RetrogeneDB ID: retro_mmul_1486

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:177765652..177766081(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.4925
• Ensembl ID: ENSMMUG00000021448
• Aliases: None
• Description: None

Sequence

>retro_mmul_1486
ATGCAGCACCGAGGCTTCCTCCTTCTCACCCTCCTCGCCCTGCTGGCGCTCACCTCTACAGAGGCCAAAAAGAAAGACAA
GGTGAAGAAGGGCCGCCCGTGGGGCGAGTGTGTGGATTGGGCCTGGGGGCCCTGCACCCCCCGCAGCAAGGATTGAGGCG
TGGGTTTCCGCGAGGGCACCTGCGGGGCCCAGACCCAGCGCATCCGGTGCAGGGTGCCCTGCAACTGGAAGAAGGAGTTT
GGAGCCGACTGCAAGTACAAGTTTGAGAACTGGGGTGCATGTGATGGGGCTACAGGCACCAAAGTCCGCCAAGGCACCGT
GAAGAAGGCCCGTTACAATGCTCAGTGCCAGGAGACCATCCGCGTCACCAAGCCCTGCACCCCCAAGACCAAAGCCAAGG
CCAAAGCCAAGAAAGGGAAGGGAAAGGAC

Alignment

ORF - retro_mmul_1486 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.01 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQHRGFLLLTLLALLALTSAVAKKKDKVKKGGPGSECAEWAWGPCTPSSKDCGVGFREGTCGAQTQRIRC
          MQHRGFLLLTLLALLALTS..AKKKDKVKKG.P..EC..WAWGPCTP.SKD.GVGFREGTCGAQTQRIRC
Retrocopy MQHRGFLLLTLLALLALTSTEAKKKDKVKKGRPWGECVDWAWGPCTPRSKD*GVGFREGTCGAQTQRIRC

Parental  RVPCNWKKEFGADCKYKFENWGACDGGTGTKVRQGTLKKARYNAQCQETIRVTKPCTPKTKAKAKXXKGK
          RVPCNWKKEFGADCKYKFENWGACDG.TGTKVRQGT.KKARYNAQCQETIRVTKPCT........XX.GK
Retrocopy RVPCNWKKEFGADCKYKFENWGACDGATGTKVRQGTVKKARYNAQCQETIRVTKPCTXXXXXXXXXXXGK

Parental  GKD
          GKD
Retrocopy GKD

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	0.11 RPM	2.69 RPM
SRP007412_brain_prefrontal_cortex	0.32 RPM	2.38 RPM
SRP007412_cerebellum	0.06 RPM	2.07 RPM
SRP007412_heart	0.59 RPM	5.89 RPM
SRP007412_kidney	0.35 RPM	3.29 RPM
SRP007412_liver	0.24 RPM	2.14 RPM
SRP007412_testis	0.38 RPM	4.30 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1486 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1486 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1486 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007740	1 retrocopy	retro_btau_655,
Echinops telfairi	ENSETEG00000016707	2 retrocopies	retro_etel_1929, retro_etel_947,
Loxodonta africana	ENSLAFG00000015119	1 retrocopy	retro_lafr_194,
Macaca mulatta	ENSMMUG00000021448	2 retrocopies	retro_mmul_1486 , retro_mmul_466,