RetrogeneDB ID: retro_mmul_2586

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:63992308..63992736(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.4817
• Ensembl ID: ENSMMUG00000008295
• Aliases: None
• Description: None

Sequence

>retro_mmul_2586
AGCGGTGGTGTTGCCCCTGTCCAGGCCCTGAGTGGCCCTGAGCATGGGCAGTCCCTGGTGGCTGCCATAGCCGAGCTACC
AGTGCTGGACTCCCACGGGCAGTGGGTGCCATTTGGAGCTCTCCTCCGGGAGCGCCGCACCATGGTACTGTTTGTGCAGC
ATTTCCTGTTTTACATTTGCAAGGAATATGTAGAGGCTCTGTGAAAAATCCTGAAGAGTTTCTTACAAGAAGCAAATGTC
ATCCTTATAGTGATTGAACAGTCATCCTACCATCCTATTGAGCCTTTTTGCAAACTGCCTGGATATTCTCATGAAATCTA
TTTCATCCTGAGAGGGAAATTTATAAAAGATTGGGAATGAAAAGAGGTGAAGAAATGGCCTCATCAGGACAGAGCCCCCA
CGTAAACTCTCAGGAAGCCTTTGGAGCT

Alignment

ORF - retro_mmul_2586 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.69 %
• Parental protein coverage: 63.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SGGTAPVPAPSGPDRGQPLAAAVAELPVLDARGQRVPFGALFRERRAVVVFVRHFLCYICKEYVEDLAKI
          SGG.APV.A.SGP..GQ.L.AA.AELPVLD..GQ.VPFGAL.RERR..V.FV.HFL.YICKEYVE.L.KI
Retrocopy SGGVAPVQALSGPEHGQSLVAAIAELPVLDSHGQWVPFGALLRERRTMVLFVQHFLFYICKEYVEAL*KI

Parental  PKSFLQEANVTLIVIGQSSYHHIEPFCRLTGYSHEIY-VDPEREIYKRLGMKRGEEIASSGQSPHVKSNL
          .KSFLQEANV.LIVI.QSSYH.IEPFC.L.GYSHEIY...PEREIYKRLGMKRGEE.ASSGQSPHV.S..
Retrocopy LKSFLQEANVILIVIEQSSYHPIEPFCKLPGYSHEIY<FHPEREIYKRLGMKRGEEMASSGQSPHVNSQE

Parental  LSGS
          ..G.
Retrocopy AFGA

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	2.35 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	2.38 RPM
SRP007412_cerebellum	0.06 RPM	3.42 RPM
SRP007412_heart	0.00 RPM	6.12 RPM
SRP007412_kidney	0.00 RPM	7.39 RPM
SRP007412_liver	0.00 RPM	4.51 RPM
SRP007412_testis	0.00 RPM	6.07 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2586 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2586 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2586 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006422	1 retrocopy	retro_chof_1792,
Choloepus hoffmanni	ENSCHOG00000007723	7 retrocopies	retro_chof_1026, retro_chof_1037, retro_chof_1808, retro_chof_2079, retro_chof_2149, retro_chof_2642, retro_chof_811,
Callithrix jacchus	ENSCJAG00000005509	1 retrocopy	retro_cjac_4168,
Dasypus novemcinctus	ENSDNOG00000024562	4 retrocopies	retro_dnov_1226, retro_dnov_1419, retro_dnov_1519, retro_dnov_1871,
Homo sapiens	ENSG00000158122	1 retrocopy	retro_hsap_4843,
Macaca mulatta	ENSMMUG00000008295	1 retrocopy	retro_mmul_2586 ,
Otolemur garnettii	ENSOGAG00000017058	1 retrocopy	retro_ogar_1866,
Procavia capensis	ENSPCAG00000003177	1 retrocopy	retro_pcap_269,
Pongo abelii	ENSPPYG00000019418	1 retrocopy	retro_pabe_3765,
Pan troglodytes	ENSPTRG00000021156	1 retrocopy	retro_ptro_3227,