RetrogeneDB ID: retro_mmul_196

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:17504782..17505091(+)
• Located in intron of: ENSMMUG00000004744

Retrocopy information

• Ensembl ID: ENSMMUG00000010727
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MMU.16721
• Ensembl ID: ENSMMUG00000012140
• Aliases: None
• Description: None

Sequence

>retro_mmul_196
ATGTCAGACGCAGCCGTAGACACCAGCTCCGAAATCACCACCAAGGACTTAAAGGAGAAGAAGGAAGTTGTGGAAGAGGC
AGAAAATGGAAGAGACGCCCCTGCTAACGGGAATGCTAATGAGGAAAATGGGGAGCAAGAGGCTGACAATGAGGTAGATG
AAGAAGAGGAAGAAGGTGGGGAGGAAGAGGAGGAGGAAGAAGAAGGTGATGGTGAGGAAGAGGATGGAGATGAAGATGAG
GAAGCTGAGTCAGCTACGGGCAAGCGGGCAGCTGAAGATGATAAGGATGACGATGTTGATACCAAGAAG

Alignment

ORF - retro_mmul_196 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.03 %
• Parental protein coverage: 93.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSDAAVDTSSEITTKDLKEKKEVVEEAENGRDAPANGNANEENGEQEADNEVDEEEEEGGEEEEEEEEGD
          MSDAAVDTSSEITTKDLKEKKEVVEEAENGRDAPANGNANEENGEQEADNEVDEEEEEGGEEEEEEEEGD
Retrocopy MSDAAVDTSSEITTKDLKEKKEVVEEAENGRDAPANGNANEENGEQEADNEVDEEEEEGGEEEEEEEEGD

Parental  GEEEDGDEDEEAESATGKRAAEDDEDDDVDTKK
          GEEEDGDEDEEAESATGKRAAEDD.DDDVDTKK
Retrocopy GEEEDGDEDEEAESATGKRAAEDDKDDDVDTKK

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	53.11 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	129.07 RPM
SRP007412_cerebellum	0.06 RPM	41.26 RPM
SRP007412_heart	0.00 RPM	102.70 RPM
SRP007412_kidney	0.12 RPM	74.53 RPM
SRP007412_liver	0.00 RPM	54.11 RPM
SRP007412_testis	0.15 RPM	137.47 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_196 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_196 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_196 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002549	2 retrocopies	retro_btau_1034, retro_btau_143,
Canis familiaris	ENSCAFG00000032596	4 retrocopies	retro_cfam_113, retro_cfam_1570, retro_cfam_282, retro_cfam_78,
Callithrix jacchus	ENSCJAG00000013611	9 retrocopies	retro_cjac_1484, retro_cjac_1976, retro_cjac_2318, retro_cjac_2507, retro_cjac_2611, retro_cjac_3035, retro_cjac_3151, retro_cjac_421, retro_cjac_647,
Felis catus	ENSFCAG00000004780	1 retrocopy	retro_fcat_1682,
Homo sapiens	ENSG00000187514	6 retrocopies	retro_hsap_1863, retro_hsap_2690, retro_hsap_3447, retro_hsap_4198, retro_hsap_4288, retro_hsap_4787,
Gorilla gorilla	ENSGGOG00000009874	4 retrocopies	retro_ggor_1551, retro_ggor_2149, retro_ggor_2981, retro_ggor_952,
Myotis lucifugus	ENSMLUG00000002628	2 retrocopies	retro_mluc_131, retro_mluc_26,
Macaca mulatta	ENSMMUG00000012140	1 retrocopy	retro_mmul_196 ,
Mus musculus	ENSMUSG00000026238	4 retrocopies	retro_mmus_3135, retro_mmus_3136, retro_mmus_414, retro_mmus_55,
Nomascus leucogenys	ENSNLEG00000014135	2 retrocopies	retro_nleu_30, retro_nleu_96,
Rattus norvegicus	ENSRNOG00000018584	1 retrocopy	retro_rnor_69,
Sus scrofa	ENSSSCG00000023690	1 retrocopy	retro_sscr_895,