RetrogeneDB ID:

retro_cfam_1512

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:32:34227877..34228337(-)
Located in intron of:ENSCAFG00000012173
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCAFG00000000071
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cfam_1512
ATGAATGTGGGGGTTGCACACAGAGAAGTAGATCTCAATACTGGAGTGATGAATAGCCTGGGCATCTGGCTGGCCTACAT
CGCCTTGGTAGGACTGCTGCATGTGGTTTTACTCAGCATCCCCTTCTTCAGCATTCCTATTTTCTGGACCCTGACCAACA
TCATCCATACCTTGGCTATGTATGTCTTCTTACATGCAGTGAAAGGGACACCCTTTGAGACACCTGACCAAGAAAAGACT
CGGCTGCTGACACACTGGGAACAGATGGACTATGGGCTCCAAAATACCTCTTCCTGCAAATTTCCTCAGCATCTCTTCTA
TCGTACTCTACCTCCTGGCCAGGTTCCACACCAAGTATGATGCTGCTCACTTTCTCATCAACACAGCCTCATTGCTCAGC
ATACTGCTGGCTAAGTTACCCCAATTCCATGGGGTTCATCTCTTTGGCATCAACAAATAC

ORF - retro_cfam_1512 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.06 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMNVGVAHSEVNPNTRVMNSRGIWLAYIILVGLLHVVLLSIPFFSIPVVWTLTNVIHNLAMYVFLHTVKGT
MNVGVAH.EV..NT.VMNS.GIWLAYI.LVGLLHVVLLSIPFFSIP..WTLTN.IH.LAMYVFLH.VKGT
RetrocopyMNVGVAHREVDLNTGVMNSLGIWLAYIALVGLLHVVLLSIPFFSIPIFWTLTNIIHTLAMYVFLHAVKGT
ParentalPFETPDQGKARLLTHWEQMDYGLQFTSSRK-FLSISPIVLYLLASFYTKYDAAHFIINTASLLSVLLPKL
PFETPDQ.K.RLLTHWEQMDYGLQ.TSS.K.FLSIS.IVLYLLA.F.TKYDAAHF.INTASLLS.LL.KL
RetrocopyPFETPDQEKTRLLTHWEQMDYGLQNTSSCK>FLSISSIVLYLLARFHTKYDAAHFLINTASLLSILLAKL
ParentalPQFHGVRLFGINKY
PQFHGV.LFGINKY
RetrocopyPQFHGVHLFGINKY

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 5 .46 RPM
SRP017611_brain 0 .24 RPM 3 .10 RPM
SRP017611_kidney 0 .07 RPM 30 .77 RPM
SRP017611_liver 0 .00 RPM 6 .09 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_1512 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_1512 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_1512 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 11 parental genes, and 20 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG00000000071 8 retrocopies
retro_cfam_1078, retro_cfam_1248, retro_cfam_1512 , retro_cfam_1786, retro_cfam_187, retro_cfam_335, retro_cfam_576, retro_cfam_972,
Choloepus hoffmanni ENSCHOG000000096011 retrocopy
retro_chof_2232,
Erinaceus europaeus ENSEEUG000000152241 retrocopy
retro_eeur_16,
Felis catus ENSFCAG000000139641 retrocopy
retro_fcat_895,
Macropus eugenii ENSMEUG000000148961 retrocopy
retro_meug_767,
Microcebus murinus ENSMICG000000109201 retrocopy
retro_mmur_212,
Myotis lucifugus ENSMLUG000000035751 retrocopy
retro_mluc_901,
Macaca mulatta ENSMMUG000000062921 retrocopy
retro_mmul_2358,
Mustela putorius furoENSMPUG000000009112 retrocopies
retro_mputfur_452, retro_mputfur_738,
Mus musculus ENSMUSG000000253531 retrocopy
retro_mmus_2646,
Otolemur garnettii ENSOGAG000000016952 retrocopies
retro_ogar_3016, retro_ogar_951,


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