RetrogeneDB ID: retro_mmul_788

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 11:8818390..8818679(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C19orf40
• Ensembl ID: ENSMMUG00000017939
• Aliases: None
• Description: chromosome 19 open reading frame 40 [Source:HGNC Symbol;Acc:28467]

Sequence

>retro_mmul_788
ATTGTGGTCACTGAGAAATAGCATGGATTCCAGCTGGTGCAGGGGATGCAAAGGAAAATTAAGCTCATTTTTCAGGATGG
TCTGACATCAGATTTTTACCTATTTAGCAGATTCTTCATTCTTTATGTCACTGAAGCTGATTTAGTAGCCAGAAAATAGC
TACATAAAGAGGCTTGGTCAGGTTAGGAATTCCAGTAATCTTCAAGGGGTTGTAGTAGTTGAAAAAGCTCATATGAGTGA
ACAATACTTTCCAGCCATACAGAAGTTCACTGTGCTTGACCTTGGGATG

Alignment

ORF - retro_mmul_788 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.2 %
• Parental protein coverage: 72.18 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IVANEKWRGSQLAQEMQGKIKLIFEDGLTPDFYLSNRCCVLYVTEADLVAG-NGYRKRLVRVRNSGNLQG
          IV..EK..G.QL.Q.MQ.KIKLIF.DGLT.DFYL..R...LYVTEADLVA..N.Y.KRL..VRNS.NLQG
Retrocopy IVVTEK*HGFQLVQGMQRKIKLIFQDGLTSDFYLFSRFFILYVTEADLVAR>NSYIKRLGQVRNSSNLQG

Parental  IVVVEKTRMSEQYFPALQKFTVLDLGM
          .VVVEK..MSEQYFPA.QKFTVLDLGM
Retrocopy VVVVEKAHMSEQYFPAIQKFTVLDLGM

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	0.08 RPM
SRP007412_cerebellum	0.00 RPM	0.32 RPM
SRP007412_heart	0.00 RPM	0.18 RPM
SRP007412_kidney	0.00 RPM	0.12 RPM
SRP007412_liver	0.00 RPM	0.16 RPM
SRP007412_testis	0.00 RPM	1.39 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_788 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_788 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_788 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000728	2 retrocopies	retro_cjac_1011, retro_cjac_3952,
Cavia porcellus	ENSCPOG00000011965	1 retrocopy	retro_cpor_1536,
Dasypus novemcinctus	ENSDNOG00000014134	4 retrocopies	retro_dnov_1817, retro_dnov_2382, retro_dnov_426, retro_dnov_942,
Echinops telfairi	ENSETEG00000002716	1 retrocopy	retro_etel_458,
Loxodonta africana	ENSLAFG00000006401	4 retrocopies	retro_lafr_165, retro_lafr_365, retro_lafr_415, retro_lafr_789,
Myotis lucifugus	ENSMLUG00000013287	1 retrocopy	retro_mluc_522,
Macaca mulatta	ENSMMUG00000017939	1 retrocopy	retro_mmul_788 ,
Procavia capensis	ENSPCAG00000009727	1 retrocopy	retro_pcap_444,
Sarcophilus harrisii	ENSSHAG00000016372	1 retrocopy	retro_shar_299,