RetrogeneDB ID: retro_mmul_1087

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 14:121373054..121373856(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000004694
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.672
• Ensembl ID: ENSMMUG00000009506
• Aliases: None
• Description: None

Sequence

>retro_mmul_1087
CAGTTCTTGATTCGTACTGGGTCTGTTGGCGGAAACAGGGCTGAAGCCTCTTTGGAGCAAGCTCAGAATCTTAACCCCAT
GGTGGATGTGAAGGTGGACACTGAGGATATACAGAAGAAACCAGAGTCATTTTTCACTCACTTTGATGCTGTGTGTCTGA
CTTGCTGCTCCAGGGATGTCATAGTTAAAGTTGACCAGATCTGTCACAAAAATAGCATCAAGTTCTTTACAGGAGATGCT
TTTGGATACCATGGATACACATTTGCCAATCTAGGAGAACATGAGTTTGTAGAAGAGAAAACTAAAGTTGCCAAAGTTAG
CCAAGGAGTAGAAGATGGGCCTGATACCAAGAGTAAAACTTGATTCTTCTAAGACAACGATGGTCAAAAAGAAGGTGGTC
TTCTGCCCCGTTAAAGAAGTCCTGGAGGTGGACTGGAGCAGTGGGAAAGCAAAGGCTACTCTGAAGCACACGACCTCTGG
CCACTTTCTGCTTCAAGTGCTCCTAAAGTTCCGCACAGAAAAAGGAAGAGATCCCAGTTCTGATACATACGGGGAAGATT
CCGAGTTGTTGCTCCAGATACGAAACGATGTGCTTGACTCACCGGGTATTAGTCCTGACCTGCTTTCTGAGGACCTTGTC
AGGTACTGCTTCTCCAAGATGGCCCCAGTGTGTGCGGTGGTTGGAGGGATTTTGGCACAGGAAATTGTGAAGGCCCTGTC
TCAGTGGGACCCTCCTCACAACAACTTCTTCTTCTTCTATGGCATGAAGGGGAATGGGATTGTGGAGTGCCTTGGCCCCA
AG

Alignment

ORF - retro_mmul_1087 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.25 %
• Parental protein coverage: 85.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QFLIRTGSVGRNRAEASLERAQNLNPMVDVKVDTEDIEKKPESFFTQFDAVCLTCCSRDVIVKVDQICHK
          QFLIRTGSVG.NRAEASLE.AQNLNPMVDVKVDTEDI.KKPESFFT.FDAVCLTCCSRDVIVKVDQICHK
Retrocopy QFLIRTGSVGGNRAEASLEQAQNLNPMVDVKVDTEDIQKKPESFFTHFDAVCLTCCSRDVIVKVDQICHK

Parental  NSIKFFTGDVFGYHGYTFANLGEHEFVEE-KTKIAKVSQGVEDGPDTKRAKLDSSETTMVKKKVVFCPVK
          NSIKFFTGD.FGYHGYTFANLGEHEFVEE.K.K..K.......G....R.KLDSS.TTMVKKKVVFCPVK
Retrocopy NSIKFFTGDAFGYHGYTFANLGEHEFVEE>KLKLPKLAKE*KMGL-IPRVKLDSSKTTMVKKKVVFCPVK

Parental  EALEVDWSSEKAKAALKRTTSDYFLLQVLLKFRTDKGRDPSSDTYEEDSELLLQIRNDVLDSLGISPDLL
          E.LEVDWSS.KAKA.LK.TTS..FLLQVLLKFRT.KGRDPSSDTY.EDSELLLQIRNDVLDS.GISPDLL
Retrocopy EVLEVDWSSGKAKATLKHTTSGHFLLQVLLKFRTEKGRDPSSDTYGEDSELLLQIRNDVLDSPGISPDLL

Parental  PEDFVSYCFSEMAPVCAVVGGILAQEIVKALSQRDPPHNNFFFFDGMKGNGIVECLGPK
          .ED.V.YCFS.MAPVCAVVGGILAQEIVKALSQ.DPPHNNFFFF.GMKGNGIVECLGPK
Retrocopy SEDLVRYCFSKMAPVCAVVGGILAQEIVKALSQWDPPHNNFFFFYGMKGNGIVECLGPK

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	140.96 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	173.73 RPM
SRP007412_cerebellum	0.06 RPM	69.03 RPM
SRP007412_heart	0.00 RPM	38.63 RPM
SRP007412_kidney	0.00 RPM	39.55 RPM
SRP007412_liver	0.00 RPM	24.26 RPM
SRP007412_testis	0.04 RPM	167.81 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1087 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1087 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1087 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_829
Pan troglodytes	retro_ptro_579
Gorilla gorilla	retro_ggor_679
Pongo abelii	retro_pabe_742

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004180	1 retrocopy	retro_cfam_1705,
Dipodomys ordii	ENSDORG00000012199	1 retrocopy	retro_dord_638,
Homo sapiens	ENSG00000142230	1 retrocopy	retro_hsap_829,
Gorilla gorilla	ENSGGOG00000013078	1 retrocopy	retro_ggor_679,
Macaca mulatta	ENSMMUG00000009506	1 retrocopy	retro_mmul_1087 ,
Nomascus leucogenys	ENSNLEG00000002965	1 retrocopy	retro_nleu_261,
Nomascus leucogenys	ENSNLEG00000002966	1 retrocopy	retro_nleu_262,
Pongo abelii	ENSPPYG00000010168	1 retrocopy	retro_pabe_742,
Pan troglodytes	ENSPTRG00000011202	1 retrocopy	retro_ptro_579,