RetrogeneDB ID: retro_mmul_2627

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:110376871..110377425(-)
• Located in intron of: None

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_2627
AAACCATAGCCAAAATCTAAAAAAAACTTCTAGCAAAGGCAGTAAAAAGGAACGGAACAGTTCTGGAATGGCAAGGAAGG
CTAAGCGAACCAAATGTCCTGAAATTCTGTCAGATGAATCTAATAGTGATGAAGATGAAAAGAAAAACAAGGAAGAGTCT
TCAGATGATGAAGATAAAGAAAGTGAAGAGGAGCCACCAAAAAAGATAGCCAAGAGAAAAACCTAAACAGAAAGCTACTT
CTAAAAGTAAAAAATCTGTGAAAAGTGCCAATGTTAAGAAAGCAGATAGCAGCACCACCAAGAAGAATCAAAACAGTTCC
AAAAAAGAAAGCGAGTCTGAGGATAGTTCAGATGATGAACCTTTAATTAAAAAGTTGAAGAAACCCCCTACAGATGAAGA
ATTAAAGGAAACAATAAAGAAATTACCGGCCAGTGCTAACTTGGAAGAAGTCACAATGAAACAGATTTGCAAAAAGGTCT
ATGAAAATTATCCTATTTATGATTTAACTGAAAGAAAATATTTCATAAAAACAACTGTAAAAGAGCTAATTTCT

Alignment

ORF - retro_mmul_2627 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.01 %
• Parental protein coverage: 94.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QPLPKSKKT-SSKGSKKERNSSGMARKAKRTKCPEILSDESSSDEDEKKNKEESSDDDDKESEEEQPP-K
          .P.PKS....SSKGSKKERNSSGMARKAKRTKCPEILSDES.SDEDEKKNKEESSDD.DKESEEE.PP.K
Retrocopy KP*PKSXXX>SSKGSKKERNSSGMARKAKRTKCPEILSDESNSDEDEKKNKEESSDDEDKESEEE-PP<K

Parental  KTAK-REKPKQKATSKSKKSVKSANVKKADSSTTKKNQNSSKKESESEDSSDDEPLIKKLKKPPTDEELK
          K....REKPKQKATSKSKKSVKSANVKKADSSTTKKNQNSSKKESESEDSSDDEPLIKKLKKPPTDEELK
Retrocopy KDSQ<REKPKQKATSKSKKSVKSANVKKADSSTTKKNQNSSKKESESEDSSDDEPLIKKLKKPPTDEELK

Parental  ETIKKLLASANLEEVTMKQICKKVYENYPTYDLTERKDFIKTTVKELIS
          ETIKKL.ASANLEEVTMKQICKKVYENYP.YDLTERK.FIKTTVKELIS
Retrocopy ETIKKLPASANLEEVTMKQICKKVYENYPIYDLTERKYFIKTTVKELIS

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	0.32 RPM	8.39 RPM
SRP007412_heart	0.06 RPM	4.24 RPM
SRP007412_kidney	0.00 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_2627 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2627 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2627 has 0 orthologous retrocopies within eutheria group .

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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,