RetrogeneDB ID:

retro_ecab_245

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:10:65356208..65356622(-)
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:ENSECAG00000000002
Aliases:None
Description:ribulose-5-phosphate-3-epimerase [Source:HGNC Symbol;Acc:10293]


Retrocopy-Parental alignment summary:






>retro_ecab_245
CATTTTGTCTCCAGCGTCACCTTTGGCCACCCTGTGGTAGAAAGTGTCCAGCTAGGCTTTGACATGCACGTGATAGCATC
CAGGCTGGAACAGTGGGTAAAACCAAAGGCTGTAGCAGGAACCCATCAATATAGTTTAATCTCGAGGTTACTGAGAAACC
AGGGGCTTTGACCAAAGACATAGTGAGAACGAGATGAAATTGACCTTGCCATCAAACCAGGAACTACAGGTGAGCATTTG
GCACCATGGGCTAATCAGATAAAGATAGCCTTGGTTATGACAGTGGGACCTGGGTTTGGAAGGCAGAAATTCATGAACGA
TGTGATGCCAAAGGTTCACTGGTTGAGGATCCAGTTCCCATCTTTGGACTTAGAGGTTGACTGTGAAGTGGGTCCTGACA
CCGCCCATAAATGT

ORF - retro_ecab_245 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.62 %
Parental protein coverage: 77.54 %
Number of stop codons detected: 0
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalHFVPNITFGHPVVESLRKQLGQDPFFDMHMMVSRPEQWVKPMAVAGANQYT-FHLEATENPGALIKDI-R
HFV...TFGHPVVES...QLG....FDMH...SR.EQWVKP.AVAG..QY..F.LE.TE.PGAL.KDI..
RetrocopyHFVSSVTFGHPVVESV--QLG----FDMHVIASRLEQWVKPKAVAGTHQYS<FNLEVTEKPGALTKDI<S
ParentalENGMK-VGLAIKPGTTVEYLAPWANQIDMALVMTVEPGFGGQKFMEDMMPKVHWLRTQFPSLDIEVDGGV
EN.MK...LAIKPGTT.E.LAPWANQI..ALVMTV.PGFG.QKFM.D.MPKVHWLR.QFPSLD.EVD..V
RetrocopyENEMK<IDLAIKPGTTGEHLAPWANQIKIALVMTVGPGFGRQKFMNDVMPKVHWLRIQFPSLDLEVDCEV
ParentalGPDTIHKC
GPDT.HKC
RetrocopyGPDTAHKC

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
SRP021940_articular_cartilage 0 .00 RPM 5 .90 RPM
SRP021940_cerebellum 0 .00 RPM 24 .41 RPM
SRP021940_embryo 0 .00 RPM 20 .56 RPM
SRP021940_placental_villous 0 .05 RPM 11 .35 RPM
SRP021940_synovial_membrane 0 .00 RPM 14 .08 RPM
SRP021940_testis 0 .06 RPM 17 .01 RPM
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_245 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_245 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_245 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 ENSCAFG000000138113 retrocopies
Choloepus hoffmanni ENSCHOG000000011105 retrocopies
Callithrix jacchus ENSCJAG000000108222 retrocopies
Dasypus novemcinctus ENSDNOG000000031931 retrocopy
Equus caballus ENSECAG00000000002 3 retrocopies
retro_ecab_245 , retro_ecab_446, retro_ecab_562,
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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