RetrogeneDB ID: retro_mmul_2001

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:38039256..38039743(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2663
• Ensembl ID: ENSMMUG00000021366
• Aliases: None
• Description: peroxiredoxin-4 precursor [Source:RefSeq peptide;Acc:NP_001180740]

Sequence

>retro_mmul_2001
AAATATTCAGATTACTGAGGAGGAGCAGCTGTGATCAATGGAGAACTTAAAGTGCTCAATTTAAATGGGTACTGTGGAAA
ATACCTATTTTTTTCCTTGATTTTACATTTGTGTGTCTAACTAAAATAATCAATTTTAGTGACAAAATTGAGATCTTAGA
CCAATAAACACTGAAGTGATACCATGCCCTGTCGATTCACAGTTTACCCATTTAATATGAAGTCCCACCCCTCTAACAAA
GAGGACTGGAGCCCTGGGAAAATTTCATTTCTTTCGGATTTTACCCATCAGATCTCAAAGTCCTATGGTGATGTATCTGG
AGAACTCAGGCCACAGTCTTAGAGGTTTCTTCACTATTGATGAAAAAGGAATCCAAAGGCAGCTTAGAATGGATGACCCT
CCTGTTAGCAGAGTAGTGAATAAAATACTGTACTGGGGTCAAGTGTCCCCATACACTGACCAGTATGGAAAAGTCTGTCC
TGCTGGA

Alignment

ORF - retro_mmul_2001 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.29 %
• Parental protein coverage: 61.25 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KPAPYWEGTAVIDGEFKELKLTDYRGKYL-VFFFYPLDFTFVCPTEIIAFGDRLE-EFRSINTEVVACSV
          K...Y..G.AVI.GE.K.L.L..Y.GKYL..FF...LDFTFVC.T.II.F.D..E...R.INTEV..C.V
Retrocopy KYSDY*GGAAVINGELKVLNLNGYCGKYL<IFF---LDFTFVCLTKIINFSDKIE<DLRPINTEVIPCPV

Parental  DSQFTHLAWINTP-RRQGGLGPIRIPLLSDLTHQISKDYG-VYLEDSGHTLRGLFIIDDKGILRQITLND
          DSQFTHL....TP........P..I..LSD.THQISK.YG..YLE.SGH.LRG.F.ID.KGI.RQ....D
Retrocopy DSQFTHLI*SPTP<SNKEDWSPGKISFLSDFTHQISKSYG>MYLENSGHSLRGFFTIDEKGIQRQLRMDD

Parental  LPVGRSVDETLRLVQAFQYTDKHGEVCPAG
          .PV.R.V...L...Q...YTD..G.VCPAG
Retrocopy PPVSRVVNKILYWGQVSPYTDQYGKVCPAG

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	3.47 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	4.05 RPM
SRP007412_cerebellum	0.00 RPM	7.04 RPM
SRP007412_heart	0.00 RPM	13.43 RPM
SRP007412_kidney	0.00 RPM	10.33 RPM
SRP007412_liver	0.00 RPM	19.24 RPM
SRP007412_testis	0.00 RPM	54.62 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2001 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2001 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2001 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3165
Gorilla gorilla	retro_ggor_1351
Equus caballus	retro_ecab_576

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006165	1 retrocopy	retro_btau_439,
Cavia porcellus	ENSCPOG00000004185	1 retrocopy	retro_cpor_353,
Equus caballus	ENSECAG00000010085	1 retrocopy	retro_ecab_576,
Homo sapiens	ENSG00000123131	1 retrocopy	retro_hsap_3165,
Gorilla gorilla	ENSGGOG00000026790	1 retrocopy	retro_ggor_1351,
Myotis lucifugus	ENSMLUG00000004904	2 retrocopies	retro_mluc_2347, retro_mluc_2619,
Macaca mulatta	ENSMMUG00000005689	2 retrocopies	retro_mmul_1780, retro_mmul_2061,
Macaca mulatta	ENSMMUG00000006221	1 retrocopy	retro_mmul_762,
Macaca mulatta	ENSMMUG00000008294	2 retrocopies	retro_mmul_1307, retro_mmul_1517,
Macaca mulatta	ENSMMUG00000021366	1 retrocopy	retro_mmul_2001 ,
Tupaia belangeri	ENSTBEG00000004454	5 retrocopies	retro_tbel_2164, retro_tbel_2467, retro_tbel_2522, retro_tbel_2811, retro_tbel_2978,
Tarsius syrichta	ENSTSYG00000000602	1 retrocopy	retro_tsyr_404,
Tursiops truncatus	ENSTTRG00000012368	1 retrocopy	retro_ttru_547,