RetrogeneDB ID: retro_mmul_533

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:132566921..132567884(-)
• Located in intron of: ENSMMUG00000014952

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.1570
• Ensembl ID: ENSMMUG00000002669
• Aliases: FCMD, FKTN
• Description: fukutin [Source:RefSeq peptide;Acc:NP_001244424]

Sequence

>retro_mmul_533
ATGAGTAGAATCAATAAGAACGTGGTTTTGGCCTTTTTAACGCTGACAAGTTCTGCATTTCTGCTGTTTCAGTTGTACTA
CTACAAGCACTATTTATCAACAATTAATGGAGCTGGTTTGTCAAAATCCAAAGGAAGCCGAATTGGATTTGATGGCACAC
AGTGGCGTGCAGTTAAAAAATTTATTATGCTAACATCCAACCAAAATGTACCAGTGTTTCTTATTGATCCTTTGGTATTG
GAATTGATTAATAAGAACTTTGAACAAGTCAAAAATACTTCTCATGGCTCCATTTCCCAATGCAGGTTTTTCTGTGTTCC
AAGAGACTTTACTGCACTTGCACTGCAGTCTCACCTATGGAGGAATGAGGAAGGCTGGTTTCGGGTAGCTGAGAATATGG
GATTTCAGTGCCTAAAGATTGAGAGTAAAGATCCCCGGCTAGACAGGATAGACTCCCTTTCTGGAACGGAAATCCCCCTG
CACTATATCTGCAAATTGGCCACTCATGCGATTCGCTTGGTAGTCTTCCATGAGAGGAGTGGCAACCACCTCTGGCTTGG
CCGCTTGAGACTTAAAGAACACATTGACAGTAAATTTGTTCCCTTCCGAAAGTTACAGTTTGGTCTTTATCCAGGAGCTT
TTGACAGGCCAGAGTTACAGCAAGTTACTGTTGATGGACTGGAAGTTCTCATTCCAAAGAATCCAATGAGCTTTGTAGAA
GAAGTACCACACTGTAGGTTTATTGAGTGTAGATATAAAGAAGCTCGAGCATTCTTTTAGCAGTACCTTGATGATAACAC
TGTGGAAGCCGTGGTCTTTCGGAAGAGTGCAAAGGAATTACTGCAACTAGCAGCAAAAACATTAAACAAATTGGGAGTAC
CATTCTGGCTGAGCAGTGGGACTTGTCTAGGATGGTATCGACAATGCAACATTATTCCTTATAGCAAAGATGTCCACCTA
GGA

Alignment

ORF - retro_mmul_533 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.21 %
• Parental protein coverage: 69.63 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSRINKNVVLALLTLTSSAFLLFQLYYYKHYLSTRNGAGLSKSKGSRIGFDSTQWRAVKKFIMLTSNQNV
          MSRINKNVVLA.LTLTSSAFLLFQLYYYKHYLST.NGAGLSKSKGSRIGFD.TQWRAVKKFIMLTSNQNV
Retrocopy MSRINKNVVLAFLTLTSSAFLLFQLYYYKHYLSTINGAGLSKSKGSRIGFDGTQWRAVKKFIMLTSNQNV

Parental  PVFLIDPLILELINKNFEQVKNTSQGSISQCTFFCVPRDFTAFALQYHLWKNEEGWFRIAENMGFQCLKI
          PVFLIDPL.LELINKNFEQVKNTS.GSISQC.FFCVPRDFTA.ALQ.HLW.NEEGWFR.AENMGFQCLKI
Retrocopy PVFLIDPLVLELINKNFEQVKNTSHGSISQCRFFCVPRDFTALALQSHLWRNEEGWFRVAENMGFQCLKI

Parental  ESKDPRLDGIDSLSGTEIPLHYICKLAAHAIHLVVFHERSGNYLWHGHLRLKEHIDRKFVPFRKLQFGRY
          ESKDPRLD.IDSLSGTEIPLHYICKLA.HAI.LVVFHERSGN.LW.G.LRLKEHID.KFVPFRKLQFG.Y
Retrocopy ESKDPRLDRIDSLSGTEIPLHYICKLATHAIRLVVFHERSGNHLWLGRLRLKEHIDSKFVPFRKLQFGLY

Parental  PGAFDRPELQQVTVDGLEVLIPKDPMHFVEEVPHSRFIECRYKEARAFFQQYLDDNTVEAMAFRKSAKEL
          PGAFDRPELQQVTVDGLEVLIPK.PM.FVEEVPH.RFIECRYKEARAFF.QYLDDNTVEA..FRKSAKEL
Retrocopy PGAFDRPELQQVTVDGLEVLIPKNPMSFVEEVPHCRFIECRYKEARAFF*QYLDDNTVEAVVFRKSAKEL

Parental  LQLAAKTLNKLGVPFWLSSGTCLGWYRQCNIIPYSKDVDLG
          LQLAAKTLNKLGVPFWLSSGTCLGWYRQCNIIPYSKDV.LG
Retrocopy LQLAAKTLNKLGVPFWLSSGTCLGWYRQCNIIPYSKDVHLG

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	16.14 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	13.72 RPM
SRP007412_cerebellum	0.00 RPM	14.85 RPM
SRP007412_heart	0.00 RPM	4.71 RPM
SRP007412_kidney	0.00 RPM	15.73 RPM
SRP007412_liver	0.00 RPM	4.47 RPM
SRP007412_testis	0.23 RPM	9.84 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_533 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_533 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_533 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000002669	1 retrocopy	retro_mmul_533 ,