RetrogeneDB ID: retro_mmul_1408

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 19:58171676..58172046(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM50A
• Ensembl ID: ENSMMUG00000032217
• Aliases: None
• Description: transmembrane protein 50A [Source:RefSeq peptide;Acc:NP_001248174]

Sequence

>retro_mmul_1408
ATGGCAGGCTTCCTAGATAATTTTCATTGGCCAGAATATGAATGTATTGACTGGGGTGAGAGAAGGAATGCTGTGGCGTC
TGTTGTAACAGGTATATTGTTTTTTACAGGCTGGTGGATAATGACGCAGCTGTGGTGTATCGTAGGCCAGAACAGTTGAA
CCATGCCTTTCACACATGTGGTGTATTTCCCACATTGGCTTTCTTCATAATAAAAATGCTGTATCCAATGCTCAGGTGAC
AGATGATAGCTGTGAAAGAGGCTGTTGAGGAAGAACAGGTGCTTGGGTTTGGCTTTTCATTGGTTTTGTGTCGATGTTTG
GGGTACTTATTGCTTCCATGTGGATTCTTTTTGGTGCATATGTTACCCAA

Alignment

ORF - retro_mmul_1408 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.48 %
• Parental protein coverage: 77.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSGFLEGLRCSE--CIDWGEKRNTIASIAAGVLFFTGWWIII-DAAVIYPTMKDFNHSYHACGVIAT-IA
          M.GFL......E..CIDWGE.RN..AS...G.LFFTG.W.I..DAAV.Y......NH..H.CGV..T.I.
Retrocopy MAGFLDNFHWPEYECIDWGERRNAVASVVTGILFFTG-WWIM<DAAVVYRRPEQLNHAFHTCGVFPT<IG

Parental  FLMI-NAVSNGQVRGDSYSEGCLGQTGARIWLFIGFMLAFGSLIASMWILFGGYVAK
          FL...NAVSN.QV..DS...GC.G.TGA..WLFIGF...FG.LIASMWILFG.YV..
Retrocopy FLHNKNAVSNAQVTDDSCERGC*GRTGAWVWLFIGFVSMFGVLIASMWILFGAYVTQ

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	56.25 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	43.16 RPM
SRP007412_cerebellum	0.00 RPM	49.85 RPM
SRP007412_heart	0.18 RPM	33.03 RPM
SRP007412_kidney	0.00 RPM	46.36 RPM
SRP007412_liver	0.04 RPM	12.51 RPM
SRP007412_testis	0.04 RPM	32.91 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1408 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1408 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1408 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2066
Pan troglodytes	retro_ptro_1379
Gorilla gorilla	retro_ggor_1487
Pongo abelii	retro_pabe_1679

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018575	1 retrocopy	retro_cjac_1677,
Cavia porcellus	ENSCPOG00000012615	1 retrocopy	retro_cpor_707,
Echinops telfairi	ENSETEG00000007483	1 retrocopy	retro_etel_2061,
Macropus eugenii	ENSMEUG00000002060	1 retrocopy	retro_meug_1270,
Macaca mulatta	ENSMMUG00000032217	1 retrocopy	retro_mmul_1408 ,
Ochotona princeps	ENSOPRG00000001182	2 retrocopies	retro_opri_546, retro_opri_62,
Pongo abelii	ENSPPYG00000001711	1 retrocopy	retro_pabe_1679,
Ictidomys tridecemlineatus	ENSSTOG00000022246	2 retrocopies	retro_itri_1228, retro_itri_1329,