RetrogeneDB ID: retro_mmul_2011

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:69154378..69155003(+)
• Located in intron of: ENSMMUG00000015422

Retrocopy information

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

Parental gene information

• Parental gene symbol: DULLARD
• Ensembl ID: ENSMMUG00000010547
• Aliases: None
• Description: None

Sequence

>retro_mmul_2011
ATGATGCGGACGTGGTGTCTGCTGGGGCTGCACACTTTCATGGCCTTCGCCAACAAGCTCTGGAGCTTCTCCACCCTTTT
GTGGTGGCAGATCTGCACGGTAATTCAGCAGCAAAGTGTTCGATATGATATCCTCCCCTTATCTTCTTGTCCCGGAATCG
GTTAGGTGAAGAGGAATATCCTCGTGCTGGATCCGGATGAGACGCTTATTCACTCCCACCATGCTGGGGTCCTGAGGCTC
ACAGTGCGGCGTGGAACGCCTCCTGACTTCATCCTCAAGGTGGTAATAGACAAACATCCTGTGCGTTTTTTTGTACATTA
AAGGCCCCATGTGGATTTCTTCTTGGAAGTGGTGAGCCAGCGGTGGGAGCTGGTGGTCTTTATAGCAAGCATGGAGATCT
ATGGCTCTGTTGTGGCAGATTAACTGGACAATTAGCAGAAGTATTCTTAAGAGGAGATACTACAGACAGCACTGCACTTT
GGAGTTGGGCAGCTACATCAAGCACCTCTCTGTGGTCCACAGTGACCTCTCCAGCACTGTGATCCTGGATAACTCCCCAG
CGGCTTACAGGAGCCATCCAGATAAGGCCATCACCATCATATCCTGGTTCAGTGACCCCAGTGAC

Alignment

ORF - retro_mmul_2011 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.08 %
• Parental protein coverage: 89.79 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MMRTQCLLGLRTFVAFAAKLWSFFIYLLRRQIRTVIQYQTVRYDILPLSPVSRNRLAQVKRKILVLDLDE
          MMRT.CLLGL.TF.AFA.KLWSF...LL..QI.TVIQ.Q.VRYDILPLS..S......VKR.ILVLD.DE
Retrocopy MMRTWCLLGLHTFMAFANKLWSFST-LLWWQICTVIQQQSVRYDILPLS--SCPGIG*VKRNILVLDPDE

Parental  TLIHSHHDGVLRPTVRPGTPPDFILKVVIDKHPVRFFVHKRPHVDFFLEVVSQWYELVVFTASMEIYGSA
          TLIHSHH.GVLR.TVR.GTPPDFILKVVIDKHPVRFFVH.RPHVDFFLEVVSQ..ELVVF.ASMEIYGS.
Retrocopy TLIHSHHAGVLRLTVRRGTPPDFILKVVIDKHPVRFFVH*RPHVDFFLEVVSQRWELVVFIASMEIYGSV

Parental  VADKLDN-SRSILKRRYYRQHCTLELGSYIKDLSVVHSDLSSIVILDNSPGAYRSHPDNAIPIKSWFSDP
          VAD.LDN.SRSILKRRYYRQHCTLELGSYIK.LSVVHSDLSS.VILDNSP.AYRSHPD.AI.I.SWFSDP
Retrocopy VAD*LDN>SRSILKRRYYRQHCTLELGSYIKHLSVVHSDLSSTVILDNSPAAYRSHPDKAITIISWFSDP

Parental  SD
          SD
Retrocopy SD

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	29.02 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	42.60 RPM
SRP007412_cerebellum	0.13 RPM	25.31 RPM
SRP007412_heart	0.00 RPM	27.68 RPM
SRP007412_kidney	0.00 RPM	28.29 RPM
SRP007412_liver	0.04 RPM	17.38 RPM
SRP007412_testis	0.08 RPM	29.82 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2011 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2011 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2011 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3188
Pan troglodytes	retro_ptro_2256
Pongo abelii	retro_pabe_2645

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019443	1 retrocopy	retro_btau_915,
Dasypus novemcinctus	ENSDNOG00000013673	2 retrocopies	retro_dnov_1802, retro_dnov_2494,
Echinops telfairi	ENSETEG00000004654	1 retrocopy	retro_etel_125,
Homo sapiens	ENSG00000175826	2 retrocopies	retro_hsap_2687, retro_hsap_3188,
Gorilla gorilla	ENSGGOG00000013777	2 retrocopies	retro_ggor_1338, retro_ggor_1874,
Macaca mulatta	ENSMMUG00000010547	1 retrocopy	retro_mmul_2011 ,
Mus musculus	ENSMUSG00000018559	1 retrocopy	retro_mmus_1023,
Otolemur garnettii	ENSOGAG00000004389	1 retrocopy	retro_ogar_1001,
Pongo abelii	ENSPPYG00000007902	2 retrocopies	retro_pabe_2294, retro_pabe_2645,
Pan troglodytes	ENSPTRG00000008668	2 retrocopies	retro_ptro_1814, retro_ptro_2256,
Drosophila melanogaster	FBgn0029067	1 retrocopy	retro_dmel_18,