RetrogeneDB ID: retro_mmul_2299

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 8:87200357..87200729(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.1104
• Ensembl ID: ENSMMUG00000003432
• Aliases: None
• Description: None

Sequence

>retro_mmul_2299
GATTACCTCTGTGCTGATCAGTGGAAAATCAAAAAGGATGAGAAGGATGACAAACACTTTTGAGCTCTGAATGAAGAGGA
TACTGCCTTGCTGAAAAATCATGGTCAGAGCACTTACTCTAGGAAGATTAAGCAGGTTGAGAATGACATTCAACAACTCC
TTAAGAAAATTATCTCAGTAGTATTAAAGAGTCTGACACTAGCCTGGCCACCACCAGCACTCTGGGATTTGGCTGCAAAT
AAGCAAATGCTCCAGGGTGAACAATGTTTACAGGTTGCAAGGTGTAGAAAGACAGTAAATGCTGATTCTGAGAACTCAAA
ATACATTGTCAGTGTGTAGCAGATTGCTAAGTTTGTGGTGGACCTCAGGGAT

Alignment

ORF - retro_mmul_2299 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.2 %
• Parental protein coverage: 63.45 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DYLGADQRKTKEDEKDDKPIRALDEGDIALLKTYGQSTYSRQIKQVEDDIQQLLKKINELTGIKESDTGL
          DYL.ADQ.K.K.DEKDDK...AL.E.D.ALLK..GQSTYSR.IKQVE.DIQQLLKKI......K......
Retrocopy DYLCADQWKIKKDEKDDKHF*ALNEEDTALLKNHGQSTYSRKIKQVENDIQQLLKKIISVV-LKSLTLAW

Parental  APPALWDLAADKQTLQSEQPLQVARCTKIINADSEDPKYIINVKQFAKFVVDLSD
          .PPALWDLAA.KQ.LQ.EQ.LQVARC.K..NADSE..KYI..V.Q.AKFVVDL.D
Retrocopy PPPALWDLAANKQMLQGEQCLQVARCRKTVNADSENSKYIVSV*QIAKFVVDLRD

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	29.58 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	20.63 RPM
SRP007412_cerebellum	0.00 RPM	30.29 RPM
SRP007412_heart	0.00 RPM	23.26 RPM
SRP007412_kidney	0.00 RPM	27.46 RPM
SRP007412_liver	0.00 RPM	25.97 RPM
SRP007412_testis	0.00 RPM	38.75 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2299 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2299 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2299 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000005729	1 retrocopy	retro_etel_1316,
Homo sapiens	ENSG00000161057	2 retrocopies	retro_hsap_2705, retro_hsap_3980,
Gorilla gorilla	ENSGGOG00000009167	3 retrocopies	retro_ggor_1885, retro_ggor_2672, retro_ggor_2673,
Myotis lucifugus	ENSMLUG00000008853	1 retrocopy	retro_mluc_1642,
Macaca mulatta	ENSMMUG00000003432	2 retrocopies	retro_mmul_1538, retro_mmul_2299 ,
Monodelphis domestica	ENSMODG00000017238	1 retrocopy	retro_mdom_868,
Mustela putorius furo	ENSMPUG00000018268	3 retrocopies	retro_mputfur_1025, retro_mputfur_232, retro_mputfur_387,
Nomascus leucogenys	ENSNLEG00000009274	2 retrocopies	retro_nleu_1578, retro_nleu_2042,
Otolemur garnettii	ENSOGAG00000005164	2 retrocopies	retro_ogar_2198, retro_ogar_2309,
Pongo abelii	ENSPPYG00000017883	2 retrocopies	retro_pabe_2257, retro_pabe_2412,
Pan troglodytes	ENSPTRG00000019553	2 retrocopies	retro_ptro_1826, retro_ptro_2702,
Tarsius syrichta	ENSTSYG00000000666	4 retrocopies	retro_tsyr_1031, retro_tsyr_1272, retro_tsyr_1857, retro_tsyr_2178,
Vicugna pacos	ENSVPAG00000008921	1 retrocopy	retro_vpac_44,