RetrogeneDB ID:

retro_ecab_1085

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:X:80712714..80713314(+)
Located in intron of:ENSECAG00000020186
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:AMMECR1L
Ensembl ID:ENSECAG00000023095
Aliases:None
Description:AMMECR1-like [Source:HGNC Symbol;Acc:28658]


Retrocopy-Parental alignment summary:






>retro_ecab_1085
ATGGGAAAAAGACATCGTGTTTCTCCACTCAAGCCCAAGTTGGCAGAATGCTGTTGTGGGGTCAAGAAGCTTAAATTACC
TGGAAATGGAACACACAGTCACAGGAACCAGTCCACAACTGTCCCCGGCTCTAGTTCAGGACATTTTCAAAACCACAAGC
ACGTGGGTGGCAGCAGTGGTCAGGAGAATGTGTTGGACTTAACTCTGGGATCCAGAAATTCTCCCTATTATACAAATGAA
TCCCTCATCAGGAGCACTGAGCCCTCTCCTCGGGCCCAATGGAACTACCAACAACACCAAAAATTTGGTGGTGACTGCAG
AGATGTGCTGCTACTGCTTTGACATCTTCTATTGTCACCTTTATGGCTTCCCACAGTCACAACTTCCTAGATTCACCAGT
GATCCCTATCTGCCTTTGGTGACATGGAAGACAGGGTAAGACAAGAAGTTTTCTGGCTATACTAGGACCTTCTCAGCCAT
AAATCTTTATTCAGGACTCAGGGAATATATGTTAACCAGTGCACTTAAGGACAGTTGATCTCCCCCTTGACCTGAGAGGA
GCTGCCTAAACTTTTCTGCTCTATCTCCTTACTAACTTCG

ORF - retro_ecab_1085 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.75 %
Parental protein coverage: 64.52 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMGKRRCVPPLEPKLAAGCCGVKKPKLSGSGTHSHGNQSTTVPGSSSGPLQNHQHVDGSSGRENVSDLTLG
MGKR..V.PL.PKLA..CCGVKK.KL.G.GTHSH.NQSTTVPGSSSG..QNH.HV.GSSG.ENV.DLTLG
RetrocopyMGKRHRVSPLKPKLAECCCGVKKLKLPGNGTHSHRNQSTTVPGSSSGHFQNHKHVGGSSGQENVLDLTLG
ParentalPGNSP-ITRMNPASGALSPLPRPNGTANTAKNLVVTAEMCCYCFDVLYCHLYGFPQPRLPRFTNDPYPLF
..NSP.I..MNP.SGALSPL..PNGT.N..KNLVVTAEMCCYCFD..YCHLYGFPQ..LPRFT.DPY...
RetrocopySRNSP>IIQMNPSSGALSPLLGPNGTTNNTKNLVVTAEMCCYCFDIFYCHLYGFPQSQLPRFTSDPYLPL
ParentalVTWKTGRDKRLRGCIGTFSAMNLHSGLREYTLTSALKDSRFP-PLTREELPKLFCSVSLLTN
VTWKTG.DK...G...TFSA.NL.SGLREY.LTSALKDS..P.PLT.EELPKLFCS.SLLT.
RetrocopyVTWKTG*DKKFSGYTRTFSAINLYSGLREYMLTSALKDS*SP<PLT*EELPKLFCSISLLTS

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 9 .62 RPM
SRP021940_cerebellum 0 .00 RPM 11 .84 RPM
SRP021940_embryo 0 .00 RPM 18 .92 RPM
SRP021940_placental_villous 0 .00 RPM 22 .23 RPM
SRP021940_synovial_membrane 0 .00 RPM 18 .59 RPM
SRP021940_testis 0 .00 RPM 29 .93 RPM
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_1085 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_1085 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_1085 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 12 parental genes, and 13 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000093731 retrocopy
Callithrix jacchus ENSCJAG000000107431 retrocopy
Equus caballus ENSECAG00000023095 1 retrocopy
retro_ecab_1085 ,
Echinops telfairi ENSETEG000000005101 retrocopy
Homo sapiens ENSG000001442331 retrocopy
Gorilla gorilla ENSGGOG000000144481 retrocopy
Myotis lucifugus ENSMLUG000000068711 retrocopy
Macaca mulatta ENSMMUG000000019871 retrocopy
Mus musculus ENSMUSG000000419152 retrocopies
Nomascus leucogenys ENSNLEG000000157931 retrocopy
Pan troglodytes ENSPTRG000000124371 retrocopy
Sarcophilus harrisii ENSSHAG000000147621 retrocopy



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