RetrogeneDB ID: retro_mmul_1399

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 19:43450305..43450847(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000021443
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.5045
• Ensembl ID: ENSMMUG00000004530
• Aliases: None
• Description: transmembrane protein 47 [Source:RefSeq peptide;Acc:NP_001253484]

Sequence

>retro_mmul_1399
ATGGCTTCGGTGGGCAGCGGCATGGAGGAGGTGCGCCTGTCGGTACTGACCCCCTTGAAGCTGGTTGGGCTGGTGTGCAT
CTTTCTGGCGCTGTGTCTGGACCTGGGGGCGGTGCTGAGCCCGGCTTGGGTCACAGCTGACCACCAGTACTACCGTGTGT
GGGAGTCCTGCCGGAAACCCGCCAGCTTGGACATCTGGCACTGCGAGTCCATGCTCAGCAGCGATTGGCAGATTGCTACT
TTGGCTTTACTCCTGGGCGGTGCTGCCATCATTCTCATTGCATTCCTGGTGGGTTTGATTTCTATCTGCGTGGGGTCTTG
AAGGCGCGTTTCTATAGACCTGTTGCGGTCATGCTTTTTGCAGCAGTTGTTTTACAGGTTTGCAGCCTGGTCCTTTACCC
AATCAAGTTCATTGAAACTGTGAGCTTGAAAATGTACCATGAGTTCAACTGGGGTTATGGCCTGGCCTGGGGTGCAACTA
TATTTTCGTTTGGGGGTGCCATCCTTTATTGCCTGAACCCTAAGAACTATGAAGACTACTAC

Alignment

ORF - retro_mmul_1399 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.08 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASAGSGMEEVRVSVLTPLKLVGLVCIFLALCLDLGAVLSPAWVTADHQYYLSLWESCRKPASLDIWHCE
          MAS.GSGMEEVR.SVLTPLKLVGLVCIFLALCLDLGAVLSPAWVTADHQYY...WESCRKPASLDIWHCE
Retrocopy MASVGSGMEEVRLSVLTPLKLVGLVCIFLALCLDLGAVLSPAWVTADHQYY-RVWESCRKPASLDIWHCE

Parental  STLSSDWQIATLALLLGGAAIILIAFLVGLISICVGS-RR-RFYRPVAVMLFAAVVLQVCSLVLYPIKFI
          S.LSSDWQIATLALLLGGAAIILIAFLVGLISICVGS.RR.RFYRPVAVMLFAAVVLQVCSLVLYPIKFI
Retrocopy SMLSSDWQIATLALLLGGAAIILIAFLVGLISICVGS*RR<RFYRPVAVMLFAAVVLQVCSLVLYPIKFI

Parental  ETVSLKIYHEFNWGYGLAWGATIFSFGGAILYCLNPKNYEDYY
          ETVSLK.YHEFNWGYGLAWGATIFSFGGAILYCLNPKNYEDYY
Retrocopy ETVSLKMYHEFNWGYGLAWGATIFSFGGAILYCLNPKNYEDYY

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	38.55 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	41.33 RPM
SRP007412_cerebellum	0.26 RPM	21.50 RPM
SRP007412_heart	0.06 RPM	29.85 RPM
SRP007412_kidney	0.00 RPM	17.96 RPM
SRP007412_liver	0.04 RPM	17.30 RPM
SRP007412_testis	0.08 RPM	1.55 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1399 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1399 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1399 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006509	1 retrocopy	retro_dnov_1659,
Macaca mulatta	ENSMMUG00000000997	1 retrocopy	retro_mmul_2156,
Macaca mulatta	ENSMMUG00000004530	1 retrocopy	retro_mmul_1399 ,
Ictidomys tridecemlineatus	ENSSTOG00000019440	1 retrocopy	retro_itri_1673,