RetrogeneDB ID:

retro_cfam_463

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:11:43106571..43107920(-)
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:ENSCAFG00000008640
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cfam_463
GAGTGTATATCGATCCACGTTGGCCAGGCAGATGTCCAGATCGGCAATGCCTGCTGGGAGCTCTATTGCCTGGAACACGG
CATTCAGCCCAATGGCCAGATGCCAAGTGACAAGACCACTGGGGGAGGAGATGACTCCTATCAACACCTTCTTCAGTGAG
ATGGGCACTGGCAAGCATGTGCCCAGGGCAGTGTTTGTAGACCTGGAGCCCACAGTCATTGATGAAGTTCACACTGGTAC
CTACCACCAGCTTTTCCACCCTGAGCAGCTCATCACAGGCAAGAAAGATGCTGCCAATAACTATGCCCAAGGGCACTACA
CCATTGGCAAGGAGATCATTGACCTTGTCTTGGACTGAATTCGGAAACTGGCTGACCAGTGCACAGGTCTTCAGGGCTTC
TTGGTTTTCCACACCTTTGGAGGGGAAACCAGTTCTGGGTTCACTTCCCTGCTGATGGAATGTCTCTCTGTCGATTATGG
CAAGAAGTCCAAGCTAGAGTTCTCCATCTACCCTGCCCCCCCAGGTGTCCACAGCTGTAGTAGAGCCCTACAACTCCATC
CTCACCACCCACACCACCCTGGAGCACTCTGATTGTGCCTTCATGGTAGACAATGAGGCCATCTATGACATCTGTCGTAG
AAACCTCGATATTGAGTGCCCAACCTACACTAATCTAAACTGGTTGATAGGTCAAATTGTGTCCTCCATCACTGATTCCC
TCAGATTTGATGGAGCCCTGAATGTGGATCTGACTGAGTTCCAGACCAACCTGGTGCCCTTTCCCTGCATCCACGTCCCT
CTGGCCACATATGCCCCTGTCATCTCTGCTGAGAAAGCCTACCATGAACAGTTTTCTGTAGCAGAGATCACCAATGCATG
CTTTGAGCCAGCCAACCAGATGGTGAAATGTGACCCTCGACATGGTAAATACATGGCTTGCTGCCTGTTGTACCATGGCG
ACGTGGTTCCCAAAGATGTCAATACTGCCATTGCCACCATCAAGACCAAGCGTACCATCCAGTTTGTGGACTGGTGCCCC
ACTGGCTTCAAAGTGGGTATTAACTACCAGCCTCCCACTGTGGTACCCGGTGGAGACCTGGCCAAAGTACAGCGAGTTGT
GTGCATGCTGAGCAACACCACAGCCATTGCTGAGGCCTGGGCTCGCCTGGACCACAAGTTTGACCTGATGTATGTCAATC
ATGCCTTTGCTCACTGGTATGTGGTTGAGGGCATGGAGGAAGGAGAGTTTTCTGAGGCCTGTGAGGACATGGCTGCCCTG
GAGAAGGATTATGAGGAGGTTGGTGTGGATTCTGTTGAAGGAGAGGGTGAAGAAGAAGGAGAGGAATAC

ORF - retro_cfam_463 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.24 %
Parental protein coverage: 99.56 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSF-NTFFSETGAGKHVPRAVFVDLE
ECISIHVGQA.VQIGNACWELYCLEHGIQP.GQMPSDKT.GGGDDS..NTFFSE.G.GKHVPRAVFVDLE
RetrocopyECISIHVGQADVQIGNACWELYCLEHGIQPNGQMPSDKTTGGGDDSY>NTFFSEMGTGKHVPRAVFVDLE
ParentalPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSF
PTVIDEV.TGTY.QLFHPEQLITGK.DAANNYA.GHYTIGKEIIDLVLD.IRKLADQCTGLQGFLVFH.F
RetrocopyPTVIDEVHTGTYHQLFHPEQLITGKKDAANNYAQGHYTIGKEIIDLVLD*IRKLADQCTGLQGFLVFHTF
ParentalGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPA-PQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIY
GG.T.SGFTSLLME.LSVDYGKKSKLEFSIYPA.PQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIY
RetrocopyGGETSSGFTSLLMECLSVDYGKKSKLEFSIYPA>PQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIY
ParentalDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEK
DICRRNLDIE.PTYTNLN.LI.QIVSSIT.SLRFDGALNVDLTEFQTNLVP.P.IH.PLATYAPVISAEK
RetrocopyDICRRNLDIECPTYTNLNWLIGQIVSSITDSLRFDGALNVDLTEFQTNLVPFPCIHVPLATYAPVISAEK
ParentalAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTG
AYHEQ.SVAEITNACFEPANQMVKCDPRHGKYMACCLLY.GDVVPKDVN.AIATIKTKR.IQFVDWCPTG
RetrocopyAYHEQFSVAEITNACFEPANQMVKCDPRHGKYMACCLLYHGDVVPKDVNTAIATIKTKRTIQFVDWCPTG
ParentalFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
FKVGINYQPPTVVPGGDLAKVQR.VCMLSNTTAIAEAWARLDHKFDLMY...AF.HWYV.EGMEEGEFSE
RetrocopyFKVGINYQPPTVVPGGDLAKVQRVVCMLSNTTAIAEAWARLDHKFDLMYVNHAFAHWYVVEGMEEGEFSE
ParentalAREDMAALEKDYEEVGVDSVEGEGEEEGEEY
A.EDMAALEKDYEEVGVDSVEGEGEEEGEEY
RetrocopyACEDMAALEKDYEEVGVDSVEGEGEEEGEEY

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 .71 RPM 465 .89 RPM
SRP017611_brain 0 .32 RPM 647 .84 RPM
SRP017611_kidney 0 .07 RPM 186 .36 RPM
SRP017611_liver 0 .00 RPM 50 .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_463 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_463 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_463 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 16 parental genes, and 41 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000068724 retrocopies
retro_amel_1162, retro_amel_1367, retro_amel_1387, retro_amel_1895,
Canis familiaris ENSCAFG000000052481 retrocopy
retro_cfam_1124,
Canis familiaris ENSCAFG00000008640 8 retrocopies
retro_cfam_1481, retro_cfam_1751, retro_cfam_1895, retro_cfam_1917, retro_cfam_1979, retro_cfam_2000, retro_cfam_463 , retro_cfam_926,
Canis familiaris ENSCAFG000000086612 retrocopies
retro_cfam_960, retro_cfam_978,
Canis familiaris ENSCAFG000000104121 retrocopy
retro_cfam_1418,
Choloepus hoffmanni ENSCHOG000000084442 retrocopies
retro_chof_179, retro_chof_360,
Cavia porcellus ENSCPOG000000130161 retrocopy
retro_cpor_96,
Felis catus ENSFCAG000000270111 retrocopy
retro_fcat_588,
Felis catus ENSFCAG000000286893 retrocopies
retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Loxodonta africana ENSLAFG000000100211 retrocopy
retro_lafr_326,
Microcebus murinus ENSMICG000000175513 retrocopies
retro_mmur_144, retro_mmur_705, retro_mmur_885,
Myotis lucifugus ENSMLUG000000026224 retrocopies
retro_mluc_154, retro_mluc_186, retro_mluc_234, retro_mluc_270,
Otolemur garnettii ENSOGAG000000094351 retrocopy
retro_ogar_240,
Tupaia belangeri ENSTBEG000000016711 retrocopy
retro_tbel_3700,
Tarsius syrichta ENSTSYG000000132667 retrocopies
retro_tsyr_1014, retro_tsyr_1278, retro_tsyr_1281, retro_tsyr_1679, retro_tsyr_1834, retro_tsyr_243, retro_tsyr_6,
Tursiops truncatus ENSTTRG000000047941 retrocopy
retro_ttru_407,


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