RetrogeneDB ID: retro_mmul_552

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:168060736..168061611(-)
• Located in intron of: ENSMMUG00000003998

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.14478
• Ensembl ID: ENSMMUG00000009587
• Aliases: None
• Description: peptidyl-prolyl cis-trans isomerase FKBP8 [Source:RefSeq peptide;Acc:NP_001247999]

Sequence

>retro_mmul_552
ATGGCATCGTGTGCTGAACCCTCTGAGCCCTCTGCCCCCGCCTCCTGCCAGGGTCCCACTGCTCGAGGACTTCGAGGTGC
TGGATGGGGTCGAGAATGCAGAGGGCAAGGAGGGAGAGGAGGAGGAAGATGACCTTAGAGAGCTGCCACTGCTGGAGGAC
ATGGGACAGCCCCTGGTGGAAGAGACTGAACAGGCCGGGACCTTGGCCCGAGAGTTCCTCACTGCCATGGAGCCTGAGCC
TGCCCCGTCCCCGGCCCCAGAAGAGTGGCCAGACATAACCAGCTGTTGAGGAAGAAGACGCTTGTCCCAGGGCCACCGGA
TTTGAGCTGCTCAGTCAAGGGCCAGGTGGTCACCATGCATTTGCAGACATCACAAGAGAATGGCATGTGGGTGCAGGAGG
AGCCGGAGCTAGTGTTCACCCTGAGCGTCTGTGAGGTCATCCAGGCCCTGGATCTCAGTGTCTAACTCATGGACGTGGGG
GAGGCAGCCATGGTCACTGCTGACTGCATGTACTGCTACAGCCCCCAGGACAGGAGCCCATACATCCCCCGCACGCGGCC
CTATGCCTGGAGGTGACCCCGAAGATGGCCGTGGACTGGCCTGACCTGGAGATGCTCATAGGGCAGGAGCGCGTGGCCTT
GGCCAACCGGAAGTGGGAGTGCGGCAGTGCCCACTACCAGTGGGCGGACTTCGTCCTGGCCACCAACTCCTATGACCTTG
CCATCAAGACCGTCACCTCCAGCGCCAAAGTGGACATGACGTTCGAGGAGGAGAAGCAGCTCCTGCAGTTGAGGGTGAGG
TGTCTGAACAACCTGGTGGCCTCACAGGTGAAGCTCGACCACTACTGCGCAGCCCTGTGCTCCTGCAACCTCGTG

Alignment

ORF - retro_mmul_552 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.41 %
• Parental protein coverage: 72.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MASCAEPSEPSAPL-PAGVPPLEDFEVLDGVEDAEGEEEEEEEEEEEDDLSELPPLEDMGQPPVEEAEQP
          MASCAEPSEPSAP..PA.VP.LEDFEVLDGVE.AEG.....E.EEEEDDL.ELP.LEDMGQP.VEE.EQ.
Retrocopy MASCAEPSEPSAPA>PARVPLLEDFEVLDGVENAEGK----EGEEEEDDLRELPLLEDMGQPLVEETEQA

Parental  GALAREFLAAMEPEPAPA-PAPEEWLDILGNGLLRKKTLVPGPPGSSRPVKGQVVTVHLQTSLENGTRVQ
          G.LAREFL.AME..P.PA.P.P........N.LLRKKTLVPGPP..S..VKGQVVT.HLQTS.ENG..VQ
Retrocopy GTLAREFLTAME--PEPA<PVPGPRRVARHNQLLRKKTLVPGPPDLSCSVKGQVVTMHLQTSQENGMWVQ

Parental  EEPELVFTLGDCDVIQALDLSVPLMDVGETAMVTADSKYCYGPQGRSPYIP-PHAALCLEVTLKTAVDGP
          EEPELVFTL..C.VIQALDLSV.LMDVGE.AMVTAD..YCY.PQ.RSPYIP.PHAALCLEVT.K.AVD.P
Retrocopy EEPELVFTLSVCEVIQALDLSV*LMDVGEAAMVTADCMYCYSPQDRSPYIP<PHAALCLEVTPKMAVDWP

Parental  DLEMLTGQERVALANRKRECGNAHYQRADFVLAANSYDLAIKAITSSAKVDMTFEEEAQLLQLKVKCLNN
          DLEML.GQERVALANRK.ECG.AHYQ.ADFVLA.NSYDLAIK..TSSAKVDMTFEEE.QLLQL.V.CLNN
Retrocopy DLEMLIGQERVALANRKWECGSAHYQWADFVLATNSYDLAIKTVTSSAKVDMTFEEEKQLLQLRVRCLNN

Parental  LAASQLKLDHYRAALRSCSLV
          L.ASQ.KLDHY.AAL.SC.LV
Retrocopy LVASQVKLDHYCAALCSCNLV

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	108.46 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	524.61 RPM
SRP007412_cerebellum	0.00 RPM	71.87 RPM
SRP007412_heart	0.18 RPM	63.48 RPM
SRP007412_kidney	0.00 RPM	56.81 RPM
SRP007412_liver	0.00 RPM	221.79 RPM
SRP007412_testis	0.15 RPM	336.83 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_552 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_552 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_552 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000007405	1 retrocopy	retro_mmul_1969,
Macaca mulatta	ENSMMUG00000009587	1 retrocopy	retro_mmul_552 ,
Macaca mulatta	ENSMMUG00000012341	1 retrocopy	retro_mmul_2171,
Macaca mulatta	ENSMMUG00000015996	1 retrocopy	retro_mmul_10,
Macaca mulatta	ENSMMUG00000016512	2 retrocopies	retro_mmul_2094, retro_mmul_735,