RetrogeneDB ID: retro_mmul_86

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:66191669..66191960(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000032435
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SEC61B
• Ensembl ID: ENSMMUG00000010661
• Aliases: None
• Description: protein transport protein Sec61 subunit beta [Source:RefSeq peptide;Acc:NP_001253867]

Sequence

>retro_mmul_86
ATGCCTGGTCCGACCCCCAGTGGTACTAACGTGGGATCCTCAGGGCTCTCTCCCAGCAAAGCCGTGGCCGCCCGGGCGGC
GGGATCCACTGTCCGGCAGAGGAAAAATGCCAGCTGTGGGACAAGGAGTGCAGGCCGCACGACCTCAGCAGGCACCGGGG
GTATGTGGCGATTCTACACAGAAGATTCACCTGGGCTCAAAGTTGGCCCTGTTCCAGTATTGGTTATGAGTCTTCTGTTC
ATCGCTTCTGTATTTATGTTGCACATTTGGGGCAAGTACACTCGTTCGTAG

Alignment

ORF - retro_mmul_86 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.96 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPGPTPSGTNVGSSGRSPSKAVAARAAGSTVRQRKNASCGTRSAGRTTSAGTGGMWRFYTEDSPGLKVGP
          MPGPTPSGTNVGSSG.SPSKAVAARAAGSTVRQRKNASCGTRSAGRTTSAGTGGMWRFYTEDSPGLKVGP
Retrocopy MPGPTPSGTNVGSSGLSPSKAVAARAAGSTVRQRKNASCGTRSAGRTTSAGTGGMWRFYTEDSPGLKVGP

Parental  VPVLVMSLLFIASVFMLHIWGKYTRS
          VPVLVMSLLFIASVFMLHIWGKYTRS
Retrocopy VPVLVMSLLFIASVFMLHIWGKYTRS

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	2.69 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	11.34 RPM
SRP007412_cerebellum	0.06 RPM	2.07 RPM
SRP007412_heart	0.00 RPM	3.77 RPM
SRP007412_kidney	0.00 RPM	7.28 RPM
SRP007412_liver	0.04 RPM	28.03 RPM
SRP007412_testis	0.04 RPM	7.92 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_86 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_86 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_86 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002457	3 retrocopies	retro_btau_1053, retro_btau_360, retro_btau_791,
Callithrix jacchus	ENSCJAG00000011279	1 retrocopy	retro_cjac_503,
Equus caballus	ENSECAG00000026930	1 retrocopy	retro_ecab_711,
Echinops telfairi	ENSETEG00000005293	4 retrocopies	retro_etel_1777, retro_etel_1889, retro_etel_483, retro_etel_695,
Homo sapiens	ENSG00000106803	1 retrocopy	retro_hsap_871,
Gorilla gorilla	ENSGGOG00000004205	1 retrocopy	retro_ggor_708,
Macropus eugenii	ENSMEUG00000000321	1 retrocopy	retro_meug_1921,
Microcebus murinus	ENSMICG00000011121	4 retrocopies	retro_mmur_1037, retro_mmur_1631, retro_mmur_435, retro_mmur_543,
Myotis lucifugus	ENSMLUG00000001097	1 retrocopy	retro_mluc_2170,
Macaca mulatta	ENSMMUG00000010661	1 retrocopy	retro_mmul_86 ,
Mus musculus	ENSMUSG00000053317	2 retrocopies	retro_mmus_1377, retro_mmus_2679,
Nomascus leucogenys	ENSNLEG00000017055	1 retrocopy	retro_nleu_2844,
Otolemur garnettii	ENSOGAG00000004168	3 retrocopies	retro_ogar_1132, retro_ogar_2671, retro_ogar_823,
Pongo abelii	ENSPPYG00000019441	1 retrocopy	retro_pabe_680,
Pan troglodytes	ENSPTRG00000021184	1 retrocopy	retro_ptro_606,
Rattus norvegicus	ENSRNOG00000006345	1 retrocopy	retro_rnor_1589,