RetrogeneDB ID: retro_mmul_2594

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:70320775..70321372(-)
• Located in intron of: ENSMMUG00000005663

Retrocopy information

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

Parental gene information

• Parental gene symbol: BCL2L2-PABPN1
• Ensembl ID: ENSMMUG00000014747
• Aliases: None
• Description: None

Sequence

>retro_mmul_2594
GACCCGGGGTATGGTGCCATTGAGGACCAAGAACTGGAAACTATCAAAACTCGAGTCAGGGAGATGGAAGAAGAAGCTGA
GAAGCTAAAGGAGCTACAGAACAGAGGTAGAGAAGCAGATGAATACAAGTCCACCTCTAGGCAATGCTGGCCCAGTGATC
ATGTCATTGAAGAGAAGATGGAGGCTGATGCCCGTTCCATCTATGTTGGCAATGTGGACTATGGTGCAACAGCAGAAGAG
CTGGAAGCTCACTTTCATGGCTGTGATTCAGTCAACCGTGTCACCATACTCTGTGACAAATTTAGTGGCCATCCCAAAGG
GTTTGCATATACAGAGTTCTCAGACAAAGAATCAGTGAGGACTTCCTTGGTCTCAGATGAGTCCCTATTTAGAGGAAGGC
AAATCAAGGTGATCCCAAAACGAACCAACAGACCAGGAATCAACACAACAGACCGGGGTTTCCCACGAGCCCGCTACGGC
GCCCAGACCACCAACTATAACAGTTACCTCTCTCGATTCTACAGTGGTTTTAACAGTAGGCCCCAGGGTCGCGTCTACAG
GGGCCGGGCTAGAGCAACATCATGGTATTCCCCTTAC

Alignment

ORF - retro_mmul_2594 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.56 %
• Parental protein coverage: 65.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DSGQGTAPALELEAIKARVREMEEEAEKLKELQN-EVEKQMNMSPPPGNAGPVIMS-IEEKMEADARSIY
          D.G.G.....ELE.IK.RVREMEEEAEKLKELQN.EVEKQMN.SPP.GNAGPVIMS.IEEKMEADARSIY
Retrocopy DPGYGAIEDQELETIKTRVREMEEEAEKLKELQN>EVEKQMNTSPPLGNAGPVIMS<IEEKMEADARSIY

Parental  VGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKVI
          VGNVDYGATAEELEAHFHGC.SVNRVTILCDKFSGHPKGFAY.EFSDKESVRTSL..DESLFRGRQIKVI
Retrocopy VGNVDYGATAEELEAHFHGCDSVNRVTILCDKFSGHPKGFAYTEFSDKESVRTSLVSDESLFRGRQIKVI

Parental  PKRTNRPGISTTDRGFPRARYRARTTNYNSSRSRFYSGFNSRPRGRVYRGRARATSWYSPY
          PKRTNRPGI.TTDRGFPRARY.A.TTNYNS..SRFYSGFNSRP.GRVYRGRARATSWYSPY
Retrocopy PKRTNRPGINTTDRGFPRARYGAQTTNYNSYLSRFYSGFNSRPQGRVYRGRARATSWYSPY

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	0.22 RPM	89.86 RPM
SRP007412_brain_prefrontal_cortex	0.32 RPM	95.75 RPM
SRP007412_cerebellum	0.77 RPM	130.63 RPM
SRP007412_heart	0.35 RPM	65.01 RPM
SRP007412_kidney	0.47 RPM	102.93 RPM
SRP007412_liver	0.16 RPM	41.76 RPM
SRP007412_testis	1.02 RPM	149.30 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2594 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2594 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2594 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4855
Pan troglodytes	retro_ptro_3232
Gorilla gorilla	retro_ggor_3030

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000100836	1 retrocopy	retro_hsap_4855,
Loxodonta africana	ENSLAFG00000031227	2 retrocopies	retro_lafr_1031, retro_lafr_233,
Macaca mulatta	ENSMMUG00000014747	1 retrocopy	retro_mmul_2594 ,
Mus musculus	ENSMUSG00000022194	1 retrocopy	retro_mmus_403,