RetrogeneDB ID: retro_mmul_2496

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:56076381..56076999(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.4256
• Ensembl ID: ENSMMUG00000006163
• Aliases: None
• Description: Malate dehydrogenase [Source:UniProtKB/TrEMBL;Acc:F7HSV9]

Sequence

>retro_mmul_2496
ATGATTAGTGTCCTGGATGGTGTCCTAATGAAACTGCAAGACTGTGCGCTTTCCCTTTGGAAAGATGTCATTGCAGCTGA
CAAAGAAGAGCTGGTCTTCAAAGACTTGGATGTGACAATTCTTGTGGTCTCCGTGCCAAGAAGGGAAGGCATGGAGAAGA
AAGATTTACTTAAAGCACATGTGAATATCTTCAAATGCCAAGATGCAGCCTTGAAGAAATATACCAAGATGTTAGTTAAA
TTTATCATAATGGAAAATCCAGTTAATACCAACTGCCTGATTTTCTTCATGTCAGCTCCATCTATCCCCAAGGAGAACTT
CAGTTGATTGATTCATTTGAATCACAACCGAGATGAAGCTCAAATCACTCTTAAACTTTGTGTGACTGCTGAAAATGTAA
AGAATGTCATTATCTAGAGGGACAATTCCTCAATTCAGTATCCATATGTCAACCATGCCAAGGAGAAATTGCAAGAAAAG
GAAATTAGTGTTTATGAAGCTCTGATAGATGACAGTTGGCTCAGGGAGAATTCATCATGCCTGCAGCAGCATGATGCTGC
TGTCATCAAAGCTTGAATACTATCCAGTGCAATGTCTACCATGAAAGCGATCTCTGAC

Alignment

ORF - retro_mmul_2496 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.08 %
• Parental protein coverage: 71.63 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMGVLDGVLMELQDCALPLLKDVIATDKEEVAFKDLDVAILVGSMPRREGMERKDLLKANVKIFKSQGAA
          M..VLDGVLM.LQDCAL.L.KDVIA.DKEE..FKDLDV.ILV.S.PRREGME.KDLLKA.V.IFK.Q.AA
Retrocopy MISVLDGVLMKLQDCALSLWKDVIAADKEELVFKDLDVTILVVSVPRREGMEKKDLLKAHVNIFKCQDAA

Parental  LDKYAKKSVKVIVVGNPANTNCLTASKSAPSIPKENFSCLTRLDHNRAKAQIALKLGVTANDVKNVIIWG
          L.KY.K..VK.I...NP.NTNCL....SAPSIPKENFS.L..L.HNR..AQI.LKL.VTA..VKNVII..
Retrocopy LKKYTKMLVKFIIMENPVNTNCLIFFMSAPSIPKENFS*LIHLNHNRDEAQITLKLCVTAENVKNVII*R

Parental  NHSSTQYPDVNHAKVKLQGKEVGVYEALKDDSWLKGEFVTTVQQRGAAVIKARKLSSAMSAAKAICD
          ..SS.QYP.VNHAK.KLQ.KE..VYEAL.DDSWL..E.....QQ..AAVIKA..LSSAMS..KAI.D
Retrocopy DNSSIQYPYVNHAKEKLQEKEISVYEALIDDSWLR-ENSSCLQQHDAAVIKA*ILSSAMSTMKAISD

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	405.62 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	348.18 RPM
SRP007412_cerebellum	0.06 RPM	267.92 RPM
SRP007412_heart	0.06 RPM	415.32 RPM
SRP007412_kidney	0.00 RPM	289.78 RPM
SRP007412_liver	0.00 RPM	90.37 RPM
SRP007412_testis	0.00 RPM	20.09 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2496 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2496 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2496 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019295	1 retrocopy	retro_btau_466,
Choloepus hoffmanni	ENSCHOG00000007281	5 retrocopies	retro_chof_1260, retro_chof_1513, retro_chof_1892, retro_chof_2001, retro_chof_90,
Callithrix jacchus	ENSCJAG00000007018	4 retrocopies	retro_cjac_1848, retro_cjac_2407, retro_cjac_2418, retro_cjac_282,
Dasypus novemcinctus	ENSDNOG00000013329	2 retrocopies	retro_dnov_109, retro_dnov_2562,
Homo sapiens	ENSG00000014641	1 retrocopy	retro_hsap_3426,
Gorilla gorilla	ENSGGOG00000007085	1 retrocopy	retro_ggor_2316,
Loxodonta africana	ENSLAFG00000016504	2 retrocopies	retro_lafr_1134, retro_lafr_972,
Macaca mulatta	ENSMMUG00000006163	2 retrocopies	retro_mmul_1750, retro_mmul_2496 ,
Nomascus leucogenys	ENSNLEG00000009823	1 retrocopy	retro_nleu_1363,
Otolemur garnettii	ENSOGAG00000014487	1 retrocopy	retro_ogar_741,
Pongo abelii	ENSPPYG00000012373	1 retrocopy	retro_pabe_2839,
Pan troglodytes	ENSPTRG00000011974	1 retrocopy	retro_ptro_2326,
Sorex araneus	ENSSARG00000007690	1 retrocopy	retro_sara_361,
Sus scrofa	ENSSSCG00000025751	1 retrocopy	retro_sscr_779,
Tarsius syrichta	ENSTSYG00000001215	2 retrocopies	retro_tsyr_1790, retro_tsyr_190,