RetrogeneDB ID: retro_mmul_845

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 11:16371507..16372170(-)
• Located in intron of: ENSMMUG00000013309

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.18378
• Ensembl ID: ENSMMUG00000000040
• Aliases: None
• Description: egl nine homolog 3 [Source:RefSeq peptide;Acc:NP_001181354]

Sequence

>retro_mmul_845
CACATCATGCCCTGTCTGCAGGAGGTCAGTTCCTGCAACCTGCAAATCTTCCTGGGCAAGGAGGTGGTGGGCAACTGCAT
CCAGGAGCACATTAAGCAGCTGCATTGCAAGGGGGCCCTGCGGGACAGCCAGCTGGCTGGGCTGTGTGCAGCGTCTCCAA
AAGGTGAACTGTGGGTGACCAGTTCATGTAGACTGGGAGCAACAAGAAGGGCTGCAAGGCCATTAGCTTCCTCCTGTCCC
TCATTGACAGGCTGGTCCTCTAGTGCAGGAGCCACTGGGAAAATACTATGTGAAGGAGAGGTCCAAGGCAATGGTGGCTT
GCTATCTTAAAAATGGAATAGGTTACATTCATCATGCGGACAACCCCAACAACAATGGCTGCTGCATCGCCTACATCCAC
TGTCTGAACAAGAATTGGGATACCAGGCTACACGGTAGGATCCTATGGCTATTTCCAGAGGAGAAATCGCTCATGGCAGA
TGTGGAGGCCATTTGTGAAAAACTCCTGTTCTGGTTAGACTGCAGGAACCCACACGAGGTGCTGTCTTCCTATGAGACCA
GATGTGCTATACTGTTTGGTACTTTGATAATGAAGAAAGGACAGAAGCCAAAAAGAAATTCAGGAATTTAATTAGGAAAC
ATCTGCCCTCACTGAAGGCTGAC

Alignment

ORF - retro_mmul_845 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.04 %
• Parental protein coverage: 92.89 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YIVPCLHEVGFCYLDNFLG-EVVGDCVLERVKQLHCTGALRDGQLAGPRAG-VSKRHLRGDQITWIGGNE
          .I.PCL.EV..C.L..FLG.EVVG.C..E..KQLHC.GALRD.QLAG..A..VSKR...GDQ....G.N.
Retrocopy HIMPCLQEVSSCNLQIFLGKEVVGNCIQEHIKQLHCKGALRDSQLAGLCAA<VSKR*TVGDQFM*TGSNK

Parental  EGCEAISFLLSLIDRLVLYCGSR-LGNYYVKERSKAMVACYPGNGTGYVRHVDNPNGDGRCITCIYYLNK
          .GC.AISFLLSLIDRLVL.C.S..LG.YYVKERSKAMVACY..NG.GY..H.DNPN..G.CI..I..LNK
Retrocopy KGCKAISFLLSLIDRLVL*CRSH<LGKYYVKERSKAMVACYLKNGIGYIHHADNPNNNGCCIAYIHCLNK

Parental  NWDAKLHGGILRIFPEGKSFIADVEPIFDRLLFFWSDRRNPHEVQPSYATRYAM-TVWYFDAEERAEAKK
          NWD..LHG.IL..FPE.KS..ADVE.I...LL.FW.D.RNPHEV..SY.TR.A..TVWYFD.EER.EAKK
Retrocopy NWDTRLHGRILWLFPEEKSLMADVEAICEKLL-FWLDCRNPHEVLSSYETRCAI<TVWYFDNEERTEAKK

Parental  KFRNLTRKTESALTED
          KFRNL.RK....L..D
Retrocopy KFRNLIRKHLPSLKAD

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	17.37 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	13.57 RPM
SRP007412_cerebellum	0.00 RPM	16.34 RPM
SRP007412_heart	0.06 RPM	95.57 RPM
SRP007412_kidney	0.00 RPM	25.35 RPM
SRP007412_liver	0.04 RPM	4.12 RPM
SRP007412_testis	0.00 RPM	1.58 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_845 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_845 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_845 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1088
Pan troglodytes	retro_ptro_740
Pongo abelii	retro_pabe_906

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000129521	1 retrocopy	retro_hsap_1088,
Macaca mulatta	ENSMMUG00000000040	1 retrocopy	retro_mmul_845 ,
Oryctolagus cuniculus	ENSOCUG00000008560	1 retrocopy	retro_ocun_1902,
Pongo abelii	ENSPPYG00000005732	1 retrocopy	retro_pabe_906,
Pan troglodytes	ENSPTRG00000006250	1 retrocopy	retro_ptro_740,