RetrogeneDB ID:

retro_cfam_1483

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:32:36073231..36074309(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCAFG00000017648
Aliases:None
Description:ATP synthase subunit alpha [Source:UniProtKB/TrEMBL;Acc:E2RNG2]


Retrocopy-Parental alignment summary:






>retro_cfam_1483
ATTAAGGCCGTGGAGAGCTTGATGCCAATTGCTCATGGTCAGCATGAGCTGATTATTGATGACCGGCAAACTGGCAAAAC
GTCAATTGCTATTGACACAATCATTAATCAGAAATGTTTCAATGACGGGACTGATGAAAAGAAGAAGCTATAGTGTATCT
ATGTCGCTATTGGTCAGAAGAGATCTACGGTTGCCCAGTTGGTGAAGAGACTTACAGATGCAGATGCCATGAAGTTCACC
ATTGTGGTGTCAGCTACTGCTTCTGATGCTGCTCCACTTCGGTGCCTGACTCCTTATTCTGGGGGCGGGGGGGGAGAATA
TTTTAGAGATCATGGCAAACATGCTTTGATCATCTACGATGACTTATCCAGACAGGCTGTTGCTTATCGTTGGATGTCTC
TGCTGCTCCGCCGGCCCCCCGGTCGTGAGGCCTATCCGGGTGATGTGTTCTACCTACATTCCCATCTGCTAGAGAGAGCA
GCCAAAATGAACAATTCTTTTGGTGGTGGCTCCTTGACTGCTTTACCAGTCATAGAAACACAAACTGGTGATGTGAATGC
TTACATTCCGACAGATGTCATTTCCATCACTGATGGACAGATCTTGGGAACAGAATTGTTCTACAAAGGTATCCGCCCTG
CCATTAACGTCAGTTTATCTGTGTCCTGTGTTGGATCTGCTGCCCAAACCAGGGCCATGAGGCAGGTGGCAGGTGCCATG
AAGCTGGAATTGGCTCAGTATTGCGAGACTGCAGCTTTTGCCCAGTTTGGTTCTGACCTTGATGCTGCCACTCAACAACC
CTTGAGTCGTGGCATGAGATTGACTGAGTTGCTGAAGCAAGGATAGTATTTTCCCATGGCTATTGAAGAACAAGTGGCTG
TTATTTATGCTGGTGTAAGAGGATATCTTGATAAATTGGAGCCCAGCAAGATCACAAAGTTTGAGCATGCTTTCTTGGCT
CGTGTTATCAGCCAGCACCAAGCCTTCTTGGACAAATATAAGGACCAATGGAAAGATCTCAGAACAGTCAGATGCTAAGC
TGAAAGAGATTGTAACAAACTTCTTGGCTGGATTTGAA

ORF - retro_cfam_1483 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.37 %
Parental protein coverage: 65.1 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalIKAVDSLVPIGRGQRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKR
IKAV.SL.PI..GQ.ELII.DRQTGKTSIAIDTIINQK.FNDGTDEKKKL.CIYVAIGQKRSTVAQLVKR
RetrocopyIKAVESLMPIAHGQHELIIDDRQTGKTSIAIDTIINQKCFNDGTDEKKKL*CIYVAIGQKRSTVAQLVKR
ParentalLTDADAMKYTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAYRQMSLLLRRPP
LTDADAMK.TIVVSATASDAAPL..L.PYS.....EYFRD.GKHALIIYDDLS.QAVAYR.MSLLLRRPP
RetrocopyLTDADAMKFTIVVSATASDAAPLRCLTPYSXXXXXEYFRDHGKHALIIYDDLSRQAVAYRWMSLLLRRPP
ParentalGREAYPGDVFYLHSRLLERAAKMNDSFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYK
GREAYPGDVFYLHS.LLERAAKMN.SFGGGSLTALPVIETQ.GDV.AYIPT.VISITDGQI.L.TELFYK
RetrocopyGREAYPGDVFYLHSHLLERAAKMNNSFGGGSLTALPVIETQTGDVNAYIPTDVISITDGQI-LGTELFYK
ParentalGIRPAINVGLSVSRVGSAAQTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLSRGVRLTELLK
GIRPAINV.LSVS.VGSAAQTRAM.QVAG.MKLELAQY.E.AAFAQFGSDLDAATQQ.LSRG.RLTELLK
RetrocopyGIRPAINVSLSVSCVGSAAQTRAMRQVAGAMKLELAQYCETAAFAQFGSDLDAATQQPLSRGMRLTELLK
ParentalQGQYSPMAIEEQVAVIYAGVRGYLDKLEPSKITKFEHAFLAHVISQHQALLG-NIRTDGKISEQSDAKLK
QG.Y.PMAIEEQVAVIYAGVRGYLDKLEPSKITKFEHAFLA.VISQHQA.L..NIRT.GKISEQSDAKLK
RetrocopyQG*YFPMAIEEQVAVIYAGVRGYLDKLEPSKITKFEHAFLARVISQHQAFLD>NIRTNGKISEQSDAKLK
ParentalEIVTNFLAGFE
EIVTNFLAGFE
RetrocopyEIVTNFLAGFE

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 394 .33 RPM
SRP017611_brain 0 .00 RPM 395 .22 RPM
SRP017611_kidney 0 .07 RPM 1120 .78 RPM
SRP017611_liver 0 .00 RPM 274 .83 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_1483 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_1483 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_1483 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 20 parental genes, and 23 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000025072 retrocopies
retro_btau_1380, retro_btau_1426,
Canis familiaris ENSCAFG00000017648 2 retrocopies
retro_cfam_1483 , retro_cfam_516,
Dasypus novemcinctus ENSDNOG000000063312 retrocopies
retro_dnov_1740, retro_dnov_2525,
Equus caballus ENSECAG000000215611 retrocopy
retro_ecab_788,
Homo sapiens ENSG000001522341 retrocopy
retro_hsap_1702,
Gorilla gorilla ENSGGOG000000165601 retrocopy
retro_ggor_1275,
Macropus eugenii ENSMEUG000000097701 retrocopy
retro_meug_151,
Meleagris gallopavo ENSMGAG000000099631 retrocopy
retro_mgal_14,
Microcebus murinus ENSMICG000000175001 retrocopy
retro_mmur_1210,
Myotis lucifugus ENSMLUG000000098561 retrocopy
retro_mluc_1198,
Macaca mulatta ENSMMUG000000035701 retrocopy
retro_mmul_1208,
Mustela putorius furoENSMPUG000000009231 retrocopy
retro_mputfur_601,
Nomascus leucogenys ENSNLEG000000109731 retrocopy
retro_nleu_1334,
Oryctolagus cuniculus ENSOCUG000000039671 retrocopy
retro_ocun_1235,
Otolemur garnettii ENSOGAG000000266841 retrocopy
retro_ogar_2623,
Pongo abelii ENSPPYG000000091301 retrocopy
retro_pabe_1363,
Pan troglodytes ENSPTRG000000099911 retrocopy
retro_ptro_1151,
Sarcophilus harrisii ENSSHAG000000171771 retrocopy
retro_shar_109,
Tarsius syrichta ENSTSYG000000078041 retrocopy
retro_tsyr_1186,
Tursiops truncatus ENSTTRG000000051181 retrocopy
retro_ttru_159,


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