RetrogeneDB ID: retro_mmul_687

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1099214725446:1150..1612(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000002193
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMMUG00000031574
• Aliases: None
• Description: None

Sequence

>retro_mmul_687
GATAGAGTGACTTGGAATCACTTTTCACCTTGTCATTTTTTGGCCAGTACAGATGATGGCTTTGTGTATAATTTGGATGC
AGGTTCAGATAAGCCAATTTTTACACTTAATGCGCACAATGATGAAATCTCTGGTCTTGATCTTAGCAGTCAAATCAAGG
GCTGTCTCGTGACTGCTTCAGTTGACAAATATGTGAAGATCTGGGACATCTTAGGAGATAGGCCAAGTCTAGTTCATTCT
AGGGACATGAAAATGGGAGTTCTCTTCTGTTCTTCATGTTGCCCTGATTTGCCATTTATTTATGCCTTTGGAGGTCAAAA
AGAAGGGCTTTGGGTCTGGGATATAAGCACAGTCTCTTCGGTAAATGAAGCATTTGGAAGACGAGAGCGGCATGTTCTCA
AGAGTGCAAGAAATTCATCTATCAGTGGCCCTTTTGGCAGCAGGAGCTCAGACACACCCATG

Alignment

ORF - retro_mmul_687 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.52 %
• Parental protein coverage: 89.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ERVTWNHFSPCHFLRMALILKVVNITCKKKSPAFIQREGKWEVKGLDLSSQIKGCLVTASADKYVKIWDI
          .RVTWNHFSPCHFL.......V.N.......P.F.......E..GLDLSSQIKGCLVTAS.DKYVKIWDI
Retrocopy DRVTWNHFSPCHFLASTDDGFVYNLDAGSDKPIFTLNAHNDEISGLDLSSQIKGCLVTASVDKYVKIWDI

Parental  LGDRPSLVHSRDMKMGVLFCSSCCPDLPFIYAFGGQKEGLRVWDISTVSSVNEAFGRRERLVLGSARNSS
          LGDRPSLVHSRDMKMGVLFCSSCCPDLPFIYAFGGQKEGL.VWDISTVSSVNEAFGRRER.VL.SARNSS
Retrocopy LGDRPSLVHSRDMKMGVLFCSSCCPDLPFIYAFGGQKEGLWVWDISTVSSVNEAFGRRERHVLKSARNSS

Parental  ISGPFGSRSSDTPM
          ISGPFGSRSSDTPM
Retrocopy ISGPFGSRSSDTPM

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	6.05 RPM	10.08 RPM
SRP007412_brain_prefrontal_cortex	4.28 RPM	7.14 RPM
SRP007412_cerebellum	4.84 RPM	9.30 RPM
SRP007412_heart	1.06 RPM	2.53 RPM
SRP007412_kidney	5.52 RPM	10.33 RPM
SRP007412_liver	1.58 RPM	2.97 RPM
SRP007412_testis	2.26 RPM	4.37 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_687 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_687 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_687 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000031574	1 retrocopy	retro_mmul_687 ,
Mus musculus	ENSMUSG00000001785	2 retrocopies	retro_mmus_1600, retro_mmus_3074,
Otolemur garnettii	ENSOGAG00000011940	2 retrocopies	retro_ogar_2999, retro_ogar_3444,
Rattus norvegicus	ENSRNOG00000005350	1 retrocopy	retro_rnor_646,
Tursiops truncatus	ENSTTRG00000011036	1 retrocopy	retro_ttru_540,