RetrogeneDB ID: retro_mmul_103

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:71388268..71389858(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000030356
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMMUG00000001027
• Aliases: None
• Description: ATP synthase subunit beta [Source:UniProtKB/TrEMBL;Acc:F6SIE0]

Sequence

>retro_mmul_103
ATGTTGGGTCTTGTGGGTAGTGTGGCCACTGCTTCCGCCTCCGGGGCCTTGCGGGGACTCACTCCTTCAGCGTCGCTACC
CCCAGCTCAGCTCTTACTGCGGGCCGCTCCGACGGCGGTCCATCCTGTCAGGGACTATGCGGCGCAAACATCTCCTTCGC
CAAAAGCGGGCGCCGCCACCGGGCGCATCGTGGCGGTCATTGGCGCAGTGGTGGACGTCCAGTTTGATGAGGGACTACCA
CCAATTCTAAATGCCCTGGAAGTGCAAGGCAGGGAGACCAGACTGGTTTTGGAGGTGGCCCAGCATTTGGGTGAGAGCAC
AGTAAGGACTATTGCTATGGATGGTACGGAAGGCTTGGTTAGAGGCCAGAAAGTACTGGATTCTGGTGCACCAATCAAAA
TTCCTGTTGGTCCTGAGACTTTGGGCAGAATCATGAATGTTATTGGAGAACCTTTTGATGAAAGAGGTCCCATCAAAACC
AAACAATTTGCTGCCATTCATGCTGAGGCTCCAGAGTTCATGGAAATGAGTGTTGAGCAGGAAATTCTGGTGACTGGTAT
CAAGGTTGTGGATCTGCTAGCTCCCTATGCCAAGGGTGGCAAAATTGGGCTTTTTGGTGGTGCCGGAGTTGGCAAGACTG
TACTGATCATGGAGTTAATCAACAATGTCGCCAAAGCCCATGGTGGTTACTCTGTGTTTGCTGGTGTTGGTGAGAGGACC
CGTGAAGGCAATGATTTATACCATGAAATGATTGAATCTGGTGTTATCAACTTAAAAGATGCCACCTCTAAGGTAGCGCT
GGTATATGGTCAAATGAATGAACCACCTGGTGCTCGTGCCCGGGTAGCTCTTACTGGACTGACTGTGGCTGAATACTTCA
GAGACCAAGAAGGTCAAGATGTACTGCTATTTATTGATAATATCTTTCGCTTCACCCAGGCTGGTTCAGAGGTGTCTGCA
TTATTGGGCAGAATCCCTTCTGCCGTGGGCTATCAGCCTACCCTCACCACTGACATGGGTACTATGCAGGAAAGAATTAC
CACTACCAAGAAGGGATCTATCACCTCTGTACAGGCTATCTATGTGCCTGCTGATGACTTGACTGACCCTGCTCCTGCTA
CTACGTTTGCCCATTTGGATGCTACCACTGTACTGTCACGTGCCATTGCTGAGCTGGGCATCTATCCAGCTGTGGATCCT
CTAGACTCCACCTCTCGCATCATGGATCCCAACATTGTTGGCAGTGAGCATTACGATGTTGCCCGTGGGGTGCAAAAAAT
CCTGCAGGACTACAAATCCCTCCAGGATATCATTGCCATCCTGGGTATGGATGAACTTTCTGAGGAAGACAAGTTGACTG
TGTCCCGTGCACGGAAAATACAGCGTTTTTTGTCTCAGCCATTCCAGGTTGCTGAGGTCTTCACAGGTCATATGGGGAAG
CTGGTACCCCTGAAGGAGACCATCAAAGGATTCCAGCAGATTTTGGCAGGTGAATATGACCATCTCCCAGAACAGGCCTT
CTATATGGTGGGACCCATTGAAGAAGCTGTGGCAAAAGCTGATAAGCTGGCTGAAGAGCATGCGTCGTGA

Alignment

ORF - retro_mmul_103 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.65 %
• Parental protein coverage: 89.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLGLVGRVATASASGALRALTPSASLPPAQLLLRAAPTAVHPVRDYAAQTSPSPKAGAATGRIVAVIGAV
          MLGLVG.VATASASGALR.LTPSASLPPAQLLLRAAPTAVHPVRDYAAQTSPSPKAGAATGRIVAVIGAV
Retrocopy MLGLVGSVATASASGALRGLTPSASLPPAQLLLRAAPTAVHPVRDYAAQTSPSPKAGAATGRIVAVIGAV

Parental  VDVQFDEGLPPILNALEVQGRETRLVLEVAQHLGESTVRTIAMDGTEGLVRGQKVLDSGAPIKIPVGPET
          VDVQFDEGLPPILNALEVQGRETRLVLEVAQHLGESTVRTIAMDGTEGLVRGQKVLDSGAPIKIPVGPET
Retrocopy VDVQFDEGLPPILNALEVQGRETRLVLEVAQHLGESTVRTIAMDGTEGLVRGQKVLDSGAPIKIPVGPET

Parental  LGRIMNVIGEPIDERGPIKTKQFAAIHAEAPEFMEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGV
          LGRIMNVIGEP.DERGPIKTKQFAAIHAEAPEFMEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGV
Retrocopy LGRIMNVIGEPFDERGPIKTKQFAAIHAEAPEFMEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGV

Parental  GKTVLIMELINNVAKAHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKVALVYGQMNEPPGARA
          GKTVLIMELINNVAKAHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKVALVYGQMNEPPGARA
Retrocopy GKTVLIMELINNVAKAHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKVALVYGQMNEPPGARA

Parental  RVALTGLTVAEYFRDQEGQDVLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGTMQERITTTK
          RVALTGLTVAEYFRDQEGQDVLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTL.TDMGTMQERITTTK
Retrocopy RVALTGLTVAEYFRDQEGQDVLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTLTTDMGTMQERITTTK

Parental  KGSITSVQAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRIMDPNIVGSEHYDV
          KGSITSVQAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRIMDPNIVGSEHYDV
Retrocopy KGSITSVQAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRIMDPNIVGSEHYDV

Parental  ARGVQKILQDWIFLSDLCDLFWSKGMQYFSNSTKLGLWRTRKTLIFLGWPQVVRNV
          ARGVQKILQD...L.D........GM...S...KL...R.RK...FL..P..V..V
Retrocopy ARGVQKILQDYKSLQDIIAIL---GMDELSEEDKLTVSRARKIQRFLSQPFQVAEV

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	49.86 RPM	93.90 RPM
SRP007412_brain_prefrontal_cortex	100.91 RPM	367.54 RPM
SRP007412_cerebellum	51.21 RPM	112.68 RPM
SRP007412_heart	61.48 RPM	259.86 RPM
SRP007412_kidney	59.04 RPM	138.14 RPM
SRP007412_liver	39.23 RPM	131.14 RPM
SRP007412_testis	8.97 RPM	43.76 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

4 EST(s) were mapped to retro_mmul_103 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BQ807538	71388332	71388524	97.4	187	5	182
CN805264	71388325	71388642	99.7	315	1	314
CN806179	71388329	71388642	98.5	308	5	303
CO048871	71388332	71388642	99.7	309	1	308

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_103 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_103 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000016752	1 retrocopy	retro_acar_181,
Bos taurus	ENSBTAG00000013315	1 retrocopy	retro_btau_1264,
Choloepus hoffmanni	ENSCHOG00000005350	1 retrocopy	retro_chof_1544,
Callithrix jacchus	ENSCJAG00000033571	2 retrocopies	retro_cjac_1488, retro_cjac_928,
Dasypus novemcinctus	ENSDNOG00000011289	1 retrocopy	retro_dnov_361,
Echinops telfairi	ENSETEG00000010208	1 retrocopy	retro_etel_2162,
Homo sapiens	ENSG00000110955	1 retrocopy	retro_hsap_2128,
Gorilla gorilla	ENSGGOG00000011596	1 retrocopy	retro_ggor_1648,
Latimeria chalumnae	ENSLACG00000009340	1 retrocopy	retro_lcha_27,
Macropus eugenii	ENSMEUG00000002875	6 retrocopies	retro_meug_1416, retro_meug_1608, retro_meug_411, retro_meug_430, retro_meug_685, retro_meug_908,
Microcebus murinus	ENSMICG00000001084	1 retrocopy	retro_mmur_495,
Macaca mulatta	ENSMMUG00000001027	1 retrocopy	retro_mmul_103 ,
Pongo abelii	ENSPPYG00000004668	2 retrocopies	retro_pabe_1921, retro_pabe_2032,
Pan troglodytes	ENSPTRG00000005107	1 retrocopy	retro_ptro_1557,
Sus scrofa	ENSSSCG00000000405	1 retrocopy	retro_sscr_453,
Tarsius syrichta	ENSTSYG00000009962	1 retrocopy	retro_tsyr_644,
Tursiops truncatus	ENSTTRG00000002144	1 retrocopy	retro_ttru_371,
Vicugna pacos	ENSVPAG00000004025	2 retrocopies	retro_vpac_405, retro_vpac_562,
Xenopus tropicalis	ENSXETG00000024665	1 retrocopy	retro_xtro_68,