RetrogeneDB ID: retro_mmul_1458

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:117067711..117068544(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.12731
• Ensembl ID: ENSMMUG00000007922
• Aliases: None
• Description: None

Sequence

>retro_mmul_1458
ATGGTGGAGAAGTTTGACTGTCTCTACTGCAGGGACCCCTTGCAGAGGAAAAAGTATGTGCACAAGGGTGACTACCACTG
CTGCCTGAAATGCTTTGACAAGTTCTGTGCCAGCATCTGCATGGAATGCTGCAAGCCCATCCGTGTGGACTCCAAGGAGG
TGCACTATAAAAACTGCTTCTGGCATGACCCCTGCTTCCACTGTGCCAAGTGCCTTCACCCCTTGGCCAATGAGACCTTT
GTGGCCAAGGACAACAAGATCCTGTGCAACAAGTTCGCCACTCAGGAGGACTCTCCCAAGTGTAAGGGATGCTTCAAGCC
CTTTGTGGCAGGAGATCAAAACTGGAGTACAAGGGGACCATCTCGCACAAAGACTGTAGCAACTGCAAGCAAGTCATGGG
GACTGGAAGCTTCTTCTCTAAAGGGAAGGACTTCTACTGTGTGACTTGCCATGAGACCAAGTTTGCTAAGTATTGCGTGA
AGTGTAACAAGGCCATCATTGCATCTGGGGGAGTCACTTACCAGGATGAGCCCTGGCATGCTGAGTGCTTTGTGTGTGTT
ACCTGCTCTAAGAAGCCGGCTGGGCAGCGTTTCACTGCTGTGGAGGACCAGTAACACTGCGTGGATTGGTACAAGAACTT
TGTGGCCAAGAAGTGTGCTGGATTCAAGCACTCCATCACTGGGTTTGGTAAAGGCTCCAGTGTGGTGGCCTATGAAGGAC
CACCCTGGCACTACTGCTGCTTCCACTGCAAAAAATGCTCCATGAATCTGGCCAACAAGCACTTTGTTTTCCACAAGGAG
CAAGTATATTGCCCTGACTGTGCCAAAGAGTTG

Alignment

ORF - retro_mmul_1458 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.56 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAEKFDCHYCRDPLQGKKYVQKDGHHCCLKCFDKFCANTCVECRKPIGADSKEVHYKNRFWHDTCFRCAK
          M.EKFDC.YCRDPLQ.KKYV.K...HCCLKCFDKFCA..C.EC.KPI..DSKEVHYKN.FWHD.CF.CAK
Retrocopy MVEKFDCLYCRDPLQRKKYVHKGDYHCCLKCFDKFCASICMECCKPIRVDSKEVHYKNCFWHDPCFHCAK

Parental  CLHPLANETFVAKDNKILCNKCTTREDSPKCKGCFKAIVAGDQN-VEYKGTVWHKDCFTCSNCKQVIGTG
          CLHPLANETFVAKDNKILCNK..T.EDSPKCKGCFK..VAGDQN..EYKGT..HKDC...SNCKQV.GTG
Retrocopy CLHPLANETFVAKDNKILCNKFATQEDSPKCKGCFKPFVAGDQN<LEYKGTISHKDC---SNCKQVMGTG

Parental  SFFPKGEDFYCVTCHETKFAKHCVKCNKA-ITSGGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYY
          SFF.KG.DFYCVTCHETKFAK.CVKCNKA.I.SGG.TYQD.PWHA.CFVCVTCSKK.AGQRFTAVEDQ..
Retrocopy SFFSKGKDFYCVTCHETKFAKYCVKCNKAIIASGGVTYQDEPWHAECFVCVTCSKKPAGQRFTAVEDQ*H

Parental  CVDCYKNFVAKKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAK
          CVD.YKNFVAKKCAG.K..ITGFGKGSSVVAYEG..WH..CFHCKKCS.NLANK.FVFH.EQVYCPDCAK
Retrocopy CVDWYKNFVAKKCAGFKHSITGFGKGSSVVAYEGPPWHYCCFHCKKCSMNLANKHFVFHKEQVYCPDCAK

Parental  KL
          .L
Retrocopy EL

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	0.34 RPM	154.63 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	141.13 RPM
SRP007412_cerebellum	0.13 RPM	173.90 RPM
SRP007412_heart	0.00 RPM	657.87 RPM
SRP007412_kidney	0.12 RPM	43.90 RPM
SRP007412_liver	0.00 RPM	10.57 RPM
SRP007412_testis	0.04 RPM	132.94 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1458 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1458 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1458 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2878
Gorilla gorilla	retro_ggor_1994
Pongo abelii	retro_pabe_2382

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000015644	2 retrocopies	retro_dord_299, retro_dord_722,
Homo sapiens	ENSG00000022267	1 retrocopy	retro_hsap_2878,
Gorilla gorilla	ENSGGOG00000010054	1 retrocopy	retro_ggor_1994,
Microcebus murinus	ENSMICG00000009342	1 retrocopy	retro_mmur_1438,
Myotis lucifugus	ENSMLUG00000014336	2 retrocopies	retro_mluc_311, retro_mluc_814,
Macaca mulatta	ENSMMUG00000003146	1 retrocopy	retro_mmul_2283,
Macaca mulatta	ENSMMUG00000004179	1 retrocopy	retro_mmul_1939,
Macaca mulatta	ENSMMUG00000007922	1 retrocopy	retro_mmul_1458 ,
Mus musculus	ENSMUSG00000023092	1 retrocopy	retro_mmus_51,
Pongo abelii	ENSPPYG00000020761	1 retrocopy	retro_pabe_2382,