RetrogeneDB ID: retro_mmul_122

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:60929283..60929493(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000030258
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MMU.1280
• Ensembl ID: ENSMMUG00000028895
• Aliases: None
• Description: ribosomal protein S28 [Source:RefSeq peptide;Acc:NP_001180365]

Sequence

>retro_mmul_122
ATGGACACCAGCCGCGTGCAGCCTATCAAGCTGGCCAGGGTCACTAAGGTCCTGGGCAGGACCGGCTCTCAGGGACAGTG
CACGCAAGTGCGCGTGGAATTCATGGACTACACGAGCCGCTCCATCATCCGCAATGTAAAAGGCCCCGTGCGCGAGGGCG
ACGTGCTCACCCTCTTGGAGTCAGAGCGAGAAGCCCGGAGGTTGCGCTGA

Alignment

ORF - retro_mmul_122 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.55 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDTSRVQPIKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLESEREARRLR
          MDTSRVQPIKLARVTKVLGRTGSQGQCTQVRVEFMD.TSRSIIRNVKGPVREGDVLTLLESEREARRLR
Retrocopy MDTSRVQPIKLARVTKVLGRTGSQGQCTQVRVEFMDYTSRSIIRNVKGPVREGDVLTLLESEREARRLR

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	19.72 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	139.94 RPM
SRP007412_cerebellum	0.00 RPM	16.92 RPM
SRP007412_heart	0.00 RPM	48.70 RPM
SRP007412_kidney	0.00 RPM	46.01 RPM
SRP007412_liver	0.12 RPM	210.15 RPM
SRP007412_testis	0.00 RPM	20.81 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_122 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_122 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_122 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004917	1 retrocopy	retro_amel_1359,
Bos taurus	ENSBTAG00000002468	1 retrocopy	retro_btau_1130,
Cavia porcellus	ENSCPOG00000022876	5 retrocopies	retro_cpor_1092, retro_cpor_1485, retro_cpor_1504, retro_cpor_176, retro_cpor_702,
Equus caballus	ENSECAG00000017256	1 retrocopy	retro_ecab_725,
Felis catus	ENSFCAG00000024931	3 retrocopies	retro_fcat_1130, retro_fcat_611, retro_fcat_752,
Homo sapiens	ENSG00000233927	9 retrocopies	retro_hsap_1192, retro_hsap_1352, retro_hsap_1725, retro_hsap_2220, retro_hsap_2279, retro_hsap_3748, retro_hsap_505, retro_hsap_523, retro_hsap_799,
Loxodonta africana	ENSLAFG00000029923	2 retrocopies	retro_lafr_168, retro_lafr_755,
Myotis lucifugus	ENSMLUG00000023621	1 retrocopy	retro_mluc_2040,
Macaca mulatta	ENSMMUG00000028895	3 retrocopies	retro_mmul_122 , retro_mmul_182, retro_mmul_807,
Monodelphis domestica	ENSMODG00000003890	1 retrocopy	retro_mdom_291,
Mus musculus	ENSMUSG00000067288	3 retrocopies	retro_mmus_2949, retro_mmus_3283, retro_mmus_91,
Oryctolagus cuniculus	ENSOCUG00000021484	2 retrocopies	retro_ocun_1230, retro_ocun_1799,
Pan troglodytes	ENSPTRG00000040141	6 retrocopies	retro_ptro_1228, retro_ptro_1613, retro_ptro_3037, retro_ptro_378, retro_ptro_391, retro_ptro_927,
Rattus norvegicus	ENSRNOG00000042886	2 retrocopies	retro_rnor_95, retro_rnor_96,
Sus scrofa	ENSSSCG00000013597	3 retrocopies	retro_sscr_132, retro_sscr_191, retro_sscr_808,