RetrogeneDB ID: retro_mmul_1311

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 17:21320606..21320930(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000009880
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.3157
• Ensembl ID: ENSMMUG00000010906
• Aliases: None
• Description: fatty acid-binding protein, adipocyte [Source:RefSeq peptide;Acc:NP_001252996]

Sequence

>retro_mmul_1311
ATGGTGGATGCCTTCCTGTGCACCTGGAAACTCTCAGACAGCAAGAATTTTGATGATTACATGAAGTTAATCGGTGTGAG
TTTTGCTACCAGGCAGGTGGCTAGCATGACAAAGCCTACCACAATCATCAAGAAGCATGGGGACATTATCACCTTAAAAA
CACAGAGCACGTTCAAGAACACAGAGGTCAGCTTTCAGCTGGGGATGGAGTTTGATGAGACAACAGCAGATGACAAACAG
GTCAAGTCCATTGTGACACTGGATGGAGGCAAACTTGTTCACTTGCAGAAGTGGGCAAGAGAGGACACTTGTGCCAGAGC
TAAG

Alignment

ORF - retro_mmul_1311 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.89 %
• Parental protein coverage: 81.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MCDAFVGTWKLVSSENFDDYMKEVGVGFATRKVAGMAKPNMIISVNGDVITIKSESTFKNTEISFKLGQE
          M.DAF..TWKL..S.NFDDYMK..GV.FATR.VA.M.KP..II...GD.IT.K..STFKNTE.SF.LG.E
Retrocopy MVDAFLCTWKLSDSKNFDDYMKLIGVSFATRQVASMTKPTTIIKKHGDIITLKTQSTFKNTEVSFQLGME

Parental  FDEVTADDRKVKSTITLDGGVLVHVQKWDGKSTTIKRK
          FDE.TADD..VKS..TLDGG.LVH.QKW....T....K
Retrocopy FDETTADDKQVKSIVTLDGGKLVHLQKWAREDTCARAK

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	0.13 RPM
SRP007412_heart	0.06 RPM	272.82 RPM
SRP007412_kidney	0.00 RPM	24.18 RPM
SRP007412_liver	0.00 RPM	2.38 RPM
SRP007412_testis	0.00 RPM	0.72 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1311 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1311 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1311 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1258
Pan troglodytes	retro_ptro_3047
Gorilla gorilla	retro_ggor_990
Pongo abelii	retro_pabe_1048

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013564	1 retrocopy	retro_acar_190,
Canis familiaris	ENSCAFG00000025410	3 retrocopies	retro_cfam_132, retro_cfam_137, retro_cfam_228,
Latimeria chalumnae	ENSLACG00000008511	3 retrocopies	retro_lcha_37, retro_lcha_45, retro_lcha_57,
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,
Oryzias latipes	ENSORLG00000008282	1 retrocopy	retro_olat_7,