RetrogeneDB ID: retro_mmul_458

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:213475435..213475701(+)
• Located in intron of: ENSMMUG00000019995

Retrocopy information

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

Parental gene information

• Parental gene symbol: FABP7
• Ensembl ID: ENSMMUG00000021907
• Aliases: None
• Description: fatty acid-binding protein, brain [Source:RefSeq peptide;Acc:NP_001244643]

Sequence

>retro_mmul_458
TCAAGAAGGAGACAAAAGGTGGTGATCAGGATTCGAAGTATGTTCAAGAACACAGAAGTTAGTTTCCATCTGGGAGAAGA
GTTTGATAAAACCACTACAGATGACAGAAACTGCAAGTTTGTTGTTAGTCTGGATAGAGACAAACTCATTCACATACAGA
AATGGGATGACAAAGAAACATATTTTATAAGAGAAGTTAAGTATGGTGAAATGGTTATGACTTAACTTTTGGTGATGATG
TGGTTGCCGTTCACTATAAGAAGGCA

Alignment

ORF - retro_mmul_458 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.11 %
• Parental protein coverage: 67.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SQEGDKVVIRTLSTFKNTEISFHLGEEFDETTADDRNCKSVVSLDGDKLVHVQKWDGKETNFVREIKDGK
          S....KVVIR..S.FKNTE.SFHLGEEFD.TT.DDRNCK.VVSLD.DKL.H.QKWD.KET.F.RE.K.G.
Retrocopy SRRRQKVVIRIRSMFKNTEVSFHLGEEFDKTTTDDRNCKFVVSLDRDKLIHIQKWDDKETYFIREVKYGE

Parental  MVMT-LTFGDVVAVRHYEKA
          MVMT.LTFGD.V...HY.KA
Retrocopy MVMT<LTFGDDVVAVHYKKA

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	0.11 RPM	31.71 RPM
SRP007412_brain_prefrontal_cortex	0.24 RPM	27.29 RPM
SRP007412_cerebellum	0.06 RPM	113.91 RPM
SRP007412_heart	0.18 RPM	0.24 RPM
SRP007412_kidney	0.00 RPM	0.12 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.08 RPM	0.04 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_458 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_458 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_458 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_536
Pan troglodytes	retro_ptro_402
Gorilla gorilla	retro_ggor_489
Pongo abelii	retro_pabe_213

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000014056	1 retrocopy	retro_cpor_34,
Homo sapiens	ENSG00000164434	1 retrocopy	retro_hsap_536,
Gorilla gorilla	ENSGGOG00000025475	1 retrocopy	retro_ggor_489,
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 ,
Oryctolagus cuniculus	ENSOCUG00000001497	1 retrocopy	retro_ocun_1874,
Otolemur garnettii	ENSOGAG00000031110	1 retrocopy	retro_ogar_2821,
Ochotona princeps	ENSOPRG00000000992	1 retrocopy	retro_opri_840,
Pongo abelii	ENSPPYG00000016979	1 retrocopy	retro_pabe_213,
Pan troglodytes	ENSPTRG00000018564	1 retrocopy	retro_ptro_402,
Sarcophilus harrisii	ENSSHAG00000003313	1 retrocopy	retro_shar_521,