RetrogeneDB ID: retro_mmul_1288

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 17:49260322..49261027(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.18098
• Ensembl ID: ENSMMUG00000007373
• Aliases: None
• Description: None

Sequence

>retro_mmul_1288
ATGGCGCCCTGGACGCTCTCTGGCTACTGCCAATGCATCATGGGCTGGGTGCCGGTGCTCTTCCTCACCTTCATGGTCAT
TTGGTCCCACTACGCGTTCGTGGTGGAGCTATGCTTGTTTACTATTTTTGGAGATGAAGAAAATGGAAAGACCGTGTTTT
CCCTTGTGGCTTTCCATCTGTTCTTTGTTATGTTTGTATGGTACTAATGGATGACAATCTTCGTATCTCCCGCTTCCCCC
TCCGAAGAGTTCTACTTGTCCAATTCTGAAAAGGAACGCTATGGAAAAGAATTCAGCCAAGAAAGACGACAAGAAATTTT
GAGAAGAGCAGCAAGAGCTTTACCTATCTACACCACGTCAGTTTCAAAAACTATCAGATACTGTGAAAAATGTCAGCTGA
TTAAACCTGATCGGGGTCATCACTGCTCAGCATGTGACTCATGTATTCTTAAGATGGATCATTACTGTCTTTGGGTGAAT
AACTGTGCTGGATTTTCTAATTACAAATTATTCCTGCTGTTTTTATTGTATTCTCTATTATATTGCCTTTTCATGGCTGC
AACAGTTTTAGAGTACTTCATAAAATTTTGGAGGAATGAACTGACAGATCCACGTGCAAAATTCCACGTCCTTTTTCTTT
TCTTTGTGTCTGCAATGTTCTTCATCAGCGTCCTCTCACTTTTCAGCTACCACTGCTGGCTAGTT

Alignment

ORF - retro_mmul_1288 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.81 %
• Parental protein coverage: 64.38 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAPWTLWRCCQRVVGWVPVLFITFVVVWSYYAYVVELCVFTIFGNEENGKTVVYLVAFHLFFVMFVWSYW
          MAPWTL...CQ...GWVPVLF.TF.V.WS.YA.VVELC.FTIFG.EENGKTV..LVAFHLFFVMFVW..W
Retrocopy MAPWTLSGYCQCIMGWVPVLFLTFMVIWSHYAFVVELCLFTIFGDEENGKTVFSLVAFHLFFVMFVWY*W

Parental  MTIFTSPASPSKEFYLSNSEKERYEKEFSQERQQEILRRAARVLPIYTTSASKTIRYCEKCQLIKPDRAH
          MTIF.SPASPS.EFYLSNSEKERY.KEFSQER.QEILRRAAR.LPIYTTS.SKTIRYCEKCQLIKPDR.H
Retrocopy MTIFVSPASPSEEFYLSNSEKERYGKEFSQERRQEILRRAARALPIYTTSVSKTIRYCEKCQLIKPDRGH

Parental  HCSACDSCILKMDHHCPWVNNCVGFSNYKFFLLFLLYSLLYCLFVAATVLEYFIKFWTNELTDTRAKFHV
          HCSACDSCILKMDH.C.WVNNC.GFSNYK.FLLFLLYSLLYCLF.AATVLEYFIKFW.NELTD.RAKFHV
Retrocopy HCSACDSCILKMDHYCLWVNNCAGFSNYKLFLLFLLYSLLYCLFMAATVLEYFIKFWRNELTDPRAKFHV

Parental  LFLFFVSAMFFISVLSLFSYHCWLV
          LFLFFVSAMFFISVLSLFSYHCWLV
Retrocopy LFLFFVSAMFFISVLSLFSYHCWLV

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	15.91 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	10.31 RPM
SRP007412_cerebellum	0.00 RPM	10.14 RPM
SRP007412_heart	0.00 RPM	2.18 RPM
SRP007412_kidney	0.00 RPM	3.87 RPM
SRP007412_liver	0.00 RPM	3.84 RPM
SRP007412_testis	1.28 RPM	55.11 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1288 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1288 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1288 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1211
Pan troglodytes	retro_ptro_829
Gorilla gorilla	retro_ggor_943

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012155	2 retrocopies	retro_chof_1627, retro_chof_2008,
Cavia porcellus	ENSCPOG00000011489	1 retrocopy	retro_cpor_303,
Equus caballus	ENSECAG00000016465	1 retrocopy	retro_ecab_683,
Homo sapiens	ENSG00000180776	1 retrocopy	retro_hsap_1211,
Gorilla gorilla	ENSGGOG00000000435	2 retrocopies	retro_ggor_1003, retro_ggor_943,
Macaca mulatta	ENSMMUG00000007373	1 retrocopy	retro_mmul_1288 ,
Macaca mulatta	ENSMMUG00000020674	1 retrocopy	retro_mmul_1448,
Pongo abelii	ENSPPYG00000005201	1 retrocopy	retro_pabe_1081,
Pan troglodytes	ENSPTRG00000005695	1 retrocopy	retro_ptro_829,
Tarsius syrichta	ENSTSYG00000003013	1 retrocopy	retro_tsyr_998,