RetrogeneDB ID: retro_mmul_1110

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 14:81957129..81957543(-)
• Located in intron of: ENSMMUG00000007921

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRABP2
• Ensembl ID: ENSMMUG00000002295
• Aliases: None
• Description: cellular retinoic acid-binding protein 2 [Source:RefSeq peptide;Acc:NP_001253818]

Sequence

>retro_mmul_1110
ATGCCCAACTTCTCTGGCAATTGGAAAATCATTCGATCAGAAAACTTCAAGGATTTGCTCAAAGTGCTGGGGGTGAATGT
GATGCTGAGGAAGACTGCTGTGGCTGCAGTGTCCAAGCCAGTAGTGGAGATCAAACAGGAGGGAGACACTTTCTACATCA
AAACCTCCACCACCGTGTGCACCACAGAGATTAACTTCAAGGTTGGGGAGGAGTTAGAGGAGCAGACTGTGGATGGGAGG
CCCTGTAAGAGCCCGGTGAAAAGGGAGAGTGAGAATAAAATGTTCTGTGAGCAGAAGCTCCTGAAGGGAGAGGGCCCCAA
GACCTCATGGACCAGAGAACTGACCAATGATAGGGAGCTGATCCTGACCATGAGGGCAGATGATGTTGTGTGTACCAGGG
TCTACGTCCGAGAG

Alignment

ORF - retro_mmul_1110 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.03 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPNFSGNWKIIRSENFEDLLKVLGVNVMLRKIAVAAASKPAVEIKQEGDTFYIKTSTTVRTTEINFKVGE
          MPNFSGNWKIIRSENF.DLLKVLGVNVMLRK.AVAA.SKP.VEIKQEGDTFYIKTSTTV.TTEINFKVGE
Retrocopy MPNFSGNWKIIRSENFKDLLKVLGVNVMLRKTAVAAVSKPVVEIKQEGDTFYIKTSTTVCTTEINFKVGE

Parental  EFEEQTVDGRPCKSLVKWESENKMVCEQKLLKGEGPKTSWTRELTNDGELILTMTADDVVCTRVYVRE
          E.EEQTVDGRPCKS.VK.ESENKM.CEQKLLKGEGPKTSWTRELTND.ELILTM.ADDVVCTRVYVRE
Retrocopy ELEEQTVDGRPCKSPVKRESENKMFCEQKLLKGEGPKTSWTRELTNDRELILTMRADDVVCTRVYVRE

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	7.51 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	5.24 RPM
SRP007412_cerebellum	0.00 RPM	3.55 RPM
SRP007412_heart	0.00 RPM	0.47 RPM
SRP007412_kidney	0.00 RPM	1.17 RPM
SRP007412_liver	0.00 RPM	0.51 RPM
SRP007412_testis	0.00 RPM	0.19 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1110 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1110 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1110 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000000486	4 retrocopies	retro_mmul_1417, retro_mmul_1920, retro_mmul_2095, retro_mmul_2230,
Macaca mulatta	ENSMMUG00000002295	1 retrocopy	retro_mmul_1110 ,
Macaca mulatta	ENSMMUG00000010906	1 retrocopy	retro_mmul_1311,
Macaca mulatta	ENSMMUG00000019337	1 retrocopy	retro_mmul_1787,
Macaca mulatta	ENSMMUG00000021907	1 retrocopy	retro_mmul_458,
Sarcophilus harrisii	ENSSHAG00000015843	1 retrocopy	retro_shar_735,
Vicugna pacos	ENSVPAG00000005002	1 retrocopy	retro_vpac_645,