RetrogeneDB ID: retro_mmul_1594

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:7407491..7407932(+)
• Located in intron of: ENSMMUG00000008504

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.19283
• Ensembl ID: ENSMMUG00000022602
• Aliases: None
• Description: methyltransferase-like protein 21A [Source:RefSeq peptide;Acc:NP_001181046]

Sequence

>retro_mmul_1594
CAGTCCCAGAGACAACTGGGAATTGCCACGGTGGTTTGGGATGTGGCCATGGTTTTCTCCACATATCTGGAGATGGGAGC
TGTGGTGCTCTTGGGCTGCCTCGCAGTGAAACTGGGTGCTGGCATAGGGCTGATAGGCAGAGTGGCTGCCTTGCTGGGTG
CTCATGTGACTATCACAGATCGAAAAGTAGCATTAGAATTTTGTAAATCGAATGGTCAAGGCAGTTTACCTCCTTGTATC
CAACCCAGAGCTTTTGTTAAGGAGTTGACTTGGGGAAAGAATTTGGGGAGTTTTACTCGTAGAGATTTTGACCTGATACT
TGGAGCCGACATCATATATTTAGAAGAAACATTCACAAATCTTCTTCAAACACTGGACCATCTCTGTTGCAATCATTCCA
TGATTCTTTTAGCTTGCTGAATTCACTATGAACAGAATAAT

Alignment

ORF - retro_mmul_1594 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.83 %
• Parental protein coverage: 67.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QDWRHLGVAAVVWDAAIVLSTYLEMGAVELRGRSAVELGAGTGLVGIVAALLGAHVTITDRKVALEFLKS
          Q..R.LG.A.VVWD.A.V.STYLEMGAV.L.G..AV.LGAG.GL.G.VAALLGAHVTITDRKVALEF.KS
Retrocopy QSQRQLGIATVVWDVAMVFSTYLEMGAVVLLGCLAVKLGAGIGLIGRVAALLGAHVTITDRKVALEFCKS

Parental  NVQANLPPHIQPKTVVKELTWGQNLGSFSPGEFDLILGADIIYLEETFTDLLQTLEHLCSNHSVILLACR
          N.Q..LPP.IQP...VKELTWG.NLGSF....FDLILGADIIYLEETFT.LLQTL.HLC.NHS.ILLAC.
Retrocopy NGQGSLPPCIQPRAFVKELTWGKNLGSFTRRDFDLILGADIIYLEETFTNLLQTLDHLCCNHSMILLAC*

Parental  IRYERDN
          I.YE..N
Retrocopy IHYEQNN

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	0.11 RPM	12.55 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	14.20 RPM
SRP007412_cerebellum	0.19 RPM	5.36 RPM
SRP007412_heart	0.12 RPM	2.94 RPM
SRP007412_kidney	0.00 RPM	4.23 RPM
SRP007412_liver	0.00 RPM	3.01 RPM
SRP007412_testis	0.00 RPM	2.79 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1594 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1594 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1594 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2532
Pan troglodytes	retro_ptro_1475
Pongo abelii	retro_pabe_1863

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000144401	1 retrocopy	retro_hsap_2532,
Macaca mulatta	ENSMMUG00000022602	1 retrocopy	retro_mmul_1594 ,
Nomascus leucogenys	ENSNLEG00000007129	2 retrocopies	retro_nleu_2926, retro_nleu_471,
Pongo abelii	ENSPPYG00000013116	1 retrocopy	retro_pabe_1863,
Pan troglodytes	ENSPTRG00000012852	1 retrocopy	retro_ptro_1475,