RetrogeneDB ID: retro_mmul_1402

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 19:45596144..45596426(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEPX1
• Ensembl ID: ENSMMUG00000007936
• Aliases: SEPX1, MSRB1
• Description: selenoprotein X, 1 [Source:RefSeq peptide;Acc:NP_001108222]

Sequence

>retro_mmul_1402
ATGTTGTTCTGCAGCTTCTTCAGGGGCGAGGTTTTCCAGAATCACTTTGAGCCAGGCGACTATATCTGTGCCAAGTGTGG
CTATGAGCTGTTCCCCGGCCGCTCACAGTGCGCATACTCATTCCCCTGACCGGCGTTCACCAAGACCATCCACTCTGACA
GCGTGGCCAAGCGCCCAGAGCGTAATCGTCCTGAAGTCTTGAAGGTGTCCTGTGGCAAGTGTGGCAATGCATCGAGCCAC
GAGTCCCTGAACCGTGGCCCCAAGCTGTAGCAGTGCCGATTC

Alignment

ORF - retro_mmul_1402 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.47 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSFCSFFGGEVFQNHFEPGVYACAKCGYELFSSRSKYAHSSPWPAFTETIHADSVAKRPEHNRPGALKVS
          M.FCSFF.GEVFQNHFEPG.Y.CAKCGYELF..RS..A.S.P.PAFT.TIH.DSVAKRPE.NRP..LKVS
Retrocopy MLFCSFFRGEVFQNHFEPGDYICAKCGYELFPGRSQCAYSFP*PAFTKTIHSDSVAKRPERNRPEVLKVS

Parental  CGKCGNGLGHEFLNDGPKPGQSRF
          CGKCGN...HE.LN.GPK..Q.RF
Retrocopy CGKCGNASSHESLNRGPKL*QCRF

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	5.49 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	15.71 RPM
SRP007412_cerebellum	0.00 RPM	4.39 RPM
SRP007412_heart	0.00 RPM	19.90 RPM
SRP007412_kidney	0.00 RPM	116.43 RPM
SRP007412_liver	0.00 RPM	144.24 RPM
SRP007412_testis	0.00 RPM	9.50 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1402 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1402 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1402 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008487	1 retrocopy	retro_amel_1468,
Homo sapiens	ENSG00000198736	1 retrocopy	retro_hsap_2057,
Microcebus murinus	ENSMICG00000011349	1 retrocopy	retro_mmur_1267,
Macaca mulatta	ENSMMUG00000007936	1 retrocopy	retro_mmul_1402 ,
Pan troglodytes	ENSPTRG00000024355	1 retrocopy	retro_ptro_1372,