RetrogeneDB ID:

retro_cfam_1663

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:4:59830416..59831161(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:DNAJC8
Ensembl ID:ENSCAFG00000011885
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cfam_1663
GGAAAGAGTGGTGCTCTGTCTGGCCAAGGGAGCGTGAAGGAAGCATGTATGACCTTCTACAATGAAGTGAAACAAATAGA
GAAGAGAGATTCAGTTCTAACATCCAAAAATCAGATCAAAAGGCTGACCTGTCTTGGCTCCTCCTACTTCACTTTGAACC
CATTTGAGGATCTTCAGATAGATCCTGAAGCGACAGATGAAGGAATAAAAAAGAAGTTTTGATAGTTACCCATATTGGTG
TATCCTGACAAAAATCAAGATGATGCTGACAACACAAAAGGCTTTGGAGGCTGTGAACAAAGCTTATAAGTTGCTACTGG
ATCAGGAGCAAAAGAGAGGGCAGGATATCATTCACGCAGGAAAATATTACACAGGACACACTGTGAGAGTGTGAGAAAAG
CAATTAAGGGGGAAGGAAAATCCTACTAATGTCGGGGAGGATGATCCTAAGCTGTTTAAACAAGCAGTATATACAAACAG
ACCACAAAACTCTTTGCTGATCTGGAAATTAAAAGGAAAGAGAGAGAAGCCAAAGAGATGCATGAAAGGAAACAACAAAG
GGAAGAAGAGATAGAAGCTGGAAAAAAAAGACAAATGAGAAAGAGAGTGGTGGAAAACCTTTGAGGAAAGTTGAGATGGT
CATGTGGACAGCTGGTGCACCTTTAGGCATATCCAAAGGGTGCAGATAGAGAAGAATAACTGGACATTCCTGAGACCATC
AAAAGTAAAAATGGAGTAGCATGAA

ORF - retro_cfam_1663 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 61.96 %
Parental protein coverage: 98.42 %
Number of stop codons detected: 6
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalGESGASAGGGSTEEAFMTFYSEVKQIEKRDSVLTSKNQIERLTRPGSSYFNLNPFEVLQIDPEVTDEEIK
G.SGA..G.GS..EA.MTFY.EVKQIEKRDSVLTSKNQI.RLT..GSSYF.LNPFE.LQIDPE.TDE.IK
RetrocopyGKSGALSGQGSVKEACMTFYNEVKQIEKRDSVLTSKNQIKRLTCLGSSYFTLNPFEDLQIDPEATDEGIK
ParentalKRFRQLSILVHPDKNQDDADRAQKAF-EAVDKAYKLLLDQEQKKRALDVIQAGKEYVEHTVKERKKQLKK
K.F..L.ILV.PDKNQDDAD...K.F.EAV.KAYKLLLDQEQ.KR..D.I.AGK.Y..HTV....KQL..
RetrocopyKKF**LPILVYPDKNQDDADNT-KGF>EAVNKAYKLLLDQEQ-KRGQDIIHAGKYYTGHTVRV*EKQLRG
ParentalEGKPTNVEEDDPELFKQAVY---KQTMKLFAELEIKR-KEREAKEMHERKRQREEEIEAQEKA-KREREW
...PTNV.EDDP.LFKQAVY....Q...L...L..KR..E..........R...EEIEA.....K.EREW
RetrocopyKENPTNVGEDDPKLFKQAVYTNRPQNSLLIWKLKGKR<REAKEMHERKQQRE--EEIEAXXXX>K*EREW
ParentalQKNFEESRDGRVDSWRNFQANTKGKKEKKNRTFLRPPKVKMEQRE
.K.FEES.DG.VDSW..F........EK.N.TFLRP.KVKME..E
RetrocopyWKTFEES*DGHVDSWCTFRHIQRVQIEKNNWTFLRPSKVKME*HE

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 56 .07 RPM
SRP017611_brain 0 .00 RPM 37 .63 RPM
SRP017611_kidney 0 .13 RPM 47 .48 RPM
SRP017611_liver 0 .07 RPM 12 .04 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_1663 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_1663 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_1663 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 23 parental genes, and 49 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000112311 retrocopy
retro_amel_703,
Bos taurus ENSBTAG000000183852 retrocopies
retro_btau_1332, retro_btau_794,
Canis familiaris ENSCAFG00000011885 2 retrocopies
retro_cfam_1506, retro_cfam_1663 ,
Choloepus hoffmanni ENSCHOG000000096491 retrocopy
retro_chof_1545,
Dasypus novemcinctus ENSDNOG000000154522 retrocopies
retro_dnov_133, retro_dnov_914,
Erinaceus europaeus ENSEEUG000000111362 retrocopies
retro_eeur_536, retro_eeur_638,
Echinops telfairi ENSETEG000000083484 retrocopies
retro_etel_374, retro_etel_502, retro_etel_745, retro_etel_846,
Felis catus ENSFCAG000000133931 retrocopy
retro_fcat_203,
Homo sapiens ENSG000001266983 retrocopies
retro_hsap_1319, retro_hsap_2840, retro_hsap_4119,
Gorilla gorilla ENSGGOG000000008212 retrocopies
retro_ggor_1030, retro_ggor_2766,
Microcebus murinus ENSMICG000000012225 retrocopies
retro_mmur_1152, retro_mmur_1355, retro_mmur_343, retro_mmur_601, retro_mmur_935,
Macaca mulatta ENSMMUG000000170804 retrocopies
retro_mmul_2004, retro_mmul_2078, retro_mmul_2168, retro_mmul_228,
Mustela putorius furoENSMPUG000000155401 retrocopy
retro_mputfur_202,
Mus musculus ENSMUSG000000544051 retrocopy
retro_mmus_916,
Nomascus leucogenys ENSNLEG000000097623 retrocopies
retro_nleu_1401, retro_nleu_1594, retro_nleu_2701,
Otolemur garnettii ENSOGAG000000155974 retrocopies
retro_ogar_2422, retro_ogar_2595, retro_ogar_3219, retro_ogar_84,
Pongo abelii ENSPPYG000000258332 retrocopies
retro_pabe_2351, retro_pabe_3382,
Pelodiscus sinensis ENSPSIG000000177211 retrocopy
retro_psin_34,
Pteropus vampyrus ENSPVAG000000176191 retrocopy
retro_pvam_1057,
Rattus norvegicus ENSRNOG000000132551 retrocopy
retro_rnor_488,
Ictidomys tridecemlineatus ENSSTOG000000128342 retrocopies
retro_itri_1361, retro_itri_1775,
Tarsius syrichta ENSTSYG000000070573 retrocopies
retro_tsyr_137, retro_tsyr_1389, retro_tsyr_885,
Tursiops truncatus ENSTTRG000000000471 retrocopy
retro_ttru_1430,


Copyright © RetrogeneDB 2014-2017