RetrogeneDB ID: retro_mmul_995

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 13:81618415..81618659(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2139
• Ensembl ID: ENSMMUG00000015255
• Aliases: None
• Description: 6-pyruvoyl tetrahydrobiopterin synthase [Source:RefSeq peptide;Acc:NP_001253543]

Sequence

>retro_mmul_995
AAGATTGATCCTGTTACAGGAATGGTTTCAAATCTGACCAACCTCATGGCATACATTGGGGAAGCAATTGTGAAACCCCT
TGATTCTCCGAATCTGGACATACTGTACTGTGCCAATGGTTTGTGTGTGACAGAAAATGCAGCTGTTACTACTGGGAAAG
ACTGGGGAAATTTCTTCCTGTGGAGTTCTTTATAAAGCAAAAGTGCATGAAACTGTCAGTAATATTGTAGTCTATAAAGG
CAAA

Alignment

ORF - retro_mmul_995 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.14 %
• Parental protein coverage: 57.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EIDPATGMVMNLADLKKYMEEAIMQPLDHKNLDMDVPYFADVVSTTENVAV-YIWDNLQKVLPV-GVLYK
          .IDP.TGMV.NL..L..Y..EAI..PLD..NLD....Y.A.....TEN.AV.Y.W..L.K.LPV.GVLYK
Retrocopy KIDPVTGMVSNLTNLMAYIGEAIVKPLDSPNLD--ILYCANGLCVTENAAV<YYWERLGKFLPV<GVLYK

Parental  VKVYETDNNIVVYKGE
          .KV.ET..NIVVYKG.
Retrocopy AKVHETVSNIVVYKGK

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	5.83 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	4.52 RPM
SRP007412_cerebellum	0.00 RPM	4.91 RPM
SRP007412_heart	0.00 RPM	2.94 RPM
SRP007412_kidney	0.00 RPM	3.99 RPM
SRP007412_liver	0.00 RPM	25.65 RPM
SRP007412_testis	0.00 RPM	2.98 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_995 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_995 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_995 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003968	3 retrocopies	retro_amel_1001, retro_amel_1480, retro_amel_691,
Bos taurus	ENSBTAG00000003770	3 retrocopies	retro_btau_1182, retro_btau_1762, retro_btau_682,
Canis familiaris	ENSCAFG00000013915	2 retrocopies	retro_cfam_1386, retro_cfam_1859,
Choloepus hoffmanni	ENSCHOG00000000013	2 retrocopies	retro_chof_1925, retro_chof_2556,
Callithrix jacchus	ENSCJAG00000012437	2 retrocopies	retro_cjac_2534, retro_cjac_2853,
Dasypus novemcinctus	ENSDNOG00000014823	1 retrocopy	retro_dnov_1747,
Echinops telfairi	ENSETEG00000008145	2 retrocopies	retro_etel_1924, retro_etel_2039,
Felis catus	ENSFCAG00000024702	3 retrocopies	retro_fcat_1546, retro_fcat_212, retro_fcat_564,
Homo sapiens	ENSG00000150787	1 retrocopy	retro_hsap_3408,
Myotis lucifugus	ENSMLUG00000023388	1 retrocopy	retro_mluc_946,
Macaca mulatta	ENSMMUG00000015255	1 retrocopy	retro_mmul_995 ,
Nomascus leucogenys	ENSNLEG00000007299	1 retrocopy	retro_nleu_1856,
Otolemur garnettii	ENSOGAG00000017191	3 retrocopies	retro_ogar_1718, retro_ogar_2790, retro_ogar_609,
Pongo abelii	ENSPPYG00000003880	1 retrocopy	retro_pabe_432,
Pan troglodytes	ENSPTRG00000004288	3 retrocopies	retro_ptro_2315, retro_ptro_2979, retro_ptro_337,
Sorex araneus	ENSSARG00000001975	2 retrocopies	retro_sara_163, retro_sara_72,
Sus scrofa	ENSSSCG00000015040	1 retrocopy	retro_sscr_284,
Ictidomys tridecemlineatus	ENSSTOG00000013277	1 retrocopy	retro_itri_1096,
Tursiops truncatus	ENSTTRG00000010526	1 retrocopy	retro_ttru_1710,
Vicugna pacos	ENSVPAG00000000061	1 retrocopy	retro_vpac_363,