RetrogeneDB ID: retro_mmul_1641

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:146682456..146682931(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NSMCE2
• Ensembl ID: ENSMMUG00000003542
• Aliases: None
• Description: None

Sequence

>retro_mmul_1641
ATGCCAGGACTTTCCAATTCAAATTCAGGTTCAACTGGTTTCATCTCCTTCAGTGGTGTAGGGTCTGCTCTCTCCTCCTT
GGAAAAACTTCCAAGCCTGTGTCACCTCTGGTATGGACACAGCTTCTAGTGTTGCTTTGGATCTTGTGGAAAGTCAGACT
GAAGTGAGTAGTGAATATAGTATGGACAAGGCGATGGTTGAATTTGCTACAATGGATCCGCAACTGAACCATTATGTAAA
GGCTGTTCAATCTACAATAAATCATGTAAAATAAGAACGTCCAGAAAAAATACCAGATTTAAAATTATTGGTGGAGAAGA
AATTTTTGGCTTTACAGAACAAGAATTCTGACGTGGACTTTCAAAATAATGACAAATTTTTAGTGTTTAAACAACAGTTG
AAAGAACTAAAGAAGCAATATGGCCTTCAAGCTGACAGAGAGGCTGACGGAACAGAAGGAGTGGATGAAGATATG

Alignment

ORF - retro_mmul_1641 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.19 %
• Parental protein coverage: 64.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPGRSSSNSGSTGFISFSGVESALSSL-KNFQACINSGMDTASSVALDLVGSQTEVSSEYSMDKAMVEFA
          MPG.S.SNSGSTGFISFSGV.SALSSL.KNFQAC..SGMDTASSVALDLV.SQTEVSSEYSMDKAMVEFA
Retrocopy MPGLSNSNSGSTGFISFSGVGSALSSL>KNFQACVTSGMDTASSVALDLVESQTEVSSEYSMDKAMVEFA

Parental  TMDRQLNHYVKAVQSTINHVKEERPEKIPDLKLLVEKKFLALQNKNSDADFQNNEKFVQFKQQLKELKKQ
          TMD.QLNHYVKAVQSTINHVK.ERPEKIPDLKLLVEKKFLALQNKNSD.DFQNN.KF..FKQQLKELKKQ
Retrocopy TMDPQLNHYVKAVQSTINHVK*ERPEKIPDLKLLVEKKFLALQNKNSDVDFQNNDKFLVFKQQLKELKKQ

Parental  YGLQADREADGTEGVDEEM
          YGLQADREADGTEGVDE.M
Retrocopy YGLQADREADGTEGVDEDM

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	5.94 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	6.82 RPM
SRP007412_cerebellum	0.00 RPM	6.20 RPM
SRP007412_heart	0.00 RPM	4.42 RPM
SRP007412_kidney	0.00 RPM	2.93 RPM
SRP007412_liver	0.00 RPM	2.06 RPM
SRP007412_testis	0.00 RPM	9.39 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1641 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1641 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1641 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009394	1 retrocopy	retro_btau_669,
Echinops telfairi	ENSETEG00000019897	1 retrocopy	retro_etel_1348,
Macaca mulatta	ENSMMUG00000003542	1 retrocopy	retro_mmul_1641 ,
Mus musculus	ENSMUSG00000059586	3 retrocopies	retro_mmus_1189, retro_mmus_1190, retro_mmus_3227,
Otolemur garnettii	ENSOGAG00000015798	1 retrocopy	retro_ogar_3039,
Rattus norvegicus	ENSRNOG00000003964	2 retrocopies	retro_rnor_2118, retro_rnor_701,
Tupaia belangeri	ENSTBEG00000005371	1 retrocopy	retro_tbel_3224,