RetrogeneDB ID: retro_mmul_487

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:46772227..46773263(-)
• Located in intron of: ENSMMUG00000015555

Retrocopy information

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

Parental gene information

• Parental gene symbol: SHMT1
• Ensembl ID: ENSMMUG00000013535
• Aliases: None
• Description: serine hydroxymethyltransferase, cytosolic [Source:RefSeq peptide;Acc:NP_001244360]

Sequence

>retro_mmul_487
CTGGGCCTGGACCTGCCAGATGGGGGCCACCTGACCCACGGGTTCATGACAGACAAGAAGAAAATCTCTGCCACATCCAT
CTTCTTTGAATCTATGCCCTATAAGGTGAACCCAGACACTGGCTACATCAACTATGGCCAGCTGGAGGAGAATGCCCGCC
TTTTCCACCTGAAGCTGATCACTGCAGGAACCAGCTGCTGCTCCTAAAACCTGGACTATGCCCGCCTGCGGAAAGACTGT
AGATGAGAATGGAGTGTATCTCATGGTGGACATGGCACATATCAGCAGGCTGGTGGCAGCTGGTGTGGTGCCCTCCCCAT
TTAAACACTGCCACGTGCTGACCACCACCACTCACAAGAACCTGAGAGGCTGCTGAGCCGGCATGATCTACGGGAAAGGA
GTGCAACGTATGGATCCCAAGACTGGCAAAGAGATTCTGTACTACCTGGAGTCTCTCATCAACTCTGCTGTGTTCCCTGG
CCTTCAGGGAGGTCCCCACAACCATGCCATTGCTGGGGTTGCTGTGACCCTGAAGCAAGCTGTGACTATGGAATTTGAAG
TTTATCAGCACCAGGTGGTGGCCAACTGCAGGGCTCTGTCTGAGGCACTGACAGAGCTGGGCTGCAAAACAGTCACAGGT
GGTTCTGACAACCATTTGATCCTCGTGGATCTCCATTCAATCAAAGGCACAGATGGCAGAAGGGCTGAGAAGGTCCTAGA
AGCCTGTTCTATTGCCTGCAACAAGAACACCTGCCCAGGTGACAGAAGCGCTCCACGGCCCAGTGGACTGCGGCTGGGGA
CGCCAGCACTGACATCCCTCGGACTTTTGGAAAAAGACTTCCAAAAAGTAGCCCCCTTTATCCACACAGGGTTAAAGCTA
ACCCCTGCAGATCTACAGCAACGTTGGCATTGGAGCCACCCTGAAAGAGTTCAAGGAGAGACTGGCAGGGGATAAATACC
GGGGGGGCGTGCAGGCTCTCTGGGAGGAGGTCGAGAGCTTCACTCTCTCTTCCCTCTGCCTGGCCTGCCTAACTTC

Alignment

ORF - retro_mmul_487 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.39 %
• Parental protein coverage: 71.43 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGLDLPDGGHLTHGFMTDKKKISATSIFFESMPYKVNPDTGYINYDQLEENARLFHPKLIIAGTSCYSRN
          .GLDLPDGGHLTHGFMTDKKKISATSIFFESMPYKVNPDTGYINY.QLEENARLFH.KLI.AGTSC.S.N
Retrocopy LGLDLPDGGHLTHGFMTDKKKISATSIFFESMPYKVNPDTGYINYGQLEENARLFHLKLITAGTSCCS*N

Parental  LDYARLRK-IADENGAYLMADMAHISGLVVAGVVPSPFEHCHVVTTTTHKTLRGCRAGMIFYRKGVKNVD
          LDYARLRK...DENG.YLM.DMAHIS.LV.AGVVPSPF.HCHV.TTTTHK.LRGC.AGMI.Y.KGV...D
Retrocopy LDYARLRK>TVDENGVYLMVDMAHISRLVAAGVVPSPFKHCHVLTTTTHKNLRGC*AGMI-YGKGVQRMD

Parental  PKTGKEILYNLESLINSAVFPGLQGGPHNHAIAGVAVALKQAMTLEFKVYQHQVVANCRALSEALMELGY
          PKTGKEILY.LESLINSAVFPGLQGGPHNHAIAGVAV.LKQA.T.EF.VYQHQVVANCRALSEAL.ELG.
Retrocopy PKTGKEILYYLESLINSAVFPGLQGGPHNHAIAGVAVTLKQAVTMEFEVYQHQVVANCRALSEALTELGC

Parental  KIVTGGSDNHLILVDLRS-KGTDGGRAEKVLEACSIACNKNTCPGDRSALRPSGLRLGTPALTSRGLLEK
          K.VTGGSDNHLILVDL.S.KGTDG.RAEKVLEACSIACNKNTCPGDRSA.RPSGLRLGTPALTS.GLLEK
Retrocopy KTVTGGSDNHLILVDLHSIKGTDGRRAEKVLEACSIACNKNTCPGDRSAPRPSGLRLGTPALTSLGLLEK

Parental  DFQKVAQFIHRGIELT-LQIQSDIGVRATLKEFKERLAGDKYQGAVQALREEVESFA-SLFPLPGLPDF
          DFQKVA.FIH.G..LT.LQI.S..G..ATLKEFKERLAGDKY.G.VQAL.EEVESF..SLFPLPGLP.F
Retrocopy DFQKVAPFIHTGLKLT>LQIYSNVGIGATLKEFKERLAGDKYRGGVQALWEEVESFT<SLFPLPGLPNF

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	2.69 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	4.44 RPM
SRP007412_cerebellum	0.00 RPM	3.75 RPM
SRP007412_heart	0.00 RPM	2.18 RPM
SRP007412_kidney	0.00 RPM	138.38 RPM
SRP007412_liver	0.04 RPM	396.47 RPM
SRP007412_testis	0.26 RPM	12.63 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_487 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_487 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_487 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_333

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000013535	1 retrocopy	retro_mmul_487 ,
Pongo abelii	ENSPPYG00000008051	1 retrocopy	retro_pabe_333,