RetrogeneDB ID: retro_mmul_2068

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:20912292..20912691(-)
• Located in intron of: ENSMMUG00000030195

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBXN2A
• Ensembl ID: ENSMMUG00000006487
• Aliases: None
• Description: UBX domain protein 2A [Source:HGNC Symbol;Acc:27265]

Sequence

>retro_mmul_2068
GTAAATGTCAGTATAAAATTATGAGAAAATGAATTATCAATCACTAATGACTTCAGACATTATTCTGATGTTGCAAGTTA
GAAATTTCTGAAATCTATTATAAAGGAGATTTACTTTTTAAAACTATGGAGAGTTTTTGATAAAGAGAATGTGGTTGCTA
AAGTTGAAGATAAAAAATAATGAAGTGTGTTTGTCTATGAAGCCTGTATTCCAGTCTTTCTCAGGATGAAGTCACAGACT
GGGAAATGCCACATGGGAAATATCTTTAAAGCAAAAAGTAGTGAAGATGAGAATAAAAATACTCTGTTTGTTGTCCCACT
AAGCAATCTGGAACCCATCATTACATTACAGATCTGGCTAACCAACTGGAAAGGGATCATTCAGAAAGCAAATATTTCC

Alignment

ORF - retro_mmul_2068 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.26 %
• Parental protein coverage: 66.17 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VDVNIKLWKNGFTVNDDFRSYSDGASQQFLNSIKKGELPSELQGIFDKEEVDVKVEDKK-NEICLSTKPV
          V.V.IKL..N......DFR.YSD.AS..FL.SI.K......L...FDKE.V..KVEDKK.NE.CLS.KPV
Retrocopy VNVSIKL*ENELSITNDFRHYSDVAS*KFLKSIIKEIYFLKLWRVFDKENVVAKVEDKK>NEVCLSMKPV

Parental  FQPFSGQGHRLGSATPKI-VSKAKNIEVENKNNLSAVPLNNLEPITNIQIWLANGKRIVQKFNIS
          FQ.FSG..HRLG.AT..I...KAK..E.ENKN.L..VPL.NLEPI...QIWL.N.K.I.QK.NIS
Retrocopy FQSFSG*SHRLGNATWEI<IFKAKSSEDENKNTLFVVPLSNLEPIITLQIWLTNWKGIIQKANIS

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	1.79 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	0.95 RPM
SRP007412_cerebellum	0.00 RPM	2.97 RPM
SRP007412_heart	0.00 RPM	1.88 RPM
SRP007412_kidney	0.00 RPM	1.29 RPM
SRP007412_liver	0.00 RPM	0.51 RPM
SRP007412_testis	0.00 RPM	2.22 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2068 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2068 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2068 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001640	5 retrocopies	retro_chof_1096, retro_chof_1171, retro_chof_2641, retro_chof_961, retro_chof_964,
Callithrix jacchus	ENSCJAG00000007665	1 retrocopy	retro_cjac_2085,
Equus caballus	ENSECAG00000020144	1 retrocopy	retro_ecab_569,
Echinops telfairi	ENSETEG00000002623	1 retrocopy	retro_etel_1116,
Homo sapiens	ENSG00000173960	1 retrocopy	retro_hsap_2025,
Gorilla gorilla	ENSGGOG00000002445	1 retrocopy	retro_ggor_1463,
Myotis lucifugus	ENSMLUG00000015640	1 retrocopy	retro_mluc_1195,
Macaca mulatta	ENSMMUG00000006487	1 retrocopy	retro_mmul_2068 ,
Macaca mulatta	ENSMMUG00000015994	1 retrocopy	retro_mmul_2337,
Mus musculus	ENSMUSG00000020634	1 retrocopy	retro_mmus_1007,
Nomascus leucogenys	ENSNLEG00000000751	1 retrocopy	retro_nleu_2612,
Oryctolagus cuniculus	ENSOCUG00000008783	1 retrocopy	retro_ocun_207,
Otolemur garnettii	ENSOGAG00000000025	1 retrocopy	retro_ogar_1909,
Procavia capensis	ENSPCAG00000011502	4 retrocopies	retro_pcap_169, retro_pcap_255, retro_pcap_271, retro_pcap_323,
Pan troglodytes	ENSPTRG00000011705	1 retrocopy	retro_ptro_1347,
Rattus norvegicus	ENSRNOG00000004950	2 retrocopies	retro_rnor_1746, retro_rnor_2966,
Sorex araneus	ENSSARG00000010108	1 retrocopy	retro_sara_272,
Sus scrofa	ENSSSCG00000026283	1 retrocopy	retro_sscr_537,
Tupaia belangeri	ENSTBEG00000012158	1 retrocopy	retro_tbel_3887,