RetrogeneDB ID: retro_mmul_1610

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:69877689..69878137(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMMUG00000000034
• Aliases: None
• Description: None

Sequence

>retro_mmul_1610
TTGCCGCTTTGCACCCTCTCCAGGCCCTGAACTTGCTCCAGTCGGCCTCTCCAGGCCCAGCTCTTCCTCCCCGCGGCCTC
TGCAGGCCCAACGCTGCCCTCGACTCGGCCTCTCCAGGGCTCGCTCCTGCTCCCGGCGGCCCCTGCGGGCCCAACTCGTC
CTCCGGTCGGCCTCCACCGGCCCAGCTCCTGCCTCTCCACGGCCTCTCCAGCTGCCAGACGTCCTCAGGTCAGCCTCTCC
TGGCCCAGCTCCTCCTGCCTGCCACTGGCCTCTTGAGGCCCAACCCCGCTCATACCTCTCAGCGGCCCTCCCGGGCCCTG
CTTCTGACTTCTGGCGGCCTCCTCAGGCCCAGGACCTGACCTCCAGTCGGCCTCTCCAGGCCCAGCCTCCTGCCTCCCGG
AGGCCTTCGCAGGCCCAGCCTCTGCCTCACAGCAGACTCTCCATGCCT

Alignment

ORF - retro_mmul_1610 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.84 %
• Parental protein coverage: 57.69 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LQLNGLCRPSVC-LLAASPGPELPQGGLSRPRCSLPDSRPGPAP-PAPGCGRAGSHG-GLSGPGSCPPSS
          L.L..L.RP..C.L..ASPGP.LP..GL.RP...L....PG.AP.P...CG...S.G.GL..P.SC....
Retrocopy LPLCTLSRP*TC<LQSASPGPALPPRGLCRPNAALDSASPGLAPAPGGPCGPNSSSG>GLHRPSSCLSTA

Parental  SPRTRLPPASLSRPRSSCLPLVASLGPA-HSSWGMAFPGPASASWLPLQAAQHLISSGPRQAQPHASRRP
          SP..R.P..SLS.P.SSCLPL.AS.GP...S....A.PGPAS..W.P.QA.Q.L.SS.P.QAQP.ASRRP
Retrocopy SPAARRPQVSLSWPSSSCLPL-AS*GPT>RSYLSAALPGPASDFWRPPQA-QDLTSSRPLQAQPPASRRP

Parental  AQAQPLPPSGLSTP
          .QAQPLP.S.LS.P
Retrocopy SQAQPLPHSRLSMP

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	0.00 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	0.56 RPM
SRP007412_cerebellum	0.00 RPM	0.13 RPM
SRP007412_heart	0.00 RPM	0.53 RPM
SRP007412_kidney	0.00 RPM	0.23 RPM
SRP007412_liver	0.04 RPM	0.91 RPM
SRP007412_testis	2.11 RPM	18.28 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1610 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1610 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1610 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000000034	1 retrocopy	retro_mmul_1610 ,
Pongo abelii	ENSPPYG00000018258	4 retrocopies	retro_pabe_133, retro_pabe_3119, retro_pabe_3126, retro_pabe_3236,