RetrogeneDB ID:

retro_cfam_648

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:15:8714816..8715828(+)
Located in intron of:ENSCAFG00000030004
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:KPNA2
Ensembl ID:ENSCAFG00000011598
Aliases:None
Description:Importin subunit alpha [Source:UniProtKB/TrEMBL;Acc:E2R6L9]


Retrocopy-Parental alignment summary:






>retro_cfam_648
AAAAGAAATGTAAGTTCATTTCTTGATAATGCTACTTCTCCACTGCAGGAAAACTATAACAACCAGGCATTGTAAATTGG
TCTGTTGATAACATTGTCAAAGACAATAAATAGCAACAATTTGGAAAGCCACCTGCAGGCTACTCAAGATGCTAAGAAAC
TGCTTTCTGGGGAAACGCAGCCCATATAGACATAATCTGGGCTGGTTTGATTCTAAAATTTGCATCCTTTTGGGGCAGAA
CTGTTCATAGTCCCATTCAATTGAATCTGCTTGAGCCCTCACTGACATTGCTTCTGGGATATCAGACAGACCACGGCTGT
GGTAGATAGAGGTGCTATCCTAGCATTCATTTCTCCATTGACATCTTCCCTTGCTCACATAAGTGAACAAGCTGTATGAG
CTCTAGGAAACATTGTACGAAATAGTTCAGTTTTCTGAGACTTGGTTATCAAATATGTTGCATTTGACCCACTCTTGGCC
CTTCTTGCAGTTCCTGATATGTCATCTTTAGCATGTGGTTACTTAGAAAAGCTTATCTGGATACTTTCAAATTTTTGTTG
CAGCAAGGATCCTGCACTTCTCTAGATGCTATTGAGCAAATTCTTCCTACTTTAGTTCATCTCCTGCATTGTAGTGACCC
AGAAGTATTAGCAGATACTAATGTTAGAACCATTTCTTACCGTACTCATGGTCCAAATGAACAGATTGAAACGGTTGTGA
AAAGAGGAGTTGTGCCCTAACATGTGAAGCTTCGAGGAGCTCCTAAATTGCTAATTGTGACCTCTGCACTAAAAGCCATA
GGAAGTATTATCACTGGGACAGATGAACAGACTTGTGTTGTAATAGGTGTTGGAGCACTTGCCATCTTTCCCAGCTTGTA
ATGCGTCCCCAAACTAATACTCAGAAGAAAGCAATGTGGACGGTGTGAAAGATGACATCTGGCTTCTAGGACCAGACACA
GTAAGTTGTGAATCAAGGATTAATTCCATTTCTCATTGGCATTCTAAGGAAG

ORF - retro_cfam_648 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.74 %
Parental protein coverage: 64.08 %
Number of stop codons detected: 7
Number of frameshifts detected: 7


Retrocopy - Parental Gene Alignment:

ParentalRRNVSSFPDDATSPLQENRNNQ-GTVNWSVDDIVKG-INSNNLESQLQATQAARKLLSREKQPPI-DNII
.RNVSSF.D.ATSPLQEN.NNQ.G.VNWSVD.IVK..INSNNLES.LQATQ.A.KLLS.E.Q.PI...II
RetrocopyKRNVSSFLDNATSPLQENYNNQ<GIVNWSVDNIVKD>INSNNLESHLQATQDAKKLLSGETQ-PI<IDII
ParentalRAGLIPKFVSFLGRTDCSPIQF-ESAWALTNIASGTSE-QTKAVVDGGAIPAFISLLASSHAHISEQAVW
.AGLI.KF.SF.GRT..SPIQ..ESA.ALT.IASG.S..QT.AVVD.GAI.AFIS.L.SS.AHISEQAV.
RetrocopyWAGLILKFASFWGRTVHSPIQL<ESA*ALTDIASGISD<QTTAVVDRGAILAFISPLTSSLAHISEQAV*
ParentalALGNIAGDGSVFRDLVIKYGAVDPLLALLAVPDMSSLACGYLRNLTWTLSNLCRNKNPA-PPLDAVEQIL
ALGNI....SVF.DLVIKY.A.DPLLALLAVPDMSSLACGYL..L.W.LSN.C..K.PA...LDA.EQIL
RetrocopyALGNIVRNSSVF*DLVIKYVAFDPLLALLAVPDMSSLACGYLEKLIWILSNFCCSKDPA<TSLDAIEQIL
ParentalPTLVRLLHHDDPEVLADT-CWAISYLTDGPNERIEMVVKTGVVPQLVKLLGATELPIVTPALRAIGNIVT
PTLV.LLH..DPEVLADT....ISY.T.GPNE.IE.VVK.GVVP..VKL.GA..L.IVT.AL.AIG.I.T
RetrocopyPTLVHLLHCSDPEVLADTNVRTISYRTHGPNEQIETVVKRGVVP*HVKLRGAPKLLIVTSALKAIGSIIT
ParentalGTDEQTQVVIDAGALAVFPS-LLTNPKTNIQKEATWTMSNITAGRQDQIQQVVNHGLVPFLVGVLSK
GTDEQT.VVI..GALA.FPS.L...P.TN.QK.A.WT....T.G..DQ.Q.VVN.GL.PFL.G.L.K
RetrocopyGTDEQTCVVIGVGALAIFPS<LVMRPQTNTQKKAMWTV*KMTSGF*DQTQ*VVNQGLIPFLIGILRK

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 .34 RPM 25 .07 RPM
SRP017611_brain 0 .16 RPM 8 .97 RPM
SRP017611_kidney 0 .07 RPM 14 .20 RPM
SRP017611_liver 0 .58 RPM 3 .55 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_648 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_648 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_648 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 24 parental genes, and 72 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000184113 retrocopies
retro_amel_1161, retro_amel_1318, retro_amel_440,
Bos taurus ENSBTAG000000122251 retrocopy
retro_btau_1830,
Canis familiaris ENSCAFG00000011598 2 retrocopies
retro_cfam_648 , retro_cfam_90,
Canis familiaris ENSCAFG000000151252 retrocopies
retro_cfam_459, retro_cfam_861,
Cavia porcellus ENSCPOG000000263181 retrocopy
retro_cpor_46,
Dasypus novemcinctus ENSDNOG000000191516 retrocopies
retro_dnov_1184, retro_dnov_1811, retro_dnov_2161, retro_dnov_2279, retro_dnov_379, retro_dnov_693,
Equus caballus ENSECAG000000205732 retrocopies
retro_ecab_1017, retro_ecab_1123,
Echinops telfairi ENSETEG000000044452 retrocopies
retro_etel_346, retro_etel_347,
Felis catus ENSFCAG000000019362 retrocopies
retro_fcat_1176, retro_fcat_921,
Homo sapiens ENSG000001824811 retrocopy
retro_hsap_2950,
Gorilla gorilla ENSGGOG000000275352 retrocopies
retro_ggor_2044, retro_ggor_2609,
Myotis lucifugus ENSMLUG000000279467 retrocopies
retro_mluc_1034, retro_mluc_1258, retro_mluc_1414, retro_mluc_288, retro_mluc_50, retro_mluc_52, retro_mluc_993,
Macaca mulatta ENSMMUG000000182563 retrocopies
retro_mmul_1140, retro_mmul_1635, retro_mmul_1947,
Monodelphis domestica ENSMODG000000038971 retrocopy
retro_mdom_271,
Mus musculus ENSMUSG000000183621 retrocopy
retro_mmus_229,
Nomascus leucogenys ENSNLEG000000017493 retrocopies
retro_nleu_1052, retro_nleu_1634, retro_nleu_208,
Oryctolagus cuniculus ENSOCUG000000159134 retrocopies
retro_ocun_1765, retro_ocun_1916, retro_ocun_426, retro_ocun_690,
Otolemur garnettii ENSOGAG000000276727 retrocopies
retro_ogar_1044, retro_ogar_1142, retro_ogar_1757, retro_ogar_2008, retro_ogar_464, retro_ogar_477, retro_ogar_936,
Pongo abelii ENSPPYG000000085691 retrocopy
retro_pabe_3501,
Pteropus vampyrus ENSPVAG000000049762 retrocopies
retro_pvam_1321, retro_pvam_1333,
Rattus norvegicus ENSRNOG000000153291 retrocopy
retro_rnor_42,
Sarcophilus harrisii ENSSHAG000000113911 retrocopy
retro_shar_165,
Tupaia belangeri ENSTBEG0000000627414 retrocopies
retro_tbel_1635, retro_tbel_2077, retro_tbel_2672, retro_tbel_2792, retro_tbel_290, retro_tbel_3638, retro_tbel_4120, retro_tbel_4358, retro_tbel_4414, retro_tbel_4435, retro_tbel_4558, retro_tbel_810, retro_tbel_97, retro_tbel_976,
Vicugna pacos ENSVPAG000000018553 retrocopies
retro_vpac_124, retro_vpac_162, retro_vpac_163,


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