RetrogeneDB ID: retro_mmul_1596

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:14879737..14880589(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FBXW11
• Ensembl ID: ENSMMUG00000016008
• Aliases: None
• Description: F-box/WD repeat-containing protein 11 [Source:RefSeq peptide;Acc:NP_001248237]

Sequence

>retro_mmul_1596
AACACTTCAGTTATGGAAGATCAAGATGAAGATGAGTCCCCAAAGAAAAATACTCCTTGGCAGATTAAGTAATGGAACAT
TGTCTGTGATTGTCTCCAGAAGCAGGCCATCAGAAGGAAACTACCAAAAAGAAAAAGACTTGTGTATTCAGTATTTTGAC
CAGTGGTCTGAATCAGATCAGGTGGAATTCGTGGAACATCTTATTTCCCGAATGTGTCATTAGCAGCATGGACGTATTAA
TTCTCACCTGAAGCCCATGTTGCAGCGGGACTTTATTGCTGCTCTACCTGAGCAAGGCTTAGATCACATAGCAGAAAATA
TTCTTTCGTACCTGGATGCCAGGTCTTTGCGTGCAGCAGAGCTGGTATGTAAAGAATGGCAGCGAGTGATCTCAGAATGA
ATGCTTTGGAAGAAGCTGATTGAACGAATGGTACGCACTGACCCCCTGTGGAAAGGACTTTCAGAAAGAAGAGGGTGGGA
TCAGTACCTCTTTAAAAACAGACCCACAGCTAGCCCTCCAAATTCATTTTATGGGTCATTATACCCAAAGATTATCCAGG
ATATAGAGACTATAGAATCCACCTGGCAGTGTGGCCGACACAGCTTGCAGAGGATTCAGTACCGCTCTGAAAATAGTAAA
GGCATCTACGCTTTACAGTACAATGATGAAAAAATTATCAGTGGCCCACAAGATAATTCTATTAAGATTTGGGATAAAAC
CAGCCTGGAATGTTTGAAAGTGTTAACGGACACACAGGCTCTGTCCTCTGTCTGCAGTATGATGAGCGTGTCATTGTAAC
TGGCTCTTCGGAGTTTACGGTGAGAGTGTGGGATGTGAACAGGGGTGAAGTT

Alignment

ORF - retro_mmul_1596 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.21 %
• Parental protein coverage: 55.25 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NTSVMEDQNEDESPKKNTLWQI-SNGTSSVIVSRKRPSEGNYQKEKDLCIKYFDQWSESDQVEFVEHLIS
          NTSVMEDQ.EDESPKKNT.WQI.SNGT.SVIVSR.RPSEGNYQKEKDLCI.YFDQWSESDQVEFVEHLIS
Retrocopy NTSVMEDQDEDESPKKNTPWQI>SNGTLSVIVSRSRPSEGNYQKEKDLCIQYFDQWSESDQVEFVEHLIS

Parental  RMCHYQHGHINSYLKPMLQRDFITALPEQGLDHIAENILSYLDARSLCAAELVCKEWQRVISEGMLWKKL
          RMCH.QHG.INS.LKPMLQRDFI.ALPEQGLDHIAENILSYLDARSL.AAELVCKEWQRVISE.MLWKKL
Retrocopy RMCH*QHGRINSHLKPMLQRDFIAALPEQGLDHIAENILSYLDARSLRAAELVCKEWQRVISE*MLWKKL

Parental  IERMVRTDPLWKGLSERRGWDQYLFKNRPTDGPPNSFYRSLYPKIIQDIETIESNWRCGRHNLQRIQCRS
          IERMVRTDPLWKGLSERRGWDQYLFKNRPT..PPNSFY.SLYPKIIQDIETIES.W.CGRH.LQRIQ.RS
Retrocopy IERMVRTDPLWKGLSERRGWDQYLFKNRPTASPPNSFYGSLYPKIIQDIETIESTWQCGRHSLQRIQYRS

Parental  ENSKGVYCLQYDDEKIISGLRDNSIKIWDKTSLECLKVLT-GHTGSVLCLQYDERVIVTGSSDSTVRVWD
          ENSKG.Y.LQY.DEKIISG..DNSIKIWDKTSLECLKVLT.GHTGSVLCLQYDERVIVTGSS..TVRVWD
Retrocopy ENSKGIYALQYNDEKIISGPQDNSIKIWDKTSLECLKVLT<GHTGSVLCLQYDERVIVTGSSEFTVRVWD

Parental  VNTGEV
          VN.GEV
Retrocopy VNRGEV

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	75.19 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	87.58 RPM
SRP007412_cerebellum	0.19 RPM	66.45 RPM
SRP007412_heart	0.00 RPM	22.85 RPM
SRP007412_kidney	0.00 RPM	23.83 RPM
SRP007412_liver	0.12 RPM	12.11 RPM
SRP007412_testis	0.11 RPM	14.25 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1596 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1596 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1596 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1576
Pongo abelii	retro_pabe_1856

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000007880	1 retrocopy	retro_ggor_1576,
Microcebus murinus	ENSMICG00000004512	1 retrocopy	retro_mmur_1457,
Macaca mulatta	ENSMMUG00000016008	1 retrocopy	retro_mmul_1596 ,
Nomascus leucogenys	ENSNLEG00000000338	1 retrocopy	retro_nleu_1445,