RetrogeneDB ID:

retro_cfam_1487

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:32:1751985..1752375(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:KRTCAP2
Ensembl ID:ENSCAFG00000017055
Aliases:KRTCAP2, KCP-2, KCP2
Description:Canis lupus familiaris keratinocyte associated protein 2 (KRTCAP2), mRNA. [Source:RefSeq mRNA;Acc:NM_001160122]


Retrocopy-Parental alignment summary:






>retro_cfam_1487
ACCGTGATGGCACTCTTCTCCCCCCAGTCCCTGATGCTCTTTGCCGGGATGCATATATATAGCCTCCAGCTGGCTTCCCC
TAAGTGGCTTACCATCAAAGGGGACGCCTGCTGGGCTCCAGCCTTTTAGTCTTCTCTCTCACCGCCTTCAGTAATCTGAT
GAATGTTGTCTTTGGCAAAGGATTCCAAGCAAAGATCTTCCCTGAGATTCTTCTCTGTCTCCTGCTGGCTCTCTTTGCAT
CTGGCCTCATCCACCAAGTCTGTGTTAGGACTTGCTTCACCTTCTTCATGGTTGGCCTCAACTACATCAACAAGATCTCC
TCTCTGTATCAGGTAACAGTTCCATTCCTCACACCAGCCAAGATCACAGGGTAAGAGCAAAAAGAGAAGC

ORF - retro_cfam_1487 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.44 %
Parental protein coverage: 95.59 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalTSLALSSLLSLLLFAGMQMYSRQLASTEWLTIQG-GLL-GSGLFVFSLTAFNNLENLVFGKGFQAKIFPE
T..AL.S..SL.LFAGM..YS.QLAS..WLTI.G.G.L.GS.L.VFSLTAF.NL.N.VFGKGFQAKIFPE
RetrocopyTVMALFSPQSLMLFAGMHIYSLQLASPKWLTIKG<GRLLGSSLLVFSLTAFSNLMNVVFGKGFQAKIFPE
ParentalILLCLLLALFASGLIHRVCVTTCFIFSMVGLYYINKISSTLYQAATPVLTPAKVT-GKGKKRN
ILLCLLLALFASGLIH.VCV.TCF.F.MVGL.YINKISS.LYQ...P.LTPAK.T.GK.KKR.
RetrocopyILLCLLLALFASGLIHQVCVRTCFTFFMVGLNYINKISS-LYQVTVPFLTPAKIT>GKSKKRS

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 71 .02 RPM
SRP017611_brain 0 .00 RPM 16 .04 RPM
SRP017611_kidney 0 .00 RPM 69 .47 RPM
SRP017611_liver 0 .00 RPM 22 .48 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_1487 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_1487 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_1487 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 16 parental genes, and 20 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000113361 retrocopy
retro_amel_1789,
Canis familiaris ENSCAFG00000017055 1 retrocopy
retro_cfam_1487 ,
Callithrix jacchus ENSCJAG000000090171 retrocopy
retro_cjac_1289,
Felis catus ENSFCAG000000250853 retrocopies
retro_fcat_1496, retro_fcat_477, retro_fcat_576,
Homo sapiens ENSG000001634631 retrocopy
retro_hsap_2100,
Gorilla gorilla ENSGGOG000000093031 retrocopy
retro_ggor_1635,
Macaca mulatta ENSMMUG000000121802 retrocopies
retro_mmul_745, retro_mmul_987,
Mustela putorius furoENSMPUG000000056471 retrocopy
retro_mputfur_1653,
Nomascus leucogenys ENSNLEG000000118641 retrocopy
retro_nleu_1306,
Oryctolagus cuniculus ENSOCUG000000003471 retrocopy
retro_ocun_157,
Otolemur garnettii ENSOGAG000000302711 retrocopy
retro_ogar_1306,
Pongo abelii ENSPPYG000000007561 retrocopy
retro_pabe_1999,
Pan troglodytes ENSPTRG000000014101 retrocopy
retro_ptro_1541,
Rattus norvegicus ENSRNOG000000205421 retrocopy
retro_rnor_2128,
Ictidomys tridecemlineatus ENSSTOG000000088291 retrocopy
retro_itri_1127,
Tarsius syrichta ENSTSYG000000132282 retrocopies
retro_tsyr_1096, retro_tsyr_531,


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