RetrogeneDB ID: retro_mmul_1150

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 15:44655174..44655690(+)
• Located in intron of: ENSMMUG00000002685

Retrocopy information

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

Parental gene information

• Parental gene symbol: DFFB
• Ensembl ID: ENSMMUG00000015174
• Aliases: None
• Description: None

Sequence

>retro_mmul_1150
GTGCTCCAGAAGCCCAAGACCGTGACGCTGCGGGCCCTGTGCAGCCAGAGGAAGTTTGGCGTGGTGGGCAGGAGCTGCAG
GGAGGTGCTGCGCAAGGGCTGCCTCCGCTTCCAGCTCCCTGAGCATGGCTCCCGGCTGTGCCTGTACAAGGATGGCATGG
AGCTGACCGAAGACTACTTCCCCAGCGTCCTCGACAATGCTGAGCTCCTGCTGCTCACCTCGGGCCAGGCCTGGCAGGGA
TATGTGAGTGACATCGGGCGTTTCCTCAGTGCTTTTCTCGAGCCGCACGCTTGGCTCATCCAGGCCGCCTGACAGCTACT
GTGTGATGAGCAGGCCCTGCAGAGGCAGAGGCTGCTGGCCGACCTCCTGTACAACATCAGCCAGAACATCACAGCCGACA
CCCAGGCTGAGGACCCGCTGTGGTTTGAAGGCTTGGAGTCCCAATTTTGGAATAAGTCTGGCTATCTGAGATATAGCTGT
GAGAGCCAGATCCGGAGTTACCTGAGAGAGGTGAGC

Alignment

ORF - retro_mmul_1150 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.88 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLQKPKSVKLRALRSPRKFGVAGRSCQEVLRKGCLRFQLPERGSRLCLYEDGTELTEDYFPSVPDNAELV
          .LQKPK.V.LRAL.S.RKFGV.GRSC.EVLRKGCLRFQLPE.GSRLCLY.DG.ELTEDYFPSV.DNAEL.
Retrocopy VLQKPKTVTLRALCSQRKFGVVGRSCREVLRKGCLRFQLPEHGSRLCLYKDGMELTEDYFPSVLDNAELL

Parental  LLTSGQAWQGYVSDIGRFLSAFHEPHAGLVQAAQQLLCDEQAPQRQRLLADLLHNVSQNIAAETRAEDPP
          LLTSGQAWQGYVSDIGRFLSAF.EPHA.L.QAA.QLLCDEQA.QRQRLLADLL.N.SQNI.A.T.AEDP.
Retrocopy LLTSGQAWQGYVSDIGRFLSAFLEPHAWLIQAA*QLLCDEQALQRQRLLADLLYNISQNITADTQAEDPL

Parental  WFEGLESRFQNKSGYLRYSCESRIRSYLREVS
          WFEGLES.F.NKSGYLRYSCES.IRSYLREVS
Retrocopy WFEGLESQFWNKSGYLRYSCESQIRSYLREVS

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	0.11 RPM
SRP007412_brain_prefrontal_cortex	0.48 RPM	1.59 RPM
SRP007412_cerebellum	0.32 RPM	0.06 RPM
SRP007412_heart	0.00 RPM	0.12 RPM
SRP007412_kidney	0.35 RPM	0.12 RPM
SRP007412_liver	0.20 RPM	0.20 RPM
SRP007412_testis	0.08 RPM	0.08 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1150 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1150 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1150 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002834	1 retrocopy	retro_cjac_616,
Homo sapiens	ENSG00000169598	1 retrocopy	retro_hsap_4240,
Gorilla gorilla	ENSGGOG00000013452	1 retrocopy	retro_ggor_2841,
Macaca mulatta	ENSMMUG00000015174	1 retrocopy	retro_mmul_1150 ,
Ornithorhynchus anatinus	ENSOANG00000013652	5 retrocopies	retro_oana_116, retro_oana_117, retro_oana_125, retro_oana_27, retro_oana_91,