RetrogeneDB ID: retro_mmul_1694

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:82879126..82879792(-)
• Located in intron of: ENSMMUG00000019015

Retrocopy information

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

Parental gene information

• Parental gene symbol: MDP1
• Ensembl ID: ENSMMUG00000012476
• Aliases: None
• Description: None

Sequence

>retro_mmul_1694
ATGAGTGGTCTCGGCAGGCTCTTCGGGAAGGGTAAGAAGGAGAAAGGGCCAACCCCTGAAGAAGCAATACAGAAACTGAA
GGAGACAGAGAAGGTACTGATCAAGAAACAGGAATTTTTGGAGCAGAAGATTCAACAGGAGCTACAAACAGCCAAGAAGT
ATGGGACCAAGAATAAGAGAGCTGCCCTACAGGCTTTGCGGAGGAAGAAAAGATTCGAACAGCAGCTGGCACAAACTGAC
GGGACATTATCCACCCTGGAGTTTCAGCGTGAGGCCATTGAGAATGCCACCACCAATGCAGAAGTCCTTCGTACCATGGA
GCTTGCTGCCCAAGGCATGAAGAAAGCCTACCAGGACATGGACATTGACAAGGTAGATGAACTGATGACTGACATCATAG
AACAACAGGAGGTGGCCCAGCAGATCTCAGATGCCATTTCTCGGCCTATGGGCTTTGGAGATGATGTGGATGAGGATGAA
CTGCTGGAGGAGCTAGAGTTGCTGGAACAGGAGGAATTGGCCCAGGAGTTGTTAAGTGTGGGCGACAAGGAGGAAGAACC
CCCAGTCAAATTGCCTGGTGTACCTTCTACTCATCTGCCGGCAGAGCCAGCTCCCAAAGCGGATGAAGATGAAGAAGCAC
TAAAGCAGTTGGCTGAGTGGGTATCC

Alignment

ORF - retro_mmul_1694 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.65 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGLGRLFGKGKKEKGPTPEEAIQKLKETEKILIKKQEFLEQKIQQELQTAKKYGTKNKRAALQALRRKK
          MSGLGRLFGKGKKEKGPTPEEAIQKLKETEK.LIKKQEFLEQKIQQELQTAKKYGTKNKRAALQALRRKK
Retrocopy MSGLGRLFGKGKKEKGPTPEEAIQKLKETEKVLIKKQEFLEQKIQQELQTAKKYGTKNKRAALQALRRKK

Parental  RFEQQLAQTDGTLSTLEFQREAIENATTNAEVLRTMELAAQGMKKAYQDMDIDKVDELMTDITEQQEVAQ
          RFEQQLAQTDGTLSTLEFQREAIENATTNAEVLRTMELAAQGMKKAYQDMDIDKVDELMTDI.EQQEVAQ
Retrocopy RFEQQLAQTDGTLSTLEFQREAIENATTNAEVLRTMELAAQGMKKAYQDMDIDKVDELMTDIIEQQEVAQ

Parental  QISDAISRPMGFGDDVDEDELLEELELLEQEELAQELLSVGDKEEEPPVKLPSVPSTHLPAEPAPKADED
          QISDAISRPMGFGDDVDEDELLEELELLEQEELAQELLSVGDKEEEPPVKLP.VPSTHLPAEPAPKADED
Retrocopy QISDAISRPMGFGDDVDEDELLEELELLEQEELAQELLSVGDKEEEPPVKLPGVPSTHLPAEPAPKADED

Parental  EEALKQLAEWVS
          EEALKQLAEWVS
Retrocopy EEALKQLAEWVS

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	12.55 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	23.09 RPM
SRP007412_cerebellum	0.06 RPM	21.96 RPM
SRP007412_heart	0.06 RPM	17.43 RPM
SRP007412_kidney	0.82 RPM	19.95 RPM
SRP007412_liver	0.00 RPM	10.29 RPM
SRP007412_testis	0.08 RPM	14.14 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1694 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1694 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1694 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000254505	1 retrocopy	retro_hsap_2284,
Gorilla gorilla	ENSGGOG00000016091	1 retrocopy	retro_ggor_1697,
Microcebus murinus	ENSMICG00000001732	1 retrocopy	retro_mmur_1101,
Macaca mulatta	ENSMMUG00000008084	1 retrocopy	retro_mmul_2178,
Macaca mulatta	ENSMMUG00000012476	2 retrocopies	retro_mmul_1035, retro_mmul_1694 ,
Pongo abelii	ENSPPYG00000005691	1 retrocopy	retro_pabe_1937,
Sorex araneus	ENSSARG00000008328	1 retrocopy	retro_sara_530,