RetrogeneDB ID:

retro_mmul_474

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:1:29086742..29087191(-)
Located in intron of:ENSMMUG00000022426
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MMU.17950
Ensembl ID:ENSMMUG00000018837
Aliases:None
Description:60S ribosomal protein L17 [Source:RefSeq peptide;Acc:NP_001180491]


Retrocopy-Parental alignment summary:






>retro_mmul_474
CAGGCCATCAAGGGTATGCATATACGAAAAGCCACGAAGTATCTGAAAGATGTCACTTTACAAAAACAGTGCGTACCAGT
CCAACGTTACAATGGTGGAGTTGGCAGGTGTGCCCAGGCCAAGCAGTGGGGCTGCACACAAGGTCGGTGGCCCAAAAAGA
GTGCTGAATTTTTGTTGCACATGCTTAAAAATGCAGAGAGTAATGCTGAACTTAAGGGTTTAGATGTAGATTCTCTGGTC
ACTGAGCACATCCAAGTGAACAAAGCACCTAAGATGCGCCGCTGGACCTACAGAGCTCATGGTTGGATTAACCCATACAT
GAGCTCTCCTTGCCACATTGAGATGATCCTTACTGAAAAGGAACAGATTGTTCCTAAACCAGAAGAGGTTGCCCAGAAGA
AAAAGATATCCCAGAAGAAACTGAAGAAACAAAACTTATGGCAGGGGAG

ORF - retro_mmul_474 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.08 %
Parental protein coverage: 82.07 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalQAIKGMHIRKATKYLKDVTLQKQCVPFRRYNGGVGRCAQAKQWGWTQGRWPKKSAEFLLHMLKNAESNAE
QAIKGMHIRKATKYLKDVTLQKQCVP..RYNGGVGRCAQAKQWG.TQGRWPKKSAEFLLHMLKNAESNAE
RetrocopyQAIKGMHIRKATKYLKDVTLQKQCVPVQRYNGGVGRCAQAKQWGCTQGRWPKKSAEFLLHMLKNAESNAE
ParentalLKGLDVDSLVIEHIQVNKAPKMRRRTYRAHGRINPYMSSPCHIEMILTEKEQIVPKPEEEVAQKKKISQK
LKGLDVDSLV.EHIQVNKAPKMRR.TYRAHG.INPYMSSPCHIEMILTEKEQIVPKP.EEVAQKKKISQK
RetrocopyLKGLDVDSLVTEHIQVNKAPKMRRWTYRAHGWINPYMSSPCHIEMILTEKEQIVPKP-EEVAQKKKISQK
ParentalKLKKQ-KLMARE
KLKKQ.KLMA.E
RetrocopyKLKKQ<KLMAGE

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
SRP007412_brain 0 .11 RPM 105 .22 RPM
SRP007412_brain_prefrontal_cortex 0 .00 RPM 147 .16 RPM
SRP007412_cerebellum 0 .19 RPM 110 .75 RPM
SRP007412_heart 0 .06 RPM 135 .38 RPM
SRP007412_kidney 0 .12 RPM 159 .50 RPM
SRP007412_liver 0 .08 RPM 114 .12 RPM
SRP007412_testis 0 .19 RPM 101 .55 RPM
Macaca mulatta was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mmul_474 retrocopy.
Macaca mulatta was not studied using FANTOM5 data.
retro_mmul_474 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_474 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_356
Pan troglodytes retro_ptro_280
Pongo abelii retro_pabe_347

Parental genes homology:
Parental genes homology involve 25 parental genes, and 552 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000000949840 retrocopies
Bos taurus ENSBTAG000000229025 retrocopies
Canis familiaris ENSCAFG000000190447 retrocopies
Callithrix jacchus ENSCJAG000000047794 retrocopies
Cavia porcellus ENSCPOG0000001933731 retrocopies
Equus caballus ENSECAG000000115479 retrocopies
Felis catus ENSFCAG0000001134243 retrocopies
Homo sapiens ENSG000002154721 retrocopy
Homo sapiens ENSG0000026568133 retrocopies
Gorilla gorilla ENSGGOG000000266971 retrocopy
Latimeria chalumnae ENSLACG000000088351 retrocopy
Loxodonta africana ENSLAFG0000000556916 retrocopies
Myotis lucifugus ENSMLUG0000002555422 retrocopies
Myotis lucifugus ENSMLUG0000002926436 retrocopies
Macaca mulatta ENSMMUG00000018837 26 retrocopies
Monodelphis domestica ENSMODG0000000353411 retrocopies
Mustela putorius furoENSMPUG000000008017 retrocopies
Mus musculus ENSMUSG0000006232880 retrocopies
Oryctolagus cuniculus ENSOCUG000000124852 retrocopies
Pan troglodytes ENSPTRG0000001001251 retrocopies
Rattus norvegicus ENSRNOG0000001868048 retrocopies
Sarcophilus harrisii ENSSHAG0000000306014 retrocopies
Sus scrofa ENSSSCG0000002964230 retrocopies
Ictidomys tridecemlineatus ENSSTOG0000000519333 retrocopies
Vicugna pacos ENSVPAG000000095681 retrocopy



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