RetrogeneDB ID: retro_mmul_1796

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:136481881..136482211(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: MMU.1921
• Ensembl ID: ENSMMUG00000009936
• Aliases: None
• Description: protein cornichon homolog 4 [Source:RefSeq peptide;Acc:NP_001247595]

Sequence

>retro_mmul_1796
GAGGACATGGTCTTTGCCTTCTTTCTCCTCAGTTGCAGGCTCATTTTTCTCTCAGTCTTCATAATTACATTGTCTGATTT
AGAGTGTGATTACATTAATGTTAGATCATGTTGCTCAAAATTAAACAAGTAGGTAATTCCAAGATTGATTGGCCATACTA
TTGTCACTGTATTAATGCTCATTTTGTTACACTGGTTCATCTTCCTTCTCAACTTACCTATTGCCACTTGGAATATATAT
TGATTCATTATGATGCCAGGCAGTAACATAGGAGTGTTTGATCCAACAGAAATACACAATCAAGGACAGCAAAAGTAACA
CATGAAAGAC

Alignment

ORF - retro_mmul_1796 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.46 %
• Parental protein coverage: 80.58 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EAVVFVFSLLDCCALIFLSVYFIITLSDLECDYINARSCCSKLNKWVIPELIGHTIVTVLMLISLHWFIF
          E..VF.F.LL.C..LIFLSV.FIITLSDLECDYIN.RSCCSKLNK.VIP.LIGHTIVTVLMLI.LHWFIF
Retrocopy EDMVFAFFLLSC-RLIFLSV-FIITLSDLECDYINVRSCCSKLNK*VIPRLIGHTIVTVLMLILLHWFIF

Parental  LLNLPVATWNIYRYIMVPSGNMGVFDPTEIHNRGQLKSHMKE
          LLNLP.ATWNIY..IM.P..N.GVFDPTEIHN.GQ.K.HMK.
Retrocopy LLNLPIATWNIY*FIMMPGSNIGVFDPTEIHNQGQQK*HMKD

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	7.17 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	5.24 RPM
SRP007412_cerebellum	0.00 RPM	7.75 RPM
SRP007412_heart	0.00 RPM	8.48 RPM
SRP007412_kidney	0.00 RPM	8.10 RPM
SRP007412_liver	0.04 RPM	8.31 RPM
SRP007412_testis	0.11 RPM	8.74 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1796 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1796 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1796 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3656
Pan troglodytes	retro_ptro_2481
Pongo abelii	retro_pabe_3003

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006544	1 retrocopy	retro_chof_327,
Callithrix jacchus	ENSCJAG00000008013	1 retrocopy	retro_cjac_2474,
Cavia porcellus	ENSCPOG00000007310	1 retrocopy	retro_cpor_777,
Dasypus novemcinctus	ENSDNOG00000007093	1 retrocopy	retro_dnov_1669,
Homo sapiens	ENSG00000143771	1 retrocopy	retro_hsap_3656,
Gorilla gorilla	ENSGGOG00000005708	1 retrocopy	retro_ggor_2470,
Myotis lucifugus	ENSMLUG00000003134	1 retrocopy	retro_mluc_1314,
Macaca mulatta	ENSMMUG00000009936	1 retrocopy	retro_mmul_1796 ,
Nomascus leucogenys	ENSNLEG00000013549	1 retrocopy	retro_nleu_514,
Ochotona princeps	ENSOPRG00000001589	1 retrocopy	retro_opri_749,
Pongo abelii	ENSPPYG00000000183	1 retrocopy	retro_pabe_3003,
Pan troglodytes	ENSPTRG00000002025	1 retrocopy	retro_ptro_2481,
Pteropus vampyrus	ENSPVAG00000014034	1 retrocopy	retro_pvam_692,
Ictidomys tridecemlineatus	ENSSTOG00000027396	2 retrocopies	retro_itri_1502, retro_itri_1552,
Vicugna pacos	ENSVPAG00000012521	2 retrocopies	retro_vpac_180, retro_vpac_215,