RetrogeneDB ID: retro_mmul_1750

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:16081115..16081931(+)
• 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_1750
GTCCTGAACAGTGTCCTAATGGAACAGCAAGACTGTGCCCTTCCCCTCCCGAAAGATGTCATCCAAACAAATAAAGAAGT
TGCCTTCAAAGACCTGGATGTGGCCATTCTCTTGGACTCTGTGCCAAGAAGGAAAGGTGTAGAGAGGAAAGATTTACTGA
AAATGTAAAAATCTTCAAATGGCAGGGTGCAGCCTTGGAGAAATATGACAAGAAGTTCATTAAGGTTATTGCTATGGGAA
ACCCAGCCAGTATCAACTGCCTGACTGCCTCCAAGTTGGCTCCATCCAGCTTCAAGGAGAACTTCAGTTGCTTGACTTGT
TTGGATCACAACCAAACTCGAGCTCAAATTACTCTTAAACCTGGTGACTGCCGACAGTGCAAAGAATGTTACACATCTGG
GGAAACCATTCCTTGACACAGTATCCAGATGTCAACCAAGCCAAGGTGAAGTTGCAAGGAAAAGAAGTTGTTTATGAAGC
TCTGAAACATGACAGCTGGCCCCAGGGAGAATTCACGACTGTGCAGCAACATGGTCCTGCTGTCCTCAAGGCTTGAAAAC
CATCCAGGGCAATGTCCACTACAAGAGCCGTCTCCAACCACCTCAGAGACATCCGGCTTGGAACCCCATAGGGAGAGTCT
GTGTCCACTGGGGTTGTCTCTGATAGTGACTCCTGTGGTATTCCCAGTCATCGTTCTACTCATTCTCTGTTGTATTCAAG
AGTAAGACCTGGACATTTGTTGAAGCTCTCTCTATTAATGATTCCTCATGTAAGAAGATGGATCTTACTGCAAAGGAACT
GGCAGGGAAGAAAAAG

Alignment

ORF - retro_mmul_1750 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.48 %
• Parental protein coverage: 95.85 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VLDGVLMELQDCALPLLKDVIATDKEEVAFKDLDVAILV-GSMPRREGMERKDLLKANVKIFKSQGAALD
          VL..VLME.QDCALPL.KDVI.T.KE.VAFKDLDVAIL..G.....E...R......NVKIFK.QGAAL.
Retrocopy VLNSVLMEQQDCALPLPKDVIQTNKE-VAFKDLDVAILL<GLCAKKERC-REERFTENVKIFKWQGAALE

Parental  KYAKKSVKVIVVGNPANTNCLTASKSAPSIPKENFSCLTRLDHNRAKAQIA-LKLGVTANDVKNVI-IWG
          KY.KK..KVI..GNPA..NCLTASK.APS..KENFSCLT.LDHN...AQI..L.L.VTA...KNV..IWG
Retrocopy KYDKKFIKVIAMGNPASINCLTASKLAPSSFKENFSCLTCLDHNQTRAQIT>LNL-VTADSAKNVT>IWG

Parental  NHSSTQYPDVNHAKVKLQGKEVGVYEALKDDSWLKGEFVTTVQQRGAAVIKARKLSSAMSAAKAICDHVR
          NHS.TQYPDVN.AKVKLQGKEV.VYEALK.DSW..GEF.TTVQQ.G.AV.KA.K.S.AMS...A...H.R
Retrocopy NHSLTQYPDVNQAKVKLQGKEV-VYEALKHDSWPQGEF-TTVQQHGPAVLKA*KPSRAMSTTRAVSNHLR

Parental  DIWFGTPEGEFVSMGVISDGNSYGVP-DDLLYSFPVVIKNKTWKLVEGLPINDFSREKMDLTAKELTEEK
          DI..GTP.GE.VS.GV.SD..S.G.P.....YSF.VV.K.KTW..VE.L.IND.S..KMDLTAKEL...K
Retrocopy DIRLGTP*GESVSTGVVSDSDSCGIP<QSSFYSFSVVFKSKTWTFVEALSINDSSCKKMDLTAKELAGKK

Parental  E
          .
Retrocopy K

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	0.00 RPM	348.18 RPM
SRP007412_cerebellum	0.00 RPM	267.92 RPM
SRP007412_heart	0.00 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_1750 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1750 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1750 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3426
Pan troglodytes	retro_ptro_2326
Gorilla gorilla	retro_ggor_2316
Pongo abelii	retro_pabe_2839

---

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,