RetrogeneDB ID: retro_mmul_1364

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 19:17613121..17613578(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: APOA1BP
• Ensembl ID: ENSMMUG00000002623
• Aliases: None
• Description: apolipoprotein A-I binding protein [Source:HGNC Symbol;Acc:18453]

Sequence

>retro_mmul_1364
AGCATGGCCCAACTTACAGAACTGGCTGGGCTCAGCTGTTCAACGTCATTGCCAAGGCATATCCTCCCATATCCATGTCC
AGGGCCCCTGCTGCTGTCCCAATCATCTGTGGCCCAGGGAATAATGGAGAAGGGAGCCTGCTCTGTGCTTGACATCCCAA
ACATTTTGGTCACCAGCCAATCATCTTTGACCCCAAAAGACCCAACAAGCCACTCTACACTATACTGGTGACCCACCATC
AGGAAAGGGTCATTCTTTTTCCTGGTGAAGTGCCCCCAGAGCCCACACTGATCAATGAGCTGTATGGGCTGGGGGTGGAT
GCCATCTTTGGCTTCAGCTTCAAGGGCAATGTTTGAAAGCCATTCTGTAACATTCTGAGTGTCCTGAATGGACTCACTGT
GCCACTGCCAATGCTGACATTCCCTTGGGATGGGACATACAGAAGGAAAACTCCGGA

Alignment

ORF - retro_mmul_1364 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.87 %
• Parental protein coverage: 62.2 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SVDQLMELAGLSCATA-IAKAYPPTSMSRSPPTVLVICGPGNNGGDGLVCARHLKLFGYEPTIYYPKRPN
          S..QL.ELAGLSC.T..IAKAYPP.SMSR.P..V..ICGPGNNG...L.CA.H.K.FG..P.I..PKRPN
Retrocopy SMAQLTELAGLSCSTS<IAKAYPPISMSRAPAAVPIICGPGNNGEGSLLCA*HPKHFGHQPIIFDPKRPN

Parental  KPLFTALVTQCQKMDIPFLGEMPSEPTMIDELYELVVDAIFGFSFKGDVREPFHSILSVLKGLTVPI-AS
          KPL.T.LVT..Q...I.F.GE.P.EPT.I.ELY.L.VDAIFGFSFKG.V..PF..ILSVL.GLTVP..A.
Retrocopy KPLYTILVTHHQERVILFPGEVPPEPTLINELYGLGVDAIFGFSFKGNV*KPFCNILSVLNGLTVPL<AN

Parental  IDIPSGAGTQKMGQG
          .DIP.G...QK...G
Retrocopy ADIPLGWDIQKENSG

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	35.74 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	48.95 RPM
SRP007412_cerebellum	0.00 RPM	30.48 RPM
SRP007412_heart	0.12 RPM	44.40 RPM
SRP007412_kidney	0.00 RPM	58.68 RPM
SRP007412_liver	0.00 RPM	61.12 RPM
SRP007412_testis	0.00 RPM	13.46 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1364 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1364 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1364 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000163382	2 retrocopies	retro_hsap_1973, retro_hsap_3275,
Gorilla gorilla	ENSGGOG00000000754	1 retrocopy	retro_ggor_2228,
Macaca mulatta	ENSMMUG00000002623	2 retrocopies	retro_mmul_1364 , retro_mmul_2060,
Nomascus leucogenys	ENSNLEG00000012663	2 retrocopies	retro_nleu_2615, retro_nleu_2992,
Pongo abelii	ENSPPYG00000000713	2 retrocopies	retro_pabe_1692, retro_pabe_2709,
Pan troglodytes	ENSPTRG00000001463	2 retrocopies	retro_ptro_1315, retro_ptro_2215,