RetrogeneDB ID: retro_mmul_1706

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:105583552..105583897(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.799
• Ensembl ID: ENSMMUG00000016059
• Aliases: None
• Description: ras-related protein Ral-A [Source:RefSeq peptide;Acc:NP_001253385]

Sequence

>retro_mmul_1706
CTCTGTGTCTTCTCTATTACAGAAATGGAATCCTTTGCAGCTACAGTTGGCTTCGGGAACAGATTTAAGAGTAAAAGAAG
ATGTGATTATTCCATTTCTACTGGTTGCTAACAAATCAGATTTAGAAGATAAAAGGCGGATTTCCGTAGAAGAGACAAAA
AACAGAACTGACTAGTGGAGTGTTAACTATGTGGAAACATCTGCTAAAACACAAGCTAATGTTGACAAGATATTTTTTGA
CTTAATGAGAGAAATTCAAGTGAGAAAGATGGAAGACAGCAAAGAAAAGAGTGGAAAAAGAAGAGGAAGAGTTTAGCCAA
GACAATCAGAGAAAGATGCTGCATT

Alignment

ORF - retro_mmul_1706 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.51 %
• Parental protein coverage: 56.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LCVFSITEMESFAATADF-REQI-LRVKEDENVPFLLVGNKSDLEDKRQVSVEEAKNRAEQWNVNYVETS
          LCVFSITEMESFAAT..F.REQI.LRVKED...PFLLV.NKSDLEDKR..SVEE.KNR...W.VNYVETS
Retrocopy LCVFSITEMESFAATVGF<REQI<LRVKEDVIIPFLLVANKSDLEDKRRISVEETKNRTD*WSVNYVETS

Parental  AKTRANVDKVFFDLMREIRARKMEDSKEKNG-KKKRKSLAKRIRERCCI
          AKT.ANVDK.FFDLMREI..RKMEDSKEK.G.KKKRKSLAK.IRERCCI
Retrocopy AKTQANVDKIFFDLMREIQVRKMEDSKEKSG<KKKRKSLAKTIRERCCI

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	11.54 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	11.42 RPM
SRP007412_cerebellum	0.00 RPM	10.20 RPM
SRP007412_heart	0.00 RPM	15.96 RPM
SRP007412_kidney	0.00 RPM	8.80 RPM
SRP007412_liver	0.00 RPM	5.94 RPM
SRP007412_testis	0.00 RPM	23.82 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1706 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1706 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1706 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3707
Pan troglodytes	retro_ptro_2511
Pongo abelii	retro_pabe_3148

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007630	1 retrocopy	retro_cjac_3313,
Dasypus novemcinctus	ENSDNOG00000017413	1 retrocopy	retro_dnov_573,
Homo sapiens	ENSG00000006451	2 retrocopies	retro_hsap_1136, retro_hsap_3707,
Macropus eugenii	ENSMEUG00000000259	1 retrocopy	retro_meug_1638,
Macaca mulatta	ENSMMUG00000011442	2 retrocopies	retro_mmul_1151, retro_mmul_1863,
Macaca mulatta	ENSMMUG00000015381	1 retrocopy	retro_mmul_1766,
Macaca mulatta	ENSMMUG00000016059	2 retrocopies	retro_mmul_1706 , retro_mmul_882,
Nomascus leucogenys	ENSNLEG00000003055	1 retrocopy	retro_nleu_935,
Pongo abelii	ENSPPYG00000017619	3 retrocopies	retro_pabe_3148, retro_pabe_3208, retro_pabe_945,
Pan troglodytes	ENSPTRG00000019108	1 retrocopy	retro_ptro_2511,
Sus scrofa	ENSSSCG00000029741	1 retrocopy	retro_sscr_634,
Ictidomys tridecemlineatus	ENSSTOG00000020292	2 retrocopies	retro_itri_1314, retro_itri_1315,
Vicugna pacos	ENSVPAG00000002810	1 retrocopy	retro_vpac_211,