RetrogeneDB ID:

retro_cfam_1443

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:31:7313094..7314042(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PRPS1
Ensembl ID:ENSCAFG00000017976
Aliases:None
Description:phosphoribosyl pyrophosphate synthetase 1 [Source:HGNC Symbol;Acc:9462]


Retrocopy-Parental alignment summary:






>retro_cfam_1443
ATGCCGAATATGAAGATCTTCAGCGGCAGCTCCCACCAGGACTTATCCCAGAAAATTGCTGACCGCCTGGGCCTGGAGCT
AGGCAAGGTGGTGACCAAGAAATTCAGCAATCAAGAGACCTGCGTGGAGATTGGAGAGGGCGTACGTGGAGAGGATGTCT
ACATTGTTCAGAGTGGTTGTGGCGAAATCAGTGACAATCTAATGGAGCTTTTGATCATGATTAATGCCTGCAAGATTGCC
TCGGCCAGCCGGGTTACCGCGGTCATCCCATGCTTCCCGTATGCCCGGCAGGATAAGAAGGAGAAGAGCCCGGCTCCCAT
CTCGGCCAAGCTTGTGGCAGATATGCTCAGGGTGGAAGGCGCGGATCGTATTATCACCGTGGACCTGCAGGCTTCTCAGA
TCCAGGGCTTTTTTGATGTCCCAGTGGACAATTTGTATGCAGCGCCAGCCGTCCTGCAGTGGATACGGGAGAGCGTCTCC
GAGTGGAGGGACTGTACTATTGTCTCACCCGACGCTGGAGGAGCTAAGACAGTGGCCTCCATCGCCGACCGGCTGAACGT
GCACTTTGCTCCGGTTCACAGAGGACGGAAGAAGGCCGACGAAGTAGACCGCGTGGTGCTGGTGGGAGACGTGAAGGATC
GAGTGGCCATCCTGGTGGATGACATGGCCGATACCTGTGGCACGATCTGCCTCGCGGCCGACAAACTCCTCTCAGCTGGA
GACTCCAGGGTGTATGCTGTCTTGACTCATGGAATCCTCTCTGGCCCGGCCATCTCTCGCATTAACAGCGCATGCTTTGA
AGCAGTCGTGGTCACCAATACCATACCTCAGGAGGATAAGACGAAGCATTGCTCCAAAATACAGGTGATCGACATCTCCG
CGATCCTGGCAGAAGCCATCAGGAGAACTCACAACGGGGAATCAGTTTCCTGCCTGTTCAGCCACGTC

ORF - retro_cfam_1443 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.92 %
Parental protein coverage: 99.37 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMPNIKIFSGSSHQDLSQKIADRLGLELGKVVTKKFSNQETCVEIGESVRGEDVYIVQSGCGEINDNLMEL
MPN.KIFSGSSHQDLSQKIADRLGLELGKVVTKKFSNQETCVEIGE.VRGEDVYIVQSGCGEI.DNLMEL
RetrocopyMPNMKIFSGSSHQDLSQKIADRLGLELGKVVTKKFSNQETCVEIGEGVRGEDVYIVQSGCGEISDNLMEL
ParentalLIMINACKIASASRVTAVIPCFPYARQDKKDKSRAPISAKLVANMLSVAGADHIITMDLHASQIQGFFDI
LIMINACKIASASRVTAVIPCFPYARQDKK.KS.APISAKLVA.ML.V.GAD.IIT.DL.ASQIQGFFD.
RetrocopyLIMINACKIASASRVTAVIPCFPYARQDKKEKSPAPISAKLVADMLRVEGADRIITVDLQASQIQGFFDV
ParentalPVDNLYAEPAVLKWIRENISEWRNCTIVSPDAGGAKRVTSIADRLNVDFALIHKERKKANEVDRMVLVGD
PVDNLYA.PAVL.WIRE..SEWR.CTIVSPDAGGAK.V.SIADRLNV.FA..H..RKKA.EVDR.VLVGD
RetrocopyPVDNLYAAPAVLQWIRESVSEWRDCTIVSPDAGGAKTVASIADRLNVHFAPVHRGRKKADEVDRVVLVGD
ParentalVKDRVAILVDDMADTCGTICHAADKLLSAGATRVYAILTHGIFSGPAISRINNACFEAVVVTNTIPQEDK
VKDRVAILVDDMADTCGTIC.AADKLLSAG..RVYA.LTHGI.SGPAISRIN.ACFEAVVVTNTIPQEDK
RetrocopyVKDRVAILVDDMADTCGTICLAADKLLSAGDSRVYAVLTHGILSGPAISRINSACFEAVVVTNTIPQEDK
ParentalMKHCSKIQVIDISMILAEAIRRTHNGESVSYLFSHV
.KHCSKIQVIDIS.ILAEAIRRTHNGESVS.LFSHV
RetrocopyTKHCSKIQVIDISAILAEAIRRTHNGESVSCLFSHV

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 35 .19 RPM
SRP017611_brain 0 .00 RPM 24 .45 RPM
SRP017611_kidney 0 .07 RPM 30 .91 RPM
SRP017611_liver 0 .00 RPM 3 .41 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_1443 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_1443 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_1443 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 25 parental genes, and 48 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000027841 retrocopy
retro_amel_22,
Bos taurus ENSBTAG000000197033 retrocopies
retro_btau_157, retro_btau_1686, retro_btau_914,
Canis familiaris ENSCAFG000000116622 retrocopies
retro_cfam_1037, retro_cfam_1433,
Canis familiaris ENSCAFG00000017976 1 retrocopy
retro_cfam_1443 ,
Equus caballus ENSECAG000000247112 retrocopies
retro_ecab_433, retro_ecab_73,
Felis catus ENSFCAG000000122861 retrocopy
retro_fcat_394,
Homo sapiens ENSG000001472241 retrocopy
retro_hsap_10,
Gorilla gorilla ENSGGOG000000124181 retrocopy
retro_ggor_2583,
Macropus eugenii ENSMEUG000000100712 retrocopies
retro_meug_1612, retro_meug_443,
Microcebus murinus ENSMICG000000019295 retrocopies
retro_mmur_1223, retro_mmur_1422, retro_mmur_514, retro_mmur_810, retro_mmur_90,
Myotis lucifugus ENSMLUG000000154982 retrocopies
retro_mluc_107, retro_mluc_356,
Macaca mulatta ENSMMUG000000046743 retrocopies
retro_mmul_1204, retro_mmul_1619, retro_mmul_305,
Mustela putorius furoENSMPUG000000037932 retrocopies
retro_mputfur_183, retro_mputfur_430,
Mus musculus ENSMUSG000000314322 retrocopies
retro_mmus_19, retro_mmus_33,
Nomascus leucogenys ENSNLEG000000139112 retrocopies
retro_nleu_1456, retro_nleu_217,
Oryctolagus cuniculus ENSOCUG000000123913 retrocopies
retro_ocun_430, retro_ocun_867, retro_ocun_912,
Ochotona princeps ENSOPRG000000131401 retrocopy
retro_opri_704,
Pongo abelii ENSPPYG000000206122 retrocopies
retro_pabe_3061, retro_pabe_46,
Pan troglodytes ENSPTRG000000221632 retrocopies
retro_ptro_2600, retro_ptro_2612,
Rattus norvegicus ENSRNOG000000251662 retrocopies
retro_rnor_249, retro_rnor_341,
Sus scrofa ENSSSCG000000125601 retrocopy
retro_sscr_1068,
Ictidomys tridecemlineatus ENSSTOG000000076382 retrocopies
retro_itri_11, retro_itri_173,
Tarsius syrichta ENSTSYG000000135562 retrocopies
retro_tsyr_1063, retro_tsyr_1567,
Tursiops truncatus ENSTTRG000000038352 retrocopies
retro_ttru_307, retro_ttru_485,
Vicugna pacos ENSVPAG000000002551 retrocopy
retro_vpac_274,


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