RetrogeneDB ID: retro_mmul_549

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:165283170..165283474(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.1735
• Ensembl ID: ENSMMUG00000017370
• Aliases: None
• Description: signal peptidase complex subunit 1 [Source:RefSeq peptide;Acc:NP_001180678]

Sequence

>retro_mmul_549
ATGTTGGAGCATATGAGCTTGCTGCCCATATGAATCGATTACAAGGGACAAAAGCTAGTTGAACAAATGTTTCAGAGAAT
TATTACTTTTTCTTCAGTCGTTGGATTTATCTATGGTTATGTGGCTGAACATTGCAGATGAACTGTCTATATAGTTATAG
CTGGATTTGCTTTTTCACATTTGCTGACACTTCACCCATGGCCCATCCATCACTGGCATCCCCTCAAGAGGTTACATGTC
CAAGACTCATCACAGAAAATGAGAAGCTGGTGATAGAAAAATTAAGAGGCATGCTAAAAATAAT

Alignment

ORF - retro_mmul_549 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.12 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MLEHLSSLPTQMDYKGQKLAEQMFQGIILFSAIVGFIYGYVAEQFGWTVYIVMAGFAFSCLLTLPPWPIY
          MLEH.S.LP...DYKGQKL.EQMFQ.II.FS..VGFIYGYVAE....TVYIV.AGFAFS.LLTL.PWPI.
Retrocopy MLEHMSLLPI*IDYKGQKLVEQMFQRIITFSSVVGFIYGYVAEHCR*TVYIVIAGFAFSHLLTLHPWPIH

Parental  RRHPLKWLPVQDSS-TDDKK-PGERKIKRHAKNN
          ..HPLK.L.VQDSS.T...K..G.RKIKRHAKNN
Retrocopy HWHPLKRLHVQDSS<TENEK<AGDRKIKRHAKNN

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	29.81 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	26.97 RPM
SRP007412_cerebellum	0.00 RPM	26.93 RPM
SRP007412_heart	0.00 RPM	38.69 RPM
SRP007412_kidney	0.00 RPM	51.64 RPM
SRP007412_liver	0.00 RPM	62.07 RPM
SRP007412_testis	0.00 RPM	187.07 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_549 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_549 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_549 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_294
Pan troglodytes	retro_ptro_241
Gorilla gorilla	retro_ggor_332
Pongo abelii	retro_pabe_380

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008426	1 retrocopy	retro_amel_1899,
Canis familiaris	ENSCAFG00000008927	1 retrocopy	retro_cfam_2079,
Equus caballus	ENSECAG00000023559	1 retrocopy	retro_ecab_86,
Erinaceus europaeus	ENSEEUG00000007914	1 retrocopy	retro_eeur_25,
Homo sapiens	ENSG00000114902	1 retrocopy	retro_hsap_294,
Gorilla gorilla	ENSGGOG00000028027	1 retrocopy	retro_ggor_332,
Microcebus murinus	ENSMICG00000014061	1 retrocopy	retro_mmur_292,
Myotis lucifugus	ENSMLUG00000000744	1 retrocopy	retro_mluc_2104,
Macaca mulatta	ENSMMUG00000017370	1 retrocopy	retro_mmul_549 ,
Otolemur garnettii	ENSOGAG00000004106	3 retrocopies	retro_ogar_2119, retro_ogar_2315, retro_ogar_2788,
Pongo abelii	ENSPPYG00000013798	1 retrocopy	retro_pabe_380,
Pan troglodytes	ENSPTRG00000015011	1 retrocopy	retro_ptro_241,
Tarsius syrichta	ENSTSYG00000006854	2 retrocopies	retro_tsyr_1359, retro_tsyr_599,
Tursiops truncatus	ENSTTRG00000008576	1 retrocopy	retro_ttru_806,
Vicugna pacos	ENSVPAG00000007380	1 retrocopy	retro_vpac_269,