RetrogeneDB ID:

retro_ecab_678

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:27:3332056..3332603(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL17
Ensembl ID:ENSECAG00000011547
Aliases:None
Description:ribosomal protein L17 [Source:HGNC Symbol;Acc:10307]


Retrocopy-Parental alignment summary:






>retro_ecab_678
AAAATGGGTCATTGCTCACTTAACCTGGAAACCCCCATAAAATCATGCAAATCAAGAGGTTCAAATCTTCGTGTTCACTT
CAAGGATACCTGTGAAACTGCCCAGGCCATGTAGGACATGCGTATCTGAAAAGCCTACTAGTCTCTGAGAGATGCCACTT
TACAGAAGCCACGTGTGCCATTAGGTGGTTACAATGGTGCCACTGTAGATGTGCCCAGACCCAACAGTGGGGTTGGACAC
AGGGTCAGGGACCCAAAAAGAGTGCTGAATTTTTGTTGCATATACTTAGACACGCAGACAGTAATGCTGACCTTCAGGAT
TTAGATGTCAGTTCTCTGGTCAAAGAGCTCACCCAGGCGAGCAAAGCCTCCAGAATGCACCTGTAGACTTGCAGAGCTCT
TGGACCGTATATAACCTCTGAGTGAGTTCCTCCAGCCGCATTGAGATCACCTTTCCTGAAACAGAATAAATTGTTCCCAA
ACCCGAAGACGAGGTTGCACAGCAGAAAAAGATATCCCAGAAGCAACAAAAGCTTATGGCTTGGGAA

ORF - retro_ecab_678 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 60.64 %
Parental protein coverage: 100. %
Number of stop codons detected: 6
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalKMVRYSLDPENPTKSCKSRGSNLRVHFKNTRETAQAIKGMHIRKATKYLKDVTLKKQCVPFRRYNGGVG-
KM...SL..E.P.KSCKSRGSNLRVHFK.T.ETAQA...M.I.KA...L.D.TL.K..VP...YNG....
RetrocopyKMGHCSLNLETPIKSCKSRGSNLRVHFKDTCETAQAM*DMRI*KAY*SLRDATLQKPRVPLGGYNGATV<
ParentalRCAQAKQWGWTQGRWPKKSAEFLLHMLKNAESNAELKGLDVDSLVIEHIQVNKAPKMRRRTYRAHG-RIN
RCAQ..QWGWTQG..PKKSAEFLLH.L..A.SNA.L..LDV.SLV.E..Q..KA..M...T.RA.G.RI.
RetrocopyRCAQTQQWGWTQGQGPKKSAEFLLHILRHADSNADLQDLDVSSLVKELTQASKASRMHL*TCRALG>RI*
ParentalPY-MSSPCHIEMILTEKEQIVPKPEEEVAQKKKISQKKLKKQKLMARE
P...SS...IE....E.E.IVPKPE.EVAQ.KKISQK....QKLMA.E
RetrocopyPL>VSSSSRIEITFPETE*IVPKPEDEVAQQKKISQK---QQKLMAWE

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 837 .99 RPM
SRP021940_cerebellum 0 .00 RPM 238 .68 RPM
SRP021940_embryo 0 .10 RPM 569 .09 RPM
SRP021940_placental_villous 0 .00 RPM 338 .75 RPM
SRP021940_synovial_membrane 0 .03 RPM 487 .80 RPM
SRP021940_testis 0 .00 RPM 215 .62 RPM
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_678 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_678 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_678 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2680
Pongo abelii retro_pabe_3253

Parental genes homology:
Parental genes homology involve 13 parental genes, and 288 retrocopies.

Species Parental gene accession Retrocopies number
Cavia porcellus ENSCPOG0000001933731 retrocopies
Equus caballus ENSECAG00000011547 9 retrocopies
Echinops telfairi ENSETEG0000001132210 retrocopies
Homo sapiens ENSG000002154721 retrocopy
Latimeria chalumnae ENSLACG000000088351 retrocopy
Macropus eugenii ENSMEUG0000001670926 retrocopies
Myotis lucifugus ENSMLUG0000002555422 retrocopies
Myotis lucifugus ENSMLUG0000002926436 retrocopies
Macaca mulatta ENSMMUG0000001883726 retrocopies
Mus musculus ENSMUSG0000006232880 retrocopies
Oryctolagus cuniculus ENSOCUG000000124852 retrocopies
Pongo abelii ENSPPYG0000000915143 retrocopies
Vicugna pacos ENSVPAG000000095681 retrocopy



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