RetrogeneDB ID: retro_mmul_1300

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 17:66701538..66702289(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX6
• Ensembl ID: ENSMMUG00000018651
• Aliases: None
• Description: None

Sequence

>retro_mmul_1300
GTAGCAAAGGTTAATCATGTCCAGATGATAGTATTGGATGAGCAGGCAGATAAGTTGCTGTCACAGAATTTTGTGCAGAA
AAATGGAGGATATTATTCTCATGCTACCTAAAAACAGGAAGATTTTACTATATTCTGCTACTTTTCCTCTTAGTGTACAG
AAGTTCATGAATTCCCATTTGCAGAAACCCTATGAGATTAACCTAATGGAGGAACTAACTCTAAAGGGAGTAACCCAGTA
CTATGCATGTGTAACGGAGCTCCAAAAAGTACACTGCCTCAATGCACTTTTCTCCAGGCTTCAGATAAACCAGTCGATCA
TTTTCTGTAACTCCTCTCAGCAAGTTGAATTGCTAGCCAAGATTTCTCAACTAGGTTATTCTTGCTTCTATATTCATGCT
AAAACGAGGCAGGAACATCAAAATTGTGTATTTCATGATTTCTGAAATGGCTTATGCCACAATCTTGTTTGCACTGATCT
GTTTACCCGAGGTGTTGATATACAAGCTGTGAATGTGTTAATAAACTTTGATTTCCCAAAGCTGGCAGAGACCTGTCTCC
ATCATATTGGAAGATCAGGTCGCTTGGGTCATCCTGGCTTAGCCATCAACTTGATCACATATGATGGTCGCTTCAACCTG
AAAAGTATTGAGGAGCAGCTGGGAACAGAAATTAAACCTATTCCAAGCAACATTGACAAGAGCCTATGTGTGGCAGAATA
CCACAGTGAGCCTGTGGAAGATGAGAAACCG

Alignment

ORF - retro_mmul_1300 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.08 %
• Parental protein coverage: 51.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VAKVDHVQMIVLDE-ADKLLSQDFVQI-MEDIILTLPKNRQILLYSATFPLSVQKFMNSHLQKPYEINLM
          VAKV.HVQMIVLDE.ADKLLSQ.FVQ..MEDIIL.LPKNR.ILLYSATFPLSVQKFMNSHLQKPYEINLM
Retrocopy VAKVNHVQMIVLDEQADKLLSQNFVQK>MEDIILMLPKNRKILLYSATFPLSVQKFMNSHLQKPYEINLM

Parental  EELTLKGVTQYYAYVTERQKVHCLNTLFSRLQINQSIIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQE
          EELTLKGVTQYYA.VTE.QKVHCLN.LFSRLQINQSIIFCNSSQ.VELLAK.ISQLGYSCFYIHAK.RQE
Retrocopy EELTLKGVTQYYACVTELQKVHCLNALFSRLQINQSIIFCNSSQQVELLAK-ISQLGYSCFYIHAKTRQE

Parental  HRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINFDFPKLAETYLHRIGRSGRFGHLGLAINLITYD
          H.N.VFHDF.NGLC.NLVCTDLFTRG.DIQAVNV.INFDFPKLAET.LH.IGRSGR.GH.GLAINLITYD
Retrocopy HQNCVFHDF*NGLCHNLVCTDLFTRGVDIQAVNVLINFDFPKLAETCLHHIGRSGRLGHPGLAINLITYD

Parental  DRFNLKSIEEQLGTEIKPIPSNIDKSLYVAEYHSEPVEDEKP
          .RFNLKSIEEQLGTEIKPIPSNIDKSL.VAEYHSEPVEDEKP
Retrocopy GRFNLKSIEEQLGTEIKPIPSNIDKSLCVAEYHSEPVEDEKP

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	47.17 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	33.40 RPM
SRP007412_cerebellum	0.00 RPM	56.31 RPM
SRP007412_heart	0.00 RPM	14.54 RPM
SRP007412_kidney	0.00 RPM	23.71 RPM
SRP007412_liver	0.00 RPM	8.15 RPM
SRP007412_testis	0.00 RPM	27.21 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1300 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1300 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1300 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1224
Pan troglodytes	retro_ptro_838
Pongo abelii	retro_pabe_1018
Callithrix jacchus	retro_cjac_379

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012442	1 retrocopy	retro_cfam_1347,
Callithrix jacchus	ENSCJAG00000013591	3 retrocopies	retro_cjac_1427, retro_cjac_1924, retro_cjac_379,
Gorilla gorilla	ENSGGOG00000016751	1 retrocopy	retro_ggor_955,
Macaca mulatta	ENSMMUG00000018651	2 retrocopies	retro_mmul_1300 , retro_mmul_1826,
Mus musculus	ENSMUSG00000032097	1 retrocopy	retro_mmus_1896,
Nomascus leucogenys	ENSNLEG00000007372	1 retrocopy	retro_nleu_695,
Otolemur garnettii	ENSOGAG00000007978	1 retrocopy	retro_ogar_2861,
Pongo abelii	ENSPPYG00000003942	2 retrocopies	retro_pabe_1018, retro_pabe_2941,
Pan troglodytes	ENSPTRG00000004353	2 retrocopies	retro_ptro_2424, retro_ptro_838,
Rattus norvegicus	ENSRNOG00000012453	4 retrocopies	retro_rnor_2546, retro_rnor_2613, retro_rnor_900, retro_rnor_901,