RetrogeneDB ID: retro_mmul_1583

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 20:56957701..56957986(-)
• Located in intron of: ENSMMUG00000029114

Retrocopy information

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

Parental gene information

• Parental gene symbol: C9H10ORF57
• Ensembl ID: ENSMMUG00000003015
• Aliases: None
• Description: None

Sequence

>retro_mmul_1583
GGATGGTCCCCAACCAACTTCATGTCTGGGTTTTTCATGATAGTGAAGTCAGAAGCCAGCAGTGCAGCTGCCACCTACTT
CTGTCCAGCCAGACCCTTGCCCTTGCTGATCACAGTCCTGGGGCTGGACTGCTTCACATAAGTTGTCTTTTGGCCTTGGA
GTATCCTTTATCAGAGCCTTGGGCCCCTGGGCTCCTTCACTCAGTACTTGGTGGGCCACCATCACACCCTCCCGTGCAGT
AGGTATTGGCTTGCCTGGCTGAGTCATGTGGGAGAATCCTTGTAT

Alignment

ORF - retro_mmul_1583 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.83 %
• Parental protein coverage: 68.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GELPVNSVSGFFKRMAKSEASNAATAYFRPARPLPSLVTVLGLGYFAWVVFWPQSIPYQSLGPLGPFTQY
          G..P.N..SGFF....KSEAS.AA..YF.PARPLP.L.TVLGL..F..VVFWP.SI.YQSLGPLG.FTQY
Retrocopy GWSPTNFMSGFFM-IVKSEASSAAATYFCPARPLPLLITVLGLDCFT*VVFWPWSILYQSLGPLGSFTQY

Parental  LVDHHHTLLHNGYWLAWLIHVGESLY
          LV.HHHTL....YWLAWL.HVGESLY
Retrocopy LVGHHHTLPCSRYWLAWLSHVGESLY

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	12.55 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	16.50 RPM
SRP007412_cerebellum	0.06 RPM	9.49 RPM
SRP007412_heart	0.00 RPM	5.12 RPM
SRP007412_kidney	0.00 RPM	23.36 RPM
SRP007412_liver	0.08 RPM	18.01 RPM
SRP007412_testis	0.04 RPM	19.98 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1583 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1583 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1583 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015748	3 retrocopies	retro_cfam_602, retro_cfam_635, retro_cfam_637,
Callithrix jacchus	ENSCJAG00000007670	1 retrocopy	retro_cjac_3839,
Dasypus novemcinctus	ENSDNOG00000024625	1 retrocopy	retro_dnov_555,
Felis catus	ENSFCAG00000026147	1 retrocopy	retro_fcat_401,
Myotis lucifugus	ENSMLUG00000007585	16 retrocopies	retro_mluc_1178, retro_mluc_2482, retro_mluc_2491, retro_mluc_2492, retro_mluc_2528, retro_mluc_2532, retro_mluc_2550, retro_mluc_2551, retro_mluc_2552, retro_mluc_2572, retro_mluc_2573, retro_mluc_2583, retro_mluc_2586, retro_mluc_2603, retro_mluc_2623, retro_mluc_766,
Macaca mulatta	ENSMMUG00000003015	1 retrocopy	retro_mmul_1583 ,
Mus musculus	ENSMUSG00000072676	1 retrocopy	retro_mmus_2102,
Oryctolagus cuniculus	ENSOCUG00000013679	1 retrocopy	retro_ocun_453,
Otolemur garnettii	ENSOGAG00000028898	1 retrocopy	retro_ogar_59,
Tarsius syrichta	ENSTSYG00000006920	1 retrocopy	retro_tsyr_103,
Tursiops truncatus	ENSTTRG00000006122	1 retrocopy	retro_ttru_454,