RetrogeneDB ID: retro_mmul_584

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:216377157..216377562(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FDX1L
• Ensembl ID: ENSMMUG00000022896
• Aliases: None
• Description: ferredoxin 1-like [Source:HGNC Symbol;Acc:30546]

Sequence

>retro_mmul_584
GTGGCTGCCTCCGAGGGCCGGGGTAGAACGAGTGCCAGGGTTCTGCTGTGGGCTGCCAGGGACACCTAGTGTAACAGACC
CAGGAGCTCTTTAGGGTCCAGGGAAGTGTAGGCGCCGGCAACAGCCAGGAAAATTCAGGAGATAGGCTGATGTGCCAGGC
AGGAAAGGAAGAGCCCAGCTCCCCCGAGCGGCCCAGGGATGTGGTGAACATGGTGTTTGTAGACCTGTCAAGCTGGGGGA
TCCTAGTGAGCTGCAGAGTCGGTGGACAATATTCTCCACCTGACCCAATGCCATGGGGTGAACCTGAAAGGCACCTGTGA
AGCCTTCCTGGCTTGCTCCGCCTGCCATGTGCATGTGAGCAAAGACCAACTGGGCCTTCTGCCTCCTCCCGAAGAGAGGA
AAGAG

Alignment

ORF - retro_mmul_584 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.93 %
• Parental protein coverage: 83.75 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAASMTRGGVSARVLLQTARGTWWNRTGGTSGSGEGVAPGTTRKFQATGSRSAGEEETGGPEQ-PG-DVV
          .AAS..RG..SARVLL..AR.T..NR.....GS.E..AP.T.RK.Q..G.....E.....P...PG.DVV
Retrocopy VAASEGRGRTSARVLLWAARDT*CNRPRSSLGSREV*APATARKIQEIG*CARQERKSPAPPSGPG<DVV

Parental  NVVFVDRSGQRIPVSGRVG-DNVLHLAQRHGVDLEGACEASLACSTCHVYVSEDHLDLLPPPEERED
          N.VFVD.S...I.VS.RVG.DN.LHL.Q.HGV.L.G.CEA.LACS.CHV.VS.D.L.LLPPPEER..
Retrocopy NMVFVDLSSWGILVSCRVG>DNILHLTQCHGVNLKGTCEAFLACSACHVHVSKDQLGLLPPPEERKE

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	1.34 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	5.95 RPM
SRP007412_cerebellum	0.00 RPM	0.52 RPM
SRP007412_heart	0.00 RPM	1.18 RPM
SRP007412_kidney	0.00 RPM	1.29 RPM
SRP007412_liver	0.00 RPM	2.85 RPM
SRP007412_testis	0.00 RPM	1.28 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_584 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_584 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_584 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_331
Pan troglodytes	retro_ptro_267
Gorilla gorilla	retro_ggor_355
Callithrix jacchus	retro_cjac_1753

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000267673	1 retrocopy	retro_hsap_331,
Gorilla gorilla	ENSGGOG00000006009	1 retrocopy	retro_ggor_355,
Macaca mulatta	ENSMMUG00000022896	1 retrocopy	retro_mmul_584 ,
Mus musculus	ENSMUSG00000079677	1 retrocopy	retro_mmus_2676,
Nomascus leucogenys	ENSNLEG00000012175	1 retrocopy	retro_nleu_1773,
Pan troglodytes	ENSPTRG00000010465	1 retrocopy	retro_ptro_267,