RetrogeneDB ID: retro_mmul_1787

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:113988572..113988916(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.19245
• Ensembl ID: ENSMMUG00000019337
• Aliases: None
• Description: fatty acid-binding protein 12 [Source:RefSeq peptide;Acc:NP_001181831]

Sequence

>retro_mmul_1787
TTCACAGATTTTGTTACTGAAGGAACAGGGAGAGCCAGCAGGAAACTGGGCTGCCTGGCAAAACCCACGGTGACCATCAG
TAGAAAGGGAGATGTGATCACTATAAAAATGAAAAGCATCTTTAAAAATAATGAGATTGCTTTTAAACCTAGAAATGAAT
GTGAGGAAACCACATCAGGTGGCCATAAAATCAAGAGTACTGTAACCTTAGATAATGACTCCCTGGCTGAGGTTCAGGAC
TGGGATCACAAGGAGACCTCATTGGGAGAAAGATGGTGGGTGAGAAGATGGGGGTGGAAAGTGGTGAGCAATATTACCTG
TGCTCAGAAACAGGGGATAGAATG

Alignment

ORF - retro_mmul_1787 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.54 %
• Parental protein coverage: 87.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FEEYLKELGIGRASRKLGCLAKPTVTISTDGDVITIKTKSIFKNSEISFKLGEEFEEITPGGHKTKSKVT
          F.....E.G.GRASRKLGCLAKPTVTIS..GDVITIK.KSIFKN.EI.FK...E.EE.T.GGHK.KS.VT
Retrocopy FTDFVTE-GTGRASRKLGCLAKPTVTISRKGDVITIKMKSIFKNNEIAFKPRNECEETTSGGHKIKSTVT

Parental  LDKESLIQVQNWDGKETT-ITRKLVDGKMVVESAVNGVICTRTYEKV
          LD..SL..VQ.WD.KET..I.RK.V..KM.VES......C..T....
Retrocopy LDNDSLAEVQDWDHKETS<IGRKMVGEKMGVESGEQYYLCSETGDRM

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	0.00 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	58.09 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1787 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1787 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1787 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3679
Pan troglodytes	retro_ptro_2493
Gorilla gorilla	retro_ggor_2488
Pongo abelii	retro_pabe_3016
Callithrix jacchus	retro_cjac_2486
Equus caballus	retro_ecab_761

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014554	1 retrocopy	retro_amel_945,
Callithrix jacchus	ENSCJAG00000000433	1 retrocopy	retro_cjac_2486,
Equus caballus	ENSECAG00000023552	1 retrocopy	retro_ecab_761,
Homo sapiens	ENSG00000197416	1 retrocopy	retro_hsap_3679,
Gorilla gorilla	ENSGGOG00000016835	1 retrocopy	retro_ggor_2488,
Latimeria chalumnae	ENSLACG00000008511	3 retrocopies	retro_lcha_37, retro_lcha_45, retro_lcha_57,
Microcebus murinus	ENSMICG00000005319	1 retrocopy	retro_mmur_1131,
Macaca mulatta	ENSMMUG00000000486	4 retrocopies	retro_mmul_1417, retro_mmul_1920, retro_mmul_2095, retro_mmul_2230,
Macaca mulatta	ENSMMUG00000002295	1 retrocopy	retro_mmul_1110,
Macaca mulatta	ENSMMUG00000010906	1 retrocopy	retro_mmul_1311,
Macaca mulatta	ENSMMUG00000019337	1 retrocopy	retro_mmul_1787 ,
Macaca mulatta	ENSMMUG00000021907	1 retrocopy	retro_mmul_458,
Nomascus leucogenys	ENSNLEG00000002515	1 retrocopy	retro_nleu_528,
Oryzias latipes	ENSORLG00000008282	1 retrocopy	retro_olat_7,
Pongo abelii	ENSPPYG00000018703	1 retrocopy	retro_pabe_3016,
Pan troglodytes	ENSPTRG00000022654	1 retrocopy	retro_ptro_2493,