RetrogeneDB ID: retro_mmul_1065

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 14:58855572..58856418(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LPAR1
• Ensembl ID: ENSMMUG00000006906
• Aliases: None
• Description: lysophosphatidic acid receptor 1 [Source:RefSeq peptide;Acc:NP_001247789]

Sequence

>retro_mmul_1065
ATGGCTGCCATCTCTACTTCCATCCCTGTAATTTCACAGCCCCAGTTCACAGCCATGAATGAACCACAGTGCTTCTACAA
CGAATCCATTGCCTTCTTTTATAACCGAAGTGGAAAGCATCTTGCCACAGAATGGAACACAGTCAGCAAGCTGGTGATGG
GACTTGGAATCACTGTTTGTATCTTCATCACGTTGGCCAATCTACTGGTCATGGTGGCAATCTATGTCAACCCCCGTTTC
CATTTTCCTATTTATTACCTAATGGCTAATCTGGCTGCTGCAGACTTCTTTGCGGGGTTGGCCTATTTCTAGCTCATGTT
CCACACAGGACCCAATACTTGGAGACTGACTGTTAGCACATGGCTCCTTCATCAGGGCCTCATTGACACCAGCCTGACGG
CATCTGTGGCCAACTTAATGACTATTGCAATCGAGAGGCACATTACGGTTTTCCGCATGCAGCTCCACACACAGATGAGC
AACCGGCGGGTAGTGGTGGTCATTGTGGTCATCTGGACTACGGCCATCGTTATGGGTGCTCTACCCAGTGTGGGCTGGAA
CTGTATCTGTGATATTGAAAATTGTTCCAACATGGCACCCCTCTACAGTGACTCTTACTTAGTCTTATGGGTCATTTTCA
ACTTGGTGACCTTTGTGGTAATGGTGGTTCTCTATGCTCACATCTTTGGCTCTATTCGCCAGAGGACTATGAGAATGTCT
CAGCATAGTTCTGGACCCTGGCGGAATCGGGATACCATGATGAGTCTTCTGAAGACTGTGGTCATTGTGCTTGGGGCCTT
TATCATCTGCTGGACTCCTGGATTGGCTTTGTTACTTCTAGACGTG

Alignment

ORF - retro_mmul_1065 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.62 %
• Parental protein coverage: 77.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAISTSIPVISQPQFTAMNEPQCFYNESIAFFYNRSGKHLATEWNTVSKLVMGLGITVCIFIMLANLLV
          MAAISTSIPVISQPQFTAMNEPQCFYNESIAFFYNRSGKHLATEWNTVSKLVMGLGITVCIFI.LANLLV
Retrocopy MAAISTSIPVISQPQFTAMNEPQCFYNESIAFFYNRSGKHLATEWNTVSKLVMGLGITVCIFITLANLLV

Parental  MVAIYVNRRFHFPIYYLMANLAAADFFAGLAYFYLMFNTGPNTRRLTVSTWLLRQGLIDTSLTASVANLL
          MVAIYVN.RFHFPIYYLMANLAAADFFAGLAYF.LMF.TGPNT.RLTVSTWLL.QGLIDTSLTASVANL.
Retrocopy MVAIYVNPRFHFPIYYLMANLAAADFFAGLAYF*LMFHTGPNTWRLTVSTWLLHQGLIDTSLTASVANLM

Parental  AIAIERHITVFRMQLHTRMSNRRVVVVIVVIWTMAIVMGAIPSVGWNCICDIENCSNMAPLYSDSYLVFW
          .IAIERHITVFRMQLHT.MSNRRVVVVIVVIWT.AIVMGA.PSVGWNCICDIENCSNMAPLYSDSYLV.W
Retrocopy TIAIERHITVFRMQLHTQMSNRRVVVVIVVIWTTAIVMGALPSVGWNCICDIENCSNMAPLYSDSYLVLW

Parental  AIFNLVTFVVMVVLYAHIFGYVRQRTMRMSRHSSGPRRNRDTMMSLLKTVVIVLGAFIICWTPGLVLLLL
          .IFNLVTFVVMVVLYAHIFG..RQRTMRMS.HSSGP.RNRDTMMSLLKTVVIVLGAFIICWTPGL.LLLL
Retrocopy VIFNLVTFVVMVVLYAHIFGSIRQRTMRMSQHSSGPWRNRDTMMSLLKTVVIVLGAFIICWTPGLALLLL

Parental  DV
          DV
Retrocopy DV

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	9.41 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	7.30 RPM
SRP007412_cerebellum	0.00 RPM	6.26 RPM
SRP007412_heart	0.06 RPM	4.89 RPM
SRP007412_kidney	0.00 RPM	1.29 RPM
SRP007412_liver	0.00 RPM	0.12 RPM
SRP007412_testis	0.00 RPM	1.06 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1065 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1065 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1065 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000006906	1 retrocopy	retro_mmul_1065 ,