RetrogeneDB ID: retro_mmul_615

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 10:67413627..67414413(+)
• Located in intron of: ENSMMUG00000023622

Retrocopy information

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

Parental gene information

• Parental gene symbol: FBXW4
• Ensembl ID: ENSMMUG00000006753
• Aliases: None
• Description: F-box/WD repeat-containing protein 4 [Source:RefSeq peptide;Acc:NP_001244875]

Sequence

>retro_mmul_615
CGACCTGCTCTGGGAGTCTTTGCTGGGCATGATGAGGACATTTGCCACTTTGTGCTGGCCAGCTTGCATATTGTCAGTGC
AGGAGGAGATGGGAAGATTGGCGTTGGTAAGATTCACAGCACCTTCACTGTCAAGTACTCGGCTCATGGACAGGAGGTGA
ACTATGTGGATTGCAAAGGGGGCATCACTGTGAGTGGCTCCAGGGACGGGATGGCCAAGGTGTGGCCTTTGGCCTCAGGC
CGGCTGGAGCAGTGTTTACACACCATCCAGATTGAAGACTGAGTCTGGTCCATTGCTATCAGCCCATTACTCAGCTCTTT
TGTGACAGGGACGGCTTGTTGCGGGCACTTCTCACCCCTGAGAGTCTGGGACCTCAACAGTGGGCAGCTGATGACATACT
TGGGCAGTGACTTTCTCCCAGGGGCTGGGGTGCTGGATGTCATGTATGAGTCCCCTTTCACACTGCTGTCCTGTGGCTAT
GACACCTACGTTCGCTACTGGGACCTCTGCACCAGTGTCCGGAAAGGTGTCATGGAGTGGGAGGAGCCCCACAGCAGCAC
CCTGTACTGTCTGCAGACAGATGGCAACCACTTGCTGGCCACAGGTTCCTCCTACTACAGTGTTGTACGGCTGTGAGACC
GGTGTCAAAGGGCCTGCGGCTGCCTGCACACCTTCCCGCTGACATCAACCCCCTCCAGCAGCCCTGTGTACTGCCTGCGT
CTCACCACCAAGCATCTCTATGCTGCACTGTCTTATGACCTCCACGTCCTGGATTTTCAAAACCCA

Alignment

ORF - retro_mmul_615 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.93 %
• Parental protein coverage: 63.41 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RRPLGVFAGHDEDVCHFVLANSHIISAGGDGKIGVHKIHSTFTVKYSAHEQEVNCVDCKGGIIVSGSRDR
          R..LGVFAGHDED.CHFVLA..HI.SAGGDGKIGV.KIHSTFTVKYSAH.QEVN.VDCKGGI.VSGSRD.
Retrocopy RPALGVFAGHDEDICHFVLASLHIVSAGGDGKIGVGKIHSTFTVKYSAHGQEVNYVDCKGGITVSGSRDG

Parental  TAKVWPLASGRLGQCLHTIQTEDRVWSIAISPLLSSFVTGTACCGHFSPLRIWDLNSGQLMTHLGSDFPP
          .AKVWPLASGRL.QCLHTIQ.ED.VWSIAISPLLSSFVTGTACCGHFSPLR.WDLNSGQLMT.LGSDF.P
Retrocopy MAKVWPLASGRLEQCLHTIQIED*VWSIAISPLLSSFVTGTACCGHFSPLRVWDLNSGQLMTYLGSDFLP

Parental  GAGVLDVMYESPFTLLSCGYDTYVRYWDLRTSVRKCVMEWEEPHDSTLYCLQTDGNHLLATGSSYYGVVR
          GAGVLDVMYESPFTLLSCGYDTYVRYWDL.TSVRK.VMEWEEPH.STLYCLQTDGNHLLATGSSYY.VVR
Retrocopy GAGVLDVMYESPFTLLSCGYDTYVRYWDLCTSVRKGVMEWEEPHSSTLYCLQTDGNHLLATGSSYYSVVR

Parental  LWDRRQRA--CLHAFPLTSTPLSSPVYCLRLTTKHLYAALSYNLHVLDFQNP
          L.DR.QRA..CLH.FPLTSTP.SSPVYCLRLTTKHLYAALSY.LHVLDFQNP
Retrocopy L*DRCQRACGCLHTFPLTSTPSSSPVYCLRLTTKHLYAALSYDLHVLDFQNP

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	0.22 RPM	16.81 RPM
SRP007412_brain_prefrontal_cortex	0.87 RPM	38.55 RPM
SRP007412_cerebellum	0.52 RPM	19.63 RPM
SRP007412_heart	0.00 RPM	33.45 RPM
SRP007412_kidney	1.06 RPM	23.36 RPM
SRP007412_liver	0.04 RPM	28.06 RPM
SRP007412_testis	0.08 RPM	13.38 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_615 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_615 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_615 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000006753	1 retrocopy	retro_mmul_615 ,
Pongo abelii	ENSPPYG00000002586	1 retrocopy	retro_pabe_1876,