RetrogeneDB ID: retro_mmul_2060

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:174735370..174736041(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000003307
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_2060
TCCGGCCTGCGGGCACTGCTGGGGCTCAGGCTGCTGGTTGCGGGCTTGCACCTGCTGCGATCAAAAGCCAGACCAGCGCC
TGCCCCTCGGGACCCAGCTGGTGGGGACCACAGCGGTGAACTCAGGTGGCCGCTGGGACTCAGCGGTCATGGAGAGCCTA
GCGGTGAAGTACCTGAGCCAGCAGGAAGCCCAGGCTGTGGACCAAGAGCTGTTTAACCAGTACCAGTTCAACGTGGACCA
ACTTACGGAGCTGGCCAGGCTGAGCTGTGCCACAGCCATCGCCAAGGCATACCCCCCACGTCCATGTTCAGGAGCCCTCT
ACTGTCCTGGTCATCTGTGGCCTGGGGAATAATGGAGGAGATGGTCTGATCTGTGCTGGACACCTCAAACTCTTTGGCTA
CCAGCCAAGTATCTATTACCCCAAAAGGCCTAACAAGCTCCTCTTCATTGCGTTGGTGACCCAGTGTCAGAAAATGGACA
TCCCTTTCCTTGGGGAAATGCGCTCAGAGCCCGTGATGATTGAGCTGTATGAGCTGGTGGTGGATGCCGCCTGTGGCTTC
AGCTTCAAGGGTGACGTTCGGGAACCGTTCCACGGCATCCTGAGTGTCCTGAAGGGACTTACTGCGTCCATTGCCAGCAT
CAACATTCCCTCAGGATGGGATGTGGAGAAG

Alignment

ORF - retro_mmul_2060 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.87 %
• Parental protein coverage: 91.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SGVRTLLGLGLLVAGSRLLR-IKSETIACRSGPTWWGPQR-LNSGGRWDSEVMASTAVKYLSQEEAQAVD
          SG.R.LLGL.LLVAG..LLR.IKS.T.AC.SGP.WWGPQR..NSGGRWDS.VM.S.AVKYLSQ.EAQAVD
Retrocopy SGLRALLGLRLLVAGLHLLR<IKSQTSACPSGPSWWGPQR<VNSGGRWDSAVMESLAVKYLSQQEAQAVD

Parental  QELFNEYQFSVDQLMELAGLSCATAIAKAYPP-TSMSRSP-PTVLVICGPGNNGGDGLVCARHLKLFGYE
          QELFN.YQF.VDQL.ELA.LSCATAIAKAYPP.TSM.RSP..TVLVICG.GNNGGDGL.CA.HLKLFGY.
Retrocopy QELFNQYQFNVDQLTELARLSCATAIAKAYPP<TSMFRSP<STVLVICGLGNNGGDGLICAGHLKLFGYQ

Parental  PTIYYPKRPNKPLFTALVTQCQKMDIPFLGEMPSEPTMIDELYELVVDAIFGFSFKGDVREPFHSILSVL
          P.IYYPKRPNK.LF.ALVTQCQKMDIPFLGEM.SEP.MI.ELYELVVDA..GFSFKGDVREPFH.ILSVL
Retrocopy PSIYYPKRPNKLLFIALVTQCQKMDIPFLGEMRSEPVMI-ELYELVVDAACGFSFKGDVREPFHGILSVL

Parental  KGLTVPIASIDIPSGAGTQK
          KGLT..IASI.IPSG....K
Retrocopy KGLTASIASINIPSGWDVEK

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	0.56 RPM	35.74 RPM
SRP007412_brain_prefrontal_cortex	1.35 RPM	48.95 RPM
SRP007412_cerebellum	0.65 RPM	30.48 RPM
SRP007412_heart	0.47 RPM	44.40 RPM
SRP007412_kidney	0.23 RPM	58.68 RPM
SRP007412_liver	0.32 RPM	61.12 RPM
SRP007412_testis	0.08 RPM	13.46 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2060 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2060 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2060 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3275
Pan troglodytes	retro_ptro_2215
Gorilla gorilla	retro_ggor_2228
Pongo abelii	retro_pabe_2709

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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,