RetrogeneDB ID: retro_mmul_2565

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:39089294..39089714(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.4666
• Ensembl ID: ENSMMUG00000010062
• Aliases: None
• Description: None

Sequence

>retro_mmul_2565
TCAGAGGCTAACGTGGGGTTCAGAGCGACCGTGGCCGTCGGCCTGACCGTCTTTGTGCTTTCTGTCGTCACTATCATCAT
CTGCTTCACCTGCTCTTGCTGCTCCCTCTACAAGATGTGCCGCTGACCGCGTCCAGTTGTGACCACCACCATGTCCCCCA
CTGTGGTGCATGCCCCTTACCTTCAGCCTCCAAGTGTGCCACCTAGCTACCCTGGACTACCAGGGCTACCACCCCATGCC
CCCCTCCCCCAGCCAGGAATGCCAGCAGCACCCTACCCAATGCAGTACCCATCACCTTACCTGGCCCAGCCCACGGGCCT
GCCGGCCTACCTCGAGACCCTGGCTAGAGGAACAGCCACACCCTACCCCACCAGCCAGCCTCCTTCCAACCCGGCCTACA
TGGATGCCTCGAAGGCGGCC

Alignment

ORF - retro_mmul_2565 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75. %
• Parental protein coverage: 84.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SDPMLGFGATLAVGLTIFVLSVVAIIICFTCSCCCLYKTCRRPRPVVTTTTSTTVVHAPYPQPPSVPPSY
          S....GF.AT.AVGLT.FVLSVV.IIICFTCSCC.LYK.CR.PRPVVTTT.S.TVVHAPY.QPPSVPPSY
Retrocopy SEANVGFRATVAVGLTVFVLSVVTIIICFTCSCCSLYKMCR*PRPVVTTTMSPTVVHAPYLQPPSVPPSY

Parental  PGPSYQGYHTMPPQPGMPAAPYPMQYPPPYPAQPMGPPAYHETLAGGAAAPYPASQPPYNPAYVDAPKAA
          PG......H...PQPGMPAAPYPMQYP.PY.AQP.G.PAY.ETLA.G.A.PYP.SQPP.NPAY.DA.KAA
Retrocopy PGLPGLPPHAPLPQPGMPAAPYPMQYPSPYLAQPTGLPAYLETLARGTATPYPTSQPPSNPAYMDASKAA

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	9.52 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	38.55 RPM
SRP007412_cerebellum	0.00 RPM	2.71 RPM
SRP007412_heart	0.00 RPM	11.42 RPM
SRP007412_kidney	0.00 RPM	12.56 RPM
SRP007412_liver	0.00 RPM	35.67 RPM
SRP007412_testis	0.00 RPM	5.43 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2565 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2565 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2565 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4812
Gorilla gorilla	retro_ggor_2996
Callithrix jacchus	retro_cjac_4152

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002915	2 retrocopies	retro_cjac_4077, retro_cjac_4152,
Homo sapiens	ENSG00000164054	2 retrocopies	retro_hsap_4706, retro_hsap_4812,
Gorilla gorilla	ENSGGOG00000028207	2 retrocopies	retro_ggor_2996, retro_ggor_86,
Macaca mulatta	ENSMMUG00000010062	1 retrocopy	retro_mmul_2565 ,
Nomascus leucogenys	ENSNLEG00000006485	1 retrocopy	retro_nleu_1984,
Pongo abelii	ENSPPYG00000013902	3 retrocopies	retro_pabe_2120, retro_pabe_3653, retro_pabe_3739,
Pan troglodytes	ENSPTRG00000014888	1 retrocopy	retro_ptro_3128,