RetrogeneDB ID: retro_mmul_2587

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:64394069..64395012(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMMUG00000020211
• Aliases: None
• Description: None

Sequence

>retro_mmul_2587
CCTCAATGCCAGCTCCAAGCTGGGCCGGCGCGCGGGGTCCGCGCGTCCGACATCTGCGAGGCGGCGTCCGGGGACGCGGT
GGCGGTAGCGCCTGCTGCCGTAGAGCCTGCCGAGTTTGATTTCGGAGAAGGTGAGGGCCACCACCTGCAGCACCTCAGTG
ACCGCGAGATGCCGGAAGATTTAGCTTTGGAGTCAAACCATTCTGACCATCCCAGGGCAAGCACAATTTTCCGGCGCAAA
TCTCAAACCGATGTGAGAGAAAAGAGGAAGAGCAATCATTTAAACTGTGTATCTCCAGGGTAGCTTACTAAAAAGTATAG
CTCACGCTCAACCATATTTCTACATGACAGCACAATCAACCAGTCTAATCTTAGAACCACAGTAAAATGTGTGACCCTAG
CAATATATCACCACATAAAGAACCGAGATGCAAATAGATCCCTAGATATTTTTGATGAGAGATCACATCCACTTACACAA
GAAAAGATTCCAGAAGAATAGTTTAAGCATGATCCTGAGCACAAATTTATTTACAGATCTGTTCATACGCCTTTTAGTGC
CGCACAACTAACAGCTGAATGTGCAATAGTAACTTTGGTTTACTTAGAAAAAATTTTAACTTATGCTGAAACCGACATTT
GTCCCACTAACTGGAAAAGGATTGGTCTGGGAGCCATTCTTCTTGCCTCCAAGATTTGGGATGATCAGGCTGTATGGAAT
ATGTACTACTGCCAGATCTTCAAGGACATTACAGTTGAGGACATGAATGAAATGGAAAGGCATTTTTTTTGAGTTTCTTC
AGTTTAATATTAATGTTCCTACCAGTGTTTATGCCAAATACTATTTTGACCTTCGCTCCTTAGCAGATGACAATAACCTT
AATTTTCTGTTCGCTCCTCTTAGCAAAGAAAGAGCACAGAACCTAGAGGCTATTTCTAGGTTG

Alignment

ORF - retro_mmul_2587 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.96 %
• Parental protein coverage: 87.57 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PKLGRRAGSTELYCASDIYEAASGDAVAVAPAAVEPAELDFGEGEGHHLQHISDREMPEDLALESNPSDH
          P.....AG......ASDI.EAASGDAVAVAPAAVEPAE.DFGEGEGHHLQH.SDREMPEDLALESN.SDH
Retrocopy PQCQLQAGPARGVRASDICEAASGDAVAVAPAAVEPAEFDFGEGEGHHLQHLSDREMPEDLALESNHSDH

Parental  PRASTIFLSKSQTDVREKRKSNHLNHVSPGQLTKKYSSCSTIFLDDSTVSQPNLRTTVKCVTLAIYYHIK
          PRASTIF..KSQTDVREKRKSNHLN.VSPG.LTKKYSS.STIFL.DST..Q.NLRTTVKCVTLAIY.HIK
Retrocopy PRASTIFRRKSQTDVREKRKSNHLNCVSPG*LTKKYSSRSTIFLHDSTINQSNLRTTVKCVTLAIYHHIK

Parental  NRDANRSLDIFDERSHPLTREKVPEEYFKHDPEHKFIYRFVRTLFSAAQLTAECAIVTLCVHIQGMVAGL
          NRDANRSLDIFDERSHPLT.EK.PEE.FKHDPEHKFIYR.V.T.FSAAQLTAECAIVTL.V.........
Retrocopy NRDANRSLDIFDERSHPLTQEKIPEE*FKHDPEHKFIYRSVHTPFSAAQLTAECAIVTL-VYLEKILTYA

Parental  GVMQCGTSNTWTKALLISLLSYNCVLSFMSSIQNSYXRIYHFYTVKYLNEMER-HFLELLQFNINVPASV
          ....C.T...W....L...L...............Y..I....TV...NEMER....E.LQFNINVP.SV
Retrocopy ETDICPTN--WKRIGLGAILLASKIWDDQAVWNMYYCQIFKDITVEDMNEMER>XXXEFLQFNINVPTSV

Parental  YAKYYFDLRSLADDNNLNFLFAPLSKERAQNLEAISRL
          YAKYYFDLRSLADDNNLNFLFAPLSKERAQNLEAISRL
Retrocopy YAKYYFDLRSLADDNNLNFLFAPLSKERAQNLEAISRL

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	3.81 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	3.73 RPM
SRP007412_cerebellum	0.00 RPM	1.81 RPM
SRP007412_heart	0.06 RPM	2.18 RPM
SRP007412_kidney	0.00 RPM	5.40 RPM
SRP007412_liver	0.00 RPM	3.44 RPM
SRP007412_testis	0.08 RPM	3.35 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2587 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2587 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2587 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4845
Pan troglodytes	retro_ptro_3228

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002901	1 retrocopy	retro_cjac_569,
Homo sapiens	ENSG00000163249	3 retrocopies	retro_hsap_1629, retro_hsap_1984, retro_hsap_4845,
Macaca mulatta	ENSMMUG00000020211	1 retrocopy	retro_mmul_2587 ,
Mus musculus	ENSMUSG00000070871	1 retrocopy	retro_mmus_3072,
Nomascus leucogenys	ENSNLEG00000007131	3 retrocopies	retro_nleu_1164, retro_nleu_2902, retro_nleu_430,
Pongo abelii	ENSPPYG00000013118	3 retrocopies	retro_pabe_1345, retro_pabe_3766, retro_pabe_76,