RetrogeneDB ID:

retro_cfam_1441

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:31:1174962..1175620(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPE
Ensembl ID:ENSCAFG00000013811
Aliases:None
Description:ribulose-5-phosphate-3-epimerase [Source:HGNC Symbol;Acc:10293]


Retrocopy-Parental alignment summary:






>retro_cfam_1441
ATGGCATCTGGCTGCAAGATTGGCCTGTCCATCCTTAACAGCGATTTGGACAATTTAGGGGCTCAGTGCCTCCGGATCCT
GGACTCTGGGGGCCGATTACTTGCACTTGGATGTAACAGACGGGCCTTTTGTTCCCAACATCACCTTTGGACACCCTGTG
GCAGAAAGCCTCTGAAAGTAGCGAGGCCAGGACCCTTTCTTTGATAATGCACATGATGATATCCAGACCAGAACAGCAGG
TAAAACCAATGGCTGTAGCAGGAGCCAATGGATACACCTTTCATCTTGAGGCAACAAAAACCCAGGGGCTTTGATTAAAG
ACATTCGGGAGAATGGGATGAAGCTTGGCCTTGCCATCAAACCAGGAACTACAGTTGATTATTTGGCACCGTGGGCTAAT
CAGATAGATATGGCCTTGGTTATGACAGTGGAACCTGGGTTTGGAGGGCAGAAATTCATGGAAGATATGATGCTGAGGGT
TAATTGGTTGAGAATGCAATTCCCATCTTTGGGCATAGAAGTCGATGGTGGAGTAGGTCCTGACACTATCCATAAGTGTG
CAGAGGCAGGAGCTAACATGATTGTGTCTGGCAGTGCCATTATGAGGAGGGATGACCCCAGATCTGTGATCAACCTGTTA
AGAAATGTTTGCTCAGAA

ORF - retro_cfam_1441 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.29 %
Parental protein coverage: 96.05 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMASGCRIGPSILNSDLANLGAECLRMLDSG-ADYLHLDVMDGHFVPNITFGHPVVESLRKQLGQDPFFD-
MASGC.IG.SILNSDL.NLGA.CLR.LDSG.ADYLHLDV.DG.FVPNITFGHPV.ESL.K..GQDPFFD.
RetrocopyMASGCKIGLSILNSDLDNLGAQCLRILDSG>ADYLHLDVTDGPFVPNITFGHPVAESL*K*RGQDPFFD>
ParentalMHMMVSRPEQWVKPMAVAGANQYTFHLEATE-NPGALIKDIRENGMKVGLAIKPGTTVEYLAPWANQIDM
MHMM.SRPEQ.VKPMAVAGAN.YTFHLEAT..NPGALIKDIRENGMK.GLAIKPGTTV.YLAPWANQIDM
RetrocopyMHMMISRPEQQVKPMAVAGANGYTFHLEATK<NPGALIKDIRENGMKLGLAIKPGTTVDYLAPWANQIDM
ParentalALVMTVEPGFGGQKFMEDMMPKVHWLRTQFPSLDIEVDGGVGPDTIHKCAEAGANMIVSGSAIMRSDDPR
ALVMTVEPGFGGQKFMEDMM..V.WLR.QFPSL.IEVDGGVGPDTIHKCAEAGANMIVSGSAIMR.DDPR
RetrocopyALVMTVEPGFGGQKFMEDMMLRVNWLRMQFPSLGIEVDGGVGPDTIHKCAEAGANMIVSGSAIMRRDDPR
ParentalSVINLLRNVCSE
SVINLLRNVCSE
RetrocopySVINLLRNVCSE

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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 8 .57 RPM
SRP017611_brain 0 .00 RPM 7 .86 RPM
SRP017611_kidney 0 .00 RPM 12 .68 RPM
SRP017611_liver 0 .00 RPM 6 .67 RPM
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1441 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1441 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_1441 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 24 parental genes, and 61 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000049653 retrocopies
Bos taurus ENSBTAG000000478062 retrocopies
Canis familiaris ENSCAFG00000013811 3 retrocopies
retro_cfam_1441 , retro_cfam_1596, retro_cfam_1623,
Choloepus hoffmanni ENSCHOG000000011105 retrocopies
Callithrix jacchus ENSCJAG000000108222 retrocopies
Dasypus novemcinctus ENSDNOG000000031931 retrocopy
Equus caballus ENSECAG000000000023 retrocopies
Homo sapiens ENSG000001977135 retrocopies
Latimeria chalumnae ENSLACG000000028001 retrocopy
Loxodonta africana ENSLAFG000000141272 retrocopies
Microcebus murinus ENSMICG000000099534 retrocopies
Macaca mulatta ENSMMUG000000105132 retrocopies
Monodelphis domestica ENSMODG000000158276 retrocopies
Mustela putorius furoENSMPUG000000079482 retrocopies
Nomascus leucogenys ENSNLEG000000071723 retrocopies
Oryctolagus cuniculus ENSOCUG000000169951 retrocopy
Otolemur garnettii ENSOGAG000000027781 retrocopy
Pongo abelii ENSPPYG000000131324 retrocopies
Pteropus vampyrus ENSPVAG000000144522 retrocopies
Sus scrofa ENSSSCG000000161521 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000103221 retrocopy
Tarsius syrichta ENSTSYG000000033045 retrocopies
Tursiops truncatus ENSTTRG000000009081 retrocopy
Vicugna pacos ENSVPAG000000115851 retrocopy



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