RetrogeneDB ID:

retro_mmul_2408

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:9:67502888..67503227(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MMU.18858
Ensembl ID:ENSMMUG00000015618
Aliases:C16H17orf61, C17orf61
Description:UPF0451 protein C17orf61 [Source:RefSeq peptide;Acc:NP_001181322]


Retrocopy-Parental alignment summary:






>retro_mmul_2408
ATGGCTGGGCCAGGAGCAGCTTTCCACTGGCGTGAGTTCCTCGTCCAGTGCTGGGGCCTTTGGCTTGGCTTCCTATCAGA
TACATGACACCCAATTCCCACATGCCTGTGGGAAGGAGCTCTTTGACAAGGCCAACAAGTACCACTTCTTACACAGTCTG
GCCCTGTTAGGGGTGCCCTCTTGCAGAAAGCCCCTCTGGGCTGGGTTACTGCTAGCCTCCAGAACGACCTTATTCTTTAC
GTCTTTTACTACCAGGCTTGGGGTGGAGACCCCAGCATCCAGACTTTGTTCCCTGTGGGAGGGAGTCTGCTACTCTTGGG
CTGGTTTGCTTTGGCTCTT

ORF - retro_mmul_2408 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.78 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMAGPAAAFRH-LGALSGAAALGLASYGAHGAQFPDAYGKELFEKANKHHFLHSLALLGVPHCRKPLWAGL
MAGP.AAF.......S.A.A.GLASY..H..QFP.A.GKELF.KANK.HFLHSLALLGVP.CRKPLWAGL
RetrocopyMAGPGAAFHW>VSSSSSAGAFGLASYQIHDTQFPHACGKELFDKANKYHFLHSLALLGVPSCRKPLWAGL
ParentalLLASGTTLFCTS-FYYQALSGDPSIQTLAPAGGTLLLLGWLALAL
LLAS.TTLF.TS.FYYQA..GDPSIQTL.P.GG.LLLLGW.ALAL
RetrocopyLLASRTTLFFTS<FYYQAWGGDPSIQTLFPVGGSLLLLGWFALAL

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






RNA-Seq - click to see more details

(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 .00 RPM 2 .69 RPM
SRP007412_brain_prefrontal_cortex 0 .00 RPM 3 .25 RPM
SRP007412_cerebellum 0 .06 RPM 2 .84 RPM
SRP007412_heart 0 .00 RPM 3 .95 RPM
SRP007412_kidney 0 .00 RPM 17 .96 RPM
SRP007412_liver 0 .00 RPM 13 .06 RPM
SRP007412_testis 0 .00 RPM 0 .79 RPM

ChIP-Seq - click to see more details

Macaca mulatta was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_mmul_2408 retrocopy.

TSS - click to see more details

Macaca mulatta was not studied using FANTOM5 data.

Lab - click to see more details

retro_mmul_2408 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_2408 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_687
Pan troglodytes retro_ptro_492
Gorilla gorilla retro_ggor_590
Pongo abelii retro_pabe_536
Parental genes homology:
Parental genes homology involve 22 parental genes, and 44 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000166835 retrocopies
retro_amel_1190, retro_amel_1360, retro_amel_285, retro_amel_504, retro_amel_577,
Bos taurus ENSBTAG000000317523 retrocopies
retro_btau_1301, retro_btau_1812, retro_btau_532,
Canis familiaris ENSCAFG000000232052 retrocopies
retro_cfam_1146, retro_cfam_1965,
Callithrix jacchus ENSCJAG000000377861 retrocopy
retro_cjac_3985,
Cavia porcellus ENSCPOG000000047601 retrocopy
retro_cpor_564,
Equus caballus ENSECAG000000164991 retrocopy
retro_ecab_682,
Echinops telfairi ENSETEG000000160763 retrocopies
retro_etel_1865, retro_etel_2014, retro_etel_693,
Felis catus ENSFCAG000000298993 retrocopies
retro_fcat_417, retro_fcat_666, retro_fcat_933,
Homo sapiens ENSG000002055442 retrocopies
retro_hsap_2212, retro_hsap_687,
Gorilla gorilla ENSGGOG000000001132 retrocopies
retro_ggor_1745, retro_ggor_590,
Microcebus murinus ENSMICG000000125501 retrocopy
retro_mmur_841,
Macaca mulatta ENSMMUG00000015618 2 retrocopies
retro_mmul_2408 , retro_mmul_929,
Mus musculus ENSMUSG000000703941 retrocopy
retro_mmus_430,
Nomascus leucogenys ENSNLEG000000094352 retrocopies
retro_nleu_2336, retro_nleu_776,
Otolemur garnettii ENSOGAG000000113781 retrocopy
retro_ogar_2039,
Ochotona princeps ENSOPRG000000149782 retrocopies
retro_opri_117, retro_opri_1200,
Pongo abelii ENSPPYG000000079153 retrocopies
retro_pabe_2084, retro_pabe_2179, retro_pabe_536,
Pan troglodytes ENSPTRG000000309872 retrocopies
retro_ptro_1678, retro_ptro_492,
Pteropus vampyrus ENSPVAG000000050611 retrocopy
retro_pvam_357,
Rattus norvegicus ENSRNOG000000375402 retrocopies
retro_rnor_1592, retro_rnor_2896,
Sus scrofa ENSSSCG000000257822 retrocopies
retro_sscr_160, retro_sscr_330,
Tursiops truncatus ENSTTRG000000097942 retrocopies
retro_ttru_1495, retro_ttru_720,




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