATGTTGCTTATGCTTTTGGTTGCAGGTGGGGACGACGACCTGACAGACTCTG
AAGACGAGTGGGACTTGTTTCATGATGAGCTAGAAGATTTTTATGACTTGGATCTA

ORF - retro_cfam_253 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.68 %
Parental protein coverage: 86.45 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalKYFMHGVCKEGDNCRYSHDLSDSPYGVVCKYFQRGYCIYGDRCRYEHSKPLKQEEVTAADLTAKSSLAAS
.YFMHGVCK.GDNCRYSHDLSDSPYGVVCKYFQRGYCIYGDRCRYEHSK.LK.EEVTAADLTAKSSLAAS
RetrocopyRYFMHGVCKDGDNCRYSHDLSDSPYGVVCKYFQRGYCIYGDRCRYEHSKLLKHEEVTAADLTAKSSLAAS
ParentalSSLSSGVGPVVEMNMGEAESRNSNFATVGAGSEDWVNAIEFVPGQPYCGRTAPSCTEAPPQGSVTKEESE
SSLSSGVGPVVEMN.GEAESRNSNFATVGAGSEDWVNAIEFVPGQPYCGRTAPSCTEAPPQGSVTKEESE
RetrocopySSLSSGVGPVVEMNTGEAESRNSNFATVGAGSEDWVNAIEFVPGQPYCGRTAPSCTEAPPQGSVTKEESE
ParentalKEQTAVETKKQLCPYAAVGECRYGENCVYLHGDSCDMCGLQVLHPMDAAQRSQHIKSCIEAHEKDMELSF
KEQTAVETKKQLCPYAAVGECRYGENCVYLHGDSCDMCGLQVLHPM.AAQRSQHIKSCIEAHEKDMELSF
RetrocopyKEQTAVETKKQLCPYAAVGECRYGENCVYLHGDSCDMCGLQVLHPMHAAQRSQHIKSCIEAHEKDMELSF
ParentalAVQRSKDMVCGICMEVVYEKANPSERRFGILSNCNHTYCLKCIRKWRSAKQFESKIIKSCPECRITSNFV
AVQ.SKDMVCGICM..VYEKANPSERRFGILSNCNHTYCLKCIRKWRS.KQFESKIIKSCPECRITSNFV
RetrocopyAVQHSKDMVCGICM--VYEKANPSERRFGILSNCNHTYCLKCIRKWRSVKQFESKIIKSCPECRITSNFV
ParentalIPSEYWVEEKEEKQKLIQKYKEAMSNKACRYFDEGRGSCPFGGNCFYKHA-YPDGRREEPQRQKVGTSSR
IPSEYWVEEKEEKQKLIQKYKEAMSNKACRYFDEGRGSCPFGGNCFYKH..YPDGRREEPQRQKVGTSSR
RetrocopyIPSEYWVEEKEEKQKLIQKYKEAMSNKACRYFDEGRGSCPFGGNCFYKHG<YPDGRREEPQRQKVGTSSR
ParentalYRAQRRNHFWELIEERENSNPFDNEEEEVVTFELGEMLLMLLAAGGDDDLTDSEDEWDLFHDELEDFYDL
YRAQRRNHFWELIEERENSNPFDNE.EEVVTFELGEMLLMLL.AGGDDDLTDSEDEWDLFHDELEDFYDL
RetrocopyYRAQRRNHFWELIEERENSNPFDNEVEEVVTFELGEMLLMLLVAGGDDDLTDSEDEWDLFHDELEDFYDL
ParentalDL
DL
RetrocopyDL

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 .00 RPM 62 .83 RPM
SRP017611_brain 0 .00 RPM 32 .07 RPM
SRP017611_kidney 0 .00 RPM 30 .38 RPM
SRP017611_liver 0 .00 RPM 12 .18 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_253 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_253 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_253 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 24 parental genes, and 53 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000083062 retrocopies
retro_btau_401, retro_btau_943,
Canis familiaris ENSCAFG00000003953 2 retrocopies
retro_cfam_2157, retro_cfam_253 ,
Choloepus hoffmanni ENSCHOG000000110153 retrocopies
retro_chof_173, retro_chof_2357, retro_chof_89,
Callithrix jacchus ENSCJAG000000134742 retrocopies
retro_cjac_210, retro_cjac_2991,
Cavia porcellus ENSCPOG000000009481 retrocopy
retro_cpor_109,
Dasypus novemcinctus ENSDNOG000000195642 retrocopies
retro_dnov_1011, retro_dnov_388,
Erinaceus europaeus ENSEEUG000000011331 retrocopy
retro_eeur_643,
Felis catus ENSFCAG000000249421 retrocopy
retro_fcat_67,
Homo sapiens ENSG000001336064 retrocopies
retro_hsap_1140, retro_hsap_4197, retro_hsap_4676, retro_hsap_4859,
Gorilla gorilla ENSGGOG000000239774 retrocopies
retro_ggor_119, retro_ggor_2813, retro_ggor_3031, retro_ggor_381,
Macropus eugenii ENSMEUG000000073991 retrocopy
retro_meug_1659,
Microcebus murinus ENSMICG000000021141 retrocopy
retro_mmur_1184,
Macaca mulatta ENSMMUG000000104203 retrocopies
retro_mmul_191, retro_mmul_2597, retro_mmul_76,
Mus musculus ENSMUSG000000299221 retrocopy
retro_mmus_2663,
Nomascus leucogenys ENSNLEG000000019214 retrocopies
retro_nleu_1027, retro_nleu_2167, retro_nleu_33, retro_nleu_939,
Otolemur garnettii ENSOGAG000000098772 retrocopies
retro_ogar_3468, retro_ogar_424,
Ochotona princeps ENSOPRG000000103531 retrocopy
retro_opri_1073,
Procavia capensis ENSPCAG000000146831 retrocopy
retro_pcap_19,
Pongo abelii ENSPPYG000000180573 retrocopies
retro_pabe_3435, retro_pabe_3776, retro_pabe_947,
Pan troglodytes ENSPTRG000000197665 retrocopies
retro_ptro_2849, retro_ptro_3106, retro_ptro_3234, retro_ptro_75, retro_ptro_776,
Sus scrofa ENSSSCG000000164982 retrocopies
retro_sscr_43, retro_sscr_637,
Tupaia belangeri ENSTBEG000000045642 retrocopies
retro_tbel_1410, retro_tbel_71,
Tarsius syrichta ENSTSYG000000099963 retrocopies
retro_tsyr_1256, retro_tsyr_1525, retro_tsyr_508,
Tursiops truncatus ENSTTRG000000095282 retrocopies
retro_ttru_1064, retro_ttru_1128,


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