RetrogeneDB ID: retro_mmul_703

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1099214730981:7079..7631(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.10090
• Ensembl ID: ENSMMUG00000006354
• Aliases: None
• Description: insulin-induced gene 2 protein [Source:RefSeq peptide;Acc:NP_001181710]

Sequence

>retro_mmul_703
CTGGTGCAGAGGAGCTTCATGCTCTTCTCAGTAGGGGCGGTCCTAGCCCTGGTGCTTAACCTGCTGCAGATCCAGAAGAA
TGTTACCCTCTTCCCAGAGGAGGTGATCGCCACCATTTTTTTCTCTGCCTGATAGGTCCCTCCCTGCTGCGGGACAGCAG
CTGCTGTTGTTGGTTTACTGTACCCTGTATCGACAGTCACCTCGGAGAACCCCACAAATTTAAGAGAGTGGGCCAGTGTC
ATGCGCTGCATAGCAGTTTTTGTTGGCATTAACCAAGCCAGTGCCAAACTGGATTTTGTCAATAAAGTCCAGCTGTCCTT
GACTTTAGCAGCCCTGTCTTAGGGCTTTTGGTGGACATTTGATGGTTCAAGAAGTGGCCTGGAGCTTGGGATCACCATAG
CCTTTCTAGCTACTCTGATCAGTCAGTTTCCGTTTGTAATGGTGTCTATGAGTACACATCCCCAGGTCTCCTCTATGTTC
CTTCTTGGTTCCCACGTATAATCTTTCTCAGGGGGTGTCACAGTGGGAAGCATAGGACGACAGTTAGCTATG

Alignment

ORF - retro_mmul_703 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.84 %
• Parental protein coverage: 78.06 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LMIRGVVLFFIGVFLALVLNLLQIQRNVTLFPPDVIASIFSSAWWVPPCCGTASAVIGLLYPCIDRHLGE
          L..R...LF..G..LALVLNLLQIQ.NVTLFP..VIA.IF.SA..VPPCCGTA.AV.GLLYP.......E
Retrocopy LVQRSFMLFSVGAVLALVLNLLQIQKNVTLFPEEVIATIFFSA**VPPCCGTAAAVVGLLYP-VSTVTSE

Parental  PHKFKREWSSVMRCVAVFVGINHASAKVDFDNNIQLSLTLAALSIGLWWTFDRSRSGFGLGVGIAFLATL
          .....REW.SVMRC.AVFVGIN.ASAK.DF.N..QLSLTLAALS.G.WWTFD.SRSG..LG..IAFLATL
Retrocopy NPTNLREWASVMRCIAVFVGINQASAKLDFVNKVQLSLTLAALS*GFWWTFDGSRSGLELGITIAFLATL

Parental  VTQ-LLVYNGVYQYTSPDFLYVRSWLPCIF-FAGGITMGNIGRQLAM
          ..Q...V.NGVY.YTSP..LYV.SW.P.I..F.GG.T.G.IGRQLAM
Retrocopy ISQ<VSVCNGVYEYTSPGLLYVPSWFPRII>FSGGVTVGSIGRQLAM

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	25.32 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	16.50 RPM
SRP007412_cerebellum	0.00 RPM	26.67 RPM
SRP007412_heart	0.00 RPM	18.96 RPM
SRP007412_kidney	0.12 RPM	21.01 RPM
SRP007412_liver	0.08 RPM	23.79 RPM
SRP007412_testis	0.00 RPM	15.15 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_703 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_703 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_703 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
Erinaceus europaeus	ENSEEUG00000008765	1 retrocopy	retro_eeur_508,
Myotis lucifugus	ENSMLUG00000028113	1 retrocopy	retro_mluc_2270,
Macaca mulatta	ENSMMUG00000006354	1 retrocopy	retro_mmul_703 ,
Monodelphis domestica	ENSMODG00000000458	2 retrocopies	retro_mdom_1872, retro_mdom_542,
Otolemur garnettii	ENSOGAG00000007739	1 retrocopy	retro_ogar_940,