RetrogeneDB ID: retro_mmul_312

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 11:81599672..81600029(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000004554
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MMU.3178
• Ensembl ID: ENSMMUG00000004552
• Aliases: None
• Description: D-dopachrome decarboxylase [Source:RefSeq peptide;Acc:NP_001244597]

Sequence

>retro_mmul_312
ATGCCGTTCGTAGAGCTGGACACGAATTTGCCCGCCAACCGAGTGCCCGCGGGGCTGGAGAAACGACTCTGCGCTGCCGC
TGCCTCCATCCTGGGCAAGCCTGCGCACCGTGTGAACGTGACGGTGCGGCCAGGCCTGACTATGGCGCTGAGCGGGTCCA
CCGAGCCCTGCGCGCAGCTGTCCGTCTCCTCCATCGGGGTAGTTGGCACCGCCGAGGACAACCGCAGCTACAGCGCCCAC
TTCTTTGAGTTTCTCACCAAGGAGCTAGCCCTGGGCCAGGACCAGATACTTATCCGCTTTTTCCCCCTGGAGTCCTGGCA
GATTGGCAAGATAGGGACGGTCGTGACATTTTTATGA

Alignment

ORF - retro_mmul_312 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.46 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPFVELDTNLPANRVPAGLEKRLCAAAASILGKPADRVNVTVRPGLTMALSGSTEPCAQLSVSSIGVVGT
          MPFVELDTNLPANRVPAGLEKRLCAAAASILGKPA.RVNVTVRPGLTMALSGSTEPCAQLSVSSIGVVGT
Retrocopy MPFVELDTNLPANRVPAGLEKRLCAAAASILGKPAHRVNVTVRPGLTMALSGSTEPCAQLSVSSIGVVGT

Parental  AEDNRSHSAHFFEFLTKELALGQDRILIRFFPLESWQIGKIGTVVTFL
          AEDNRS.SAHFFEFLTKELALGQD.ILIRFFPLESWQIGKIGTVVTFL
Retrocopy AEDNRSYSAHFFEFLTKELALGQDQILIRFFPLESWQIGKIGTVVTFL

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	1.68 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	8.41 RPM
SRP007412_cerebellum	0.19 RPM	0.77 RPM
SRP007412_heart	0.00 RPM	2.24 RPM
SRP007412_kidney	0.59 RPM	6.46 RPM
SRP007412_liver	16.86 RPM	168.39 RPM
SRP007412_testis	0.30 RPM	1.77 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_312 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_312 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_312 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013811	1 retrocopy	retro_amel_1024,
Felis catus	ENSFCAG00000009408	1 retrocopy	retro_fcat_1172,
Macaca mulatta	ENSMMUG00000004552	1 retrocopy	retro_mmul_312 ,
Mustela putorius furo	ENSMPUG00000002935	1 retrocopy	retro_mputfur_1365,