RetrogeneDB ID: retro_mmul_1266

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 16:57445958..57446254(-)
• Located in intron of: ENSMMUG00000010588

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.1618
• Ensembl ID: ENSMMUG00000019763
• Aliases: None
• Description: protein DEK [Source:RefSeq peptide;Acc:NP_001244457]

Sequence

>retro_mmul_1266
GTGAAAAGTGTCAATGTTAAGAAAGCAGATGGCAGCACCACCAAGAAGAATCAAAACAGTTCCAAAAAAGAAAGTGAGTC
TGAGGACAGTTCAGATGATGAACCTTTAATTAAAAAGTTGAAGAAACCCCCTACAGATGAAGAATTAAAGGAAACAATAA
ATTACTGGCCAGTGCTAACTTGGAAGAAGTCACAATGAAACAGATTTGCAAAAAGGTCTATGAAAATTATCCTACTTATG
ATTTAACTGAAAAAAAAGATTTCATATAAACAGCTAATGTAAAAGAGCTAATTTCT

Alignment

ORF - retro_mmul_1266 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.14 %
• Parental protein coverage: 50.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VKSANVKKADSSTTKKNQNSSKKESESEDSSDDEPLIKKLKKPPTDEELKETI-KKLLASANLEEVTMKQ
          VKS.NVKKAD.STTKKNQNSSKKESESEDSSDDEPLIKKLKKPPTDEELKETI.K.L....NLEEVTMKQ
Retrocopy VKSVNVKKADGSTTKKNQNSSKKESESEDSSDDEPLIKKLKKPPTDEELKETI<KLLASA-NLEEVTMKQ

Parental  ICKKVYENYPTYDLTERKDFIKT-TVKELIS
          ICKKVYENYPTYDLT...DFI.T..VKELIS
Retrocopy ICKKVYENYPTYDLTXXXDFI*TANVKELIS

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	4.82 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	4.28 RPM
SRP007412_cerebellum	0.00 RPM	8.39 RPM
SRP007412_heart	0.00 RPM	4.24 RPM
SRP007412_kidney	0.12 RPM	5.99 RPM
SRP007412_liver	0.00 RPM	1.31 RPM
SRP007412_testis	0.00 RPM	1.47 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1266 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1266 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1266 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010184	1 retrocopy	retro_cfam_1362,
Echinops telfairi	ENSETEG00000018188	1 retrocopy	retro_etel_1367,
Loxodonta africana	ENSLAFG00000004470	1 retrocopy	retro_lafr_517,
Macaca mulatta	ENSMMUG00000019763	2 retrocopies	retro_mmul_1266 , retro_mmul_2627,
Oryctolagus cuniculus	ENSOCUG00000003869	4 retrocopies	retro_ocun_1583, retro_ocun_1791, retro_ocun_1851, retro_ocun_1857,
Otolemur garnettii	ENSOGAG00000007750	1 retrocopy	retro_ogar_3258,
Sus scrofa	ENSSSCG00000001075	1 retrocopy	retro_sscr_203,