RetrogeneDB ID: retro_mmul_1981

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:137382626..137382955(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000004440
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMMUG00000013949
• Aliases: None
• Description: None

Sequence

>retro_mmul_1981
GAGCTGAAGAAGAAGTTGTTCAAAGGCCGGCGGGTGCTGAATCGGGAGCGGCGTCTGAGGCACCGCGTGGTCGGGGCTGT
GATAGACCAAGGGCTGATCACGCGGCACCATCTCAAGAAGCGGGCGTCCAGTGCACATGCCAACATTACTCTGTCAGGGA
AGAAGCCAGAAAACTCCTCCAGCAGATCCGGCTTGCCCAGAAAGAGAAGGCGGCCATGGAAGTGGAAGCCCCTTCAAAGC
CAGCCAGGACTAGTGAACCACAGCTTAAAAGGCAAAAGAAGACAAAAGCTCCCCAGGATGTAGAAATGAAGGACCTTGAA
GATGAGAGC

Alignment

ORF - retro_mmul_1981 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.5 %
• Parental protein coverage: 68.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ELKKKLFKRRRVLNRERRLRHRVVGAVIDQGLITRHHLKKRASSARANITLSGKK-RRKLLQQIRLAQKE
          ELKKKLFK.RRVLNRERRLRHRVVGAVIDQGLITRHHLKKRASSA.ANITLSGKK..RKLLQQIRLAQKE
Retrocopy ELKKKLFKGRRVLNRERRLRHRVVGAVIDQGLITRHHLKKRASSAHANITLSGKK<ARKLLQQIRLAQKE

Parental  KAAMEVEAPSKPARTSEPRLKRQKKTKAPQDVEMKDLEDES
          KAAMEVEAPSKPARTSEP.LKRQKKTKAPQDVEMKDLEDES
Retrocopy KAAMEVEAPSKPARTSEPQLKRQKKTKAPQDVEMKDLEDES

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	2.80 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	5.39 RPM
SRP007412_cerebellum	0.00 RPM	3.23 RPM
SRP007412_heart	0.06 RPM	2.18 RPM
SRP007412_kidney	0.00 RPM	2.35 RPM
SRP007412_liver	0.00 RPM	2.97 RPM
SRP007412_testis	0.04 RPM	29.44 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1981 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1981 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1981 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006512	1 retrocopy	retro_amel_1386,
Bos taurus	ENSBTAG00000010465	2 retrocopies	retro_btau_1195, retro_btau_1799,
Canis familiaris	ENSCAFG00000015719	2 retrocopies	retro_cfam_1104, retro_cfam_757,
Felis catus	ENSFCAG00000025454	2 retrocopies	retro_fcat_1722, retro_fcat_773,
Macaca mulatta	ENSMMUG00000013949	4 retrocopies	retro_mmul_1186, retro_mmul_1541, retro_mmul_1785, retro_mmul_1981 ,
Mus musculus	ENSMUSG00000071653	2 retrocopies	retro_mmus_1809, retro_mmus_759,
Otolemur garnettii	ENSOGAG00000033103	1 retrocopy	retro_ogar_811,
Rattus norvegicus	ENSRNOG00000019701	4 retrocopies	retro_rnor_1066, retro_rnor_1955, retro_rnor_851, retro_rnor_883,
Sus scrofa	ENSSSCG00000023323	2 retrocopies	retro_sscr_1162, retro_sscr_1163,