RetrogeneDB ID: retro_mmul_749

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1099214792487:1681..2707(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PEX12
• Ensembl ID: ENSMMUG00000006047
• Aliases: None
• Description: None

Sequence

>retro_mmul_749
GAGCAGCCATCCATCTTTGTGGTGGTAGCACAGGACAGTTTAACGACAGCAGTGAGATCTGCTCTTCAGCATGTGGTCAA
GGTTCTTGCAGAATCACATCCCACCCACTATAGCTTCTTGTGGAGGTGGTTTGATGAAATCTTTACTCTGCTACATCTCC
GGCTCCAACAGTATAACTGTCTAGAACCAGTGCCTCATTTTCTGAAAACTTTTGTGGCTTAAAGAGAATCATAATGGGGG
ACACTCACAAGTCTCAGAGATTGGCTAGCACTGGTCTCCTAAGGAAGCAGCTTTGGAAATCAATTATGCTCCTGGTTCTT
CTTTTCTATCTGAAAATGAAGCTGGAGAAGCTGGCTTCTAGCCGAGAGAAGAGGATGAATATTCTATTCATCCCCCTTCT
TCCAACTGGAAACCACTTTACAGACCCTTCCTGGCAACCTACCCATTTGTTAACATGGCCTGGGCAGGAGGGTTTCTTGT
ACAACTTCGGTACATCCTAGGAAAATCTCAGCATCACTCACCACTGCTGAGACTGGCTGGAGTTCAGCTAGGTCGACTGA
CAGTTCAGGATATACAAGCTCTGGAGCATAGACCAGCTGAAGCCAGCATGATATAGCAACCAGCCAGGAGTGTTAGTGAG
AAGATAAAGTCAGCTCTGAAGAAAGCTGTGAGGAGTGTTGCCTTATCCCTGTCTACTGGCCTTTCTGTCAGTGTATTCTT
CTTACAGTTCCTTGACTGGTGGTACTCATCTGAAAACCAATAAACCATCAATCATTGTCTGCCTCGCCTACTCCACCACC
ACCTGTCCACCTAGACTATAACTCTGATTGTCGCCTCTTACCCAAAATGCAGACTGTATGCCCCCTGTATCGTAAAACCC
AGGTGAACGATACTGTTATTGCTGCTTCTAGCTATGTGTTTTGTTACGGCTGTGTGTTTCATTATGTGAGGAGTCACTAA
GCTTGTCCCATTACAGGTTATCCAACAGAAGTACAACATCTGATTAAATTCTACTCCCCTGAGAAC

Alignment

ORF - retro_mmul_749 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.86 %
• Parental protein coverage: 95.82 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DQPSIFEVVAQDSLMTAVRPALQHVVKVLAESNPTHYGFLWRWFDEIFTLLDLLVQQHY-LSRTSASFSE
          .QPSIF.VVAQDSL.TAVR.ALQHVVKVLAES.PTHY.FLWRWFDEIFTLL.L..QQ...LSRTSASFSE
Retrocopy EQPSIFVVVAQDSLTTAVRSALQHVVKVLAESHPTHYSFLWRWFDEIFTLLHLRLQQYN<LSRTSASFSE

Parental  NFYGLKRIAMGDTHKSQRLASAGLPKKQLWKSIMVLVLLPYLKVKLEKLVSSL-REEDEYSIHPPSSRWK
          NF.GLKRI.MGDTHKSQRLAS.GL..KQLWKSIM.LVLL.YLK.KLEKL.SS..REEDEYSIHPPSS.WK
Retrocopy NFCGLKRIIMGDTHKSQRLASTGLLRKQLWKSIMLLVLLFYLKMKLEKLASSR<REEDEYSIHPPSSNWK

Parental  RFYRAFLAAYPFVNMAWEGWFLVQQLRYILGKAQHHSPLLRLAGVRLGRLTVQDIQALEHKPAKASMMQQ
          ..YR.FLA.YPFVNMAW.G.FLVQ.LRYILGK.QHHSPLLRLAGV.LGRLTVQDIQALEH.PA.ASM..Q
Retrocopy PLYRPFLATYPFVNMAWAGGFLVQ-LRYILGKSQHHSPLLRLAGVQLGRLTVQDIQALEHRPAEASMI*Q

Parental  PARSVSEKIKSALKKAVGGVALSLSTGLSVGVFFLQFLDWWYSSENQETI-KSLTALPTPPPPVHLDYNS
          PARSVSEKIKSALKKAV..VALSLSTGLSV.VFFLQFLDWWYSSENQ.TI..SL.A.PTPPPPVHLDYNS
Retrocopy PARSVSEKIKSALKKAVRSVALSLSTGLSVSVFFLQFLDWWYSSENQ*TI<QSLSASPTPPPPVHLDYNS

Parental  DSPLLPKMKTVCPLCRKTRVNDTVLATSGYVFCYRCVFHYVRSHQACPITGYPTEVQHLIKLYSPEN
          D..LLPKM.TVCPL.RKT.VNDTV.A.S.YVFCY.CVFHYVRSH.ACPITGYPTEVQHLIK.YSPEN
Retrocopy DCRLLPKMQTVCPLYRKTQVNDTVIAASSYVFCYGCVFHYVRSH*ACPITGYPTEVQHLIKFYSPEN

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	9.08 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	9.76 RPM
SRP007412_cerebellum	0.00 RPM	9.23 RPM
SRP007412_heart	0.00 RPM	9.89 RPM
SRP007412_kidney	0.00 RPM	8.22 RPM
SRP007412_liver	0.00 RPM	5.07 RPM
SRP007412_testis	0.08 RPM	29.36 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_749 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_749 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_749 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000003330	1 retrocopy	retro_ggor_957,
Macaca mulatta	ENSMMUG00000006047	1 retrocopy	retro_mmul_749 ,
Monodelphis domestica	ENSMODG00000019129	1 retrocopy	retro_mdom_557,
Nomascus leucogenys	ENSNLEG00000013933	1 retrocopy	retro_nleu_697,
Pan troglodytes	ENSPTRG00000009020	1 retrocopy	retro_ptro_839,