RetrogeneDB ID: retro_mmul_2418

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 9:96863292..96863624(+)
• Located in intron of: ENSMMUG00000010428

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.4015
• Ensembl ID: ENSMMUG00000007011
• Aliases: None
• Description: sialomucin core protein 24 precursor [Source:RefSeq peptide;Acc:NP_001252672]

Sequence

>retro_mmul_2418
ACTGCTATGGGTCGCAACTCCAAGATAACCCCAGTGCCAGTGACATCCTTCCCATCAGTCACCACTCCAGCACCAGAAAC
CTATGAAGACTGCAACAGCTGTGTTTCCTGTTTTAAAGCACTGTTAATAATACCTGCTTTTAGATAGAATGTAAAGAAGA
TGAGAGCTACTGTTCACATAATTCAACAGTTAGAGACTGTGGTGTGGTGAACAGGACAGACTTCTGTTCTGTGCCAACTG
CCACTCTGGTGCCAATCAATTCCACAGTGACACATAGATCCAGTGTTTCACACTCAGTGAATCTAAGCAGATTTGCTGAG
GCTTTGTATGTT

Alignment

ORF - retro_mmul_2418 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.54 %
• Parental protein coverage: 64.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TSLAPTSNITSAPVTSLPLVTTPAPETCEGRNSCVSCFNASTV-NTTCFWIECK-DESYCSHNSTVSDCQ
          T.....S.IT..PVTS.P.VTTPAPET.E..NSCVSCF.A....NT.CF.IECK.DESYCSHNSTV.DC.
Retrocopy TAMGRNSKITPVPVTSFPSVTTPAPETYEDCNSCVSCFKALLI<NT-CF*IECKEDESYCSHNSTVRDCG

Parental  VGNTTDFCSVPTATLVPTANSTGTTNTTVTPTSQPVRKSTFDAASFI
          V.N.TDFCSVPTATLVP..NST.T....V...S..V..S.F..A...
Retrocopy VVNRTDFCSVPTATLVP-INSTVTHRSSV---SHSVNLSRFAEALYV

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	27.68 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	25.46 RPM
SRP007412_cerebellum	0.00 RPM	33.39 RPM
SRP007412_heart	0.00 RPM	48.82 RPM
SRP007412_kidney	0.00 RPM	146.12 RPM
SRP007412_liver	0.00 RPM	74.73 RPM
SRP007412_testis	0.00 RPM	64.42 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2418 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2418 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2418 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017992	3 retrocopies	retro_btau_477, retro_btau_479, retro_btau_503,
Macaca mulatta	ENSMMUG00000007011	1 retrocopy	retro_mmul_2418 ,
Otolemur garnettii	ENSOGAG00000015500	2 retrocopies	retro_ogar_2245, retro_ogar_3252,
Tursiops truncatus	ENSTTRG00000004181	2 retrocopies	retro_ttru_436, retro_ttru_532,