RetrogeneDB ID: retro_mmul_1777

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:85153819..85154632(+)
• Located in intron of: ENSMMUG00000019530

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.8572
• Ensembl ID: ENSMMUG00000029059
• Aliases: None
• Description: None

Sequence

>retro_mmul_1777
ATGAGGGAGATCGTGCACATTCAGGGCGGCCAGTGCGGCTACTACATCGGGGCCAAGTTCTGGGAAGTCATCAGTGATGA
GCATGGCATAGACCCCAGCAGCAACTACGTGGGGGACTCGGACTTGCAGCTGGAGCGGATCAGCATCTACTACAATGAGG
CCTCTTCTCACAAGTATGTGCCTCAGGCCATTCTGGTCGACCTGGAGGCTGGGACCATGGACAGTGTCCGCTCGGGGCCT
TTTGGACATTTTTTCAGGCCTGATAATTTCATCTTTGGTCAGAGTGGGGCCGGCAACAACTGGGCCAGGGGTCACTACAC
GGAGGGTGCGGAGCTGGTGGATCCCGTCCTGGATGTGCGGAAGGAGTGTGAGAACTGCGACTGTCTGTAGGGTTTCCAGC
TGACCCACTCGCTGGCTGAGGGCACAGCCTCGGGCATGGGCATGCTACTCATCAGCAAGGTGCATGAGGAGTATCCCGAC
CGCATCATGAACACCTTCAGCGTAGTTCCCTCGCCCAAGGTGTCAGACACGGTGGTGGAGCCCTACAACCCCACGCTGTC
CATCGACCAGCTGGTGGAGAATACAGGTGAGACCTACCGCATAGACAAGGAGGTTCTCTACGACATCTGCGTCTGCACCC
TCAGGCTGGCCACGCCCACCTATGGGGACCTCTGCCACCTGGTGTTGGCCACCATGAGCGGGATCACCACCTCCTTGCGC
TTCCTGGGCCAGCTCAACAAGGACCTGCACAAGCGGGTGGTGAACATGGTGCCCTTCCCCCACCTGCACTTCTTCATGCC
CAGCATGAAGCCC

Alignment

ORF - retro_mmul_1777 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.66 %
• Parental protein coverage: 60.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPSGNYVGDSDLQLERISVYYNEASSHKYVPRAILVDLEP
          MREIVHIQ.GQCG..IGAKFWEVISDEHGIDPS.NYVGDSDLQLERIS.YYNEASSHKYVP.AILVDLE.
Retrocopy MREIVHIQGGQCGYYIGAKFWEVISDEHGIDPSSNYVGDSDLQLERISIYYNEASSHKYVPQAILVDLEA

Parental  GTMDSVRSGAFGHLFRPDNFIFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKECENCDCLQGFQLTHSLG
          GTMDSVRSG.FGH.FRPDNFIFGQSGAGNNWA.GHYTEGAELVD.VLDV.RKECENCDCL.GFQLTHSL.
Retrocopy GTMDSVRSGPFGHFFRPDNFIFGQSGAGNNWARGHYTEGAELVDPVLDV-RKECENCDCL*GFQLTHSLA

Parental  GGTGSGMGTLLISKVREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSIHQLVENTDETYCIDNEALYDI
          .GT.SGMG.LLISKV.EEYPDRIMNTFSVVPSPKVSDTVVEPYN.TLSI.QLVENT.ETY.ID.E.LYDI
Retrocopy EGTASGMGMLLISKVHEEYPDRIMNTFSVVPSPKVSDTVVEPYNPTLSIDQLVENTGETYRIDKEVLYDI

Parental  CFRTLKLATPTYGDLNHLVSATMSGVTTSLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAP
          C..TL.LATPTYGDL.HLV.ATMSG.TTSLRF.GQLN.DL.K..VNMVPFP.LHFFMP...P
Retrocopy CVCTLRLATPTYGDLCHLVLATMSGITTSLRFLGQLNKDLHKRVVNMVPFPHLHFFMPSMKP

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	85.38 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	389.43 RPM
SRP007412_cerebellum	0.06 RPM	56.05 RPM
SRP007412_heart	0.00 RPM	0.94 RPM
SRP007412_kidney	0.00 RPM	0.12 RPM
SRP007412_liver	0.00 RPM	0.99 RPM
SRP007412_testis	0.00 RPM	15.68 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1777 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1777 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1777 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2369
Gorilla gorilla	retro_ggor_2364

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000258947	1 retrocopy	retro_hsap_155,
Macaca mulatta	ENSMMUG00000012164	2 retrocopies	retro_mmul_1849, retro_mmul_2533,
Macaca mulatta	ENSMMUG00000023684	2 retrocopies	retro_mmul_2501, retro_mmul_375,
Macaca mulatta	ENSMMUG00000029059	1 retrocopy	retro_mmul_1777 ,