RetrogeneDB ID: retro_mmul_395

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:95921572..95922034(+)
• Located in intron of: ENSMMUG00000005073

Retrocopy information

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

Parental gene information

• Parental gene symbol: MND1
• Ensembl ID: ENSMMUG00000004937
• Aliases: None
• Description: meiotic nuclear division protein 1 homolog [Source:RefSeq peptide;Acc:NP_001245035]

Sequence

>retro_mmul_395
AAAAAAGTCCTTCAAAGTTTAGTTGATAATGATATGGTTGGTGAGAGAACTGGAACTTCTCATTATTATCAGGCTTTTCC
AAGTAAAATTCTTCATGCAAGGACCTGTAAATTGGAGGTTCTGAAATCTCAGTTGTTTCAGAGAATCCAAAAGCATGCAA
ACTTACAGAAAAGCATCAGAAAAACTAAAACTGGCCAACATGAGATGAAGGAGTGAACCATGCTAGCCAAAGAGCATTCT
TCACTCTGGGATCAAAGGGAACAGCTAAAGACAGAAGTTGAAAAATGCAAATAATGTGACCCGCAAGTTGTTGAAGAAAT
ACATCAGGCAAATAAAGTACTTGTTAACAGATGGACTGATAACATATTTGCAATAAAATCTTGGGCCAAAAGAAAATTTG
GGTTTGAAGAAAATAAAATTGATAAAACTTCTGGAATTCCAGAAGACTTTAAGTACATTGAC

Alignment

ORF - retro_mmul_395 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.32 %
• Parental protein coverage: 77.07 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KEVLQSLVDDGMVDCERIGTSNYYWAFPSKALHARKRKLEVLESQLSEGSQKHASLQKSIEKAKIGRCET
          K.VLQSLVD..MV..ER.GTS.YY.AFPSK.LHAR..KLEVL.SQL....QKHA.LQKSI.K.K.G..E.
Retrocopy KKVLQSLVDNDMVG-ERTGTSHYYQAFPSKILHARTCKLEVLKSQLFQRIQKHANLQKSIRKTKTGQHEM

Parental  EERTRLAKELSSLRDQREQLKAEVEKYKDCDPQVVEEIRQANKVAKEAANRWTDNIFAIKSWAKRKFGFE
          .E.T.LAKE.SSL.DQREQLK.EVEK.K.CDPQVVEEI.QANKV.....NRWTDNIFAIKSWAKRKFGFE
Retrocopy KE*TMLAKEHSSLWDQREQLKTEVEKCK*CDPQVVEEIHQANKV---LVNRWTDNIFAIKSWAKRKFGFE

Parental  ENKIDKTFGIPEDFDYID
          ENKIDKT.GIPEDF.YID
Retrocopy ENKIDKTSGIPEDFKYID

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	0.22 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.19 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.29 RPM
SRP007412_kidney	0.00 RPM	0.23 RPM
SRP007412_liver	0.00 RPM	0.36 RPM
SRP007412_testis	0.04 RPM	11.46 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_395 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_395 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_395 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018446	1 retrocopy	retro_amel_1745,
Callithrix jacchus	ENSCJAG00000001993	5 retrocopies	retro_cjac_1495, retro_cjac_1907, retro_cjac_2624, retro_cjac_2946, retro_cjac_3979,
Dipodomys ordii	ENSDORG00000004514	1 retrocopy	retro_dord_99,
Felis catus	ENSFCAG00000022084	1 retrocopy	retro_fcat_1833,
Macaca mulatta	ENSMMUG00000004937	1 retrocopy	retro_mmul_395 ,
Mus musculus	ENSMUSG00000033752	2 retrocopies	retro_mmus_1172, retro_mmus_3281,
Nomascus leucogenys	ENSNLEG00000005936	1 retrocopy	retro_nleu_998,
Oryctolagus cuniculus	ENSOCUG00000004594	2 retrocopies	retro_ocun_1865, retro_ocun_360,
Ochotona princeps	ENSOPRG00000015738	1 retrocopy	retro_opri_1121,
Sorex araneus	ENSSARG00000011001	1 retrocopy	retro_sara_417,