RetrogeneDB ID: retro_mmul_269

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 17:30871429..30871669(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000030714
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MMU.3201
• Ensembl ID: ENSMMUG00000012534
• Aliases: None
• Description: cyclin-dependent kinases regulatory subunit 2 [Source:RefSeq peptide;Acc:NP_001254472]

Sequence

>retro_mmul_269
ATGTCGCACAAACAGATTTACTATTTGGACAAATACGACGACGAGGAGTTTGAGTATCGACATGTCATGCTGCCCAAGGA
CATAGCCAAGCTGGTCCCTAAAACTCATTTGATGTCTGAATCTGAATGGAGGAATCTTGGCGTTCAGCAGAGTCAGGGAT
GGGTCCATTATATGATCCAGGAACCAGAACCTCACATCTTGCTCTTCCGGCGCCCACTACCCAAGAAGCCAAAGAAATGA

Alignment

ORF - retro_mmul_269 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.48 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAHKQIYYSDKYFDEHYEYRHVMLPRELSKQVPKTHLMSEEEWRRLGVQQSLGWVHYMIHEPEPHILLFR
          M.HKQIYY.DKY.DE..EYRHVMLP....K.VPKTHLMSE.EWR.LGVQQS.GWVHYMI.EPEPHILLFR
Retrocopy MSHKQIYYLDKYDDEEFEYRHVMLPKDIAKLVPKTHLMSESEWRNLGVQQSQGWVHYMIQEPEPHILLFR

Parental  RPLPKDQQK
          RPLPK...K
Retrocopy RPLPKKPKK

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	0.45 RPM	0.34 RPM
SRP007412_brain_prefrontal_cortex	0.24 RPM	0.00 RPM
SRP007412_cerebellum	0.13 RPM	0.71 RPM
SRP007412_heart	0.06 RPM	0.24 RPM
SRP007412_kidney	0.35 RPM	1.88 RPM
SRP007412_liver	0.00 RPM	3.05 RPM
SRP007412_testis	0.00 RPM	71.20 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_269 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_269 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_269 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002194	2 retrocopies	retro_cfam_1495, retro_cfam_472,
Callithrix jacchus	ENSCJAG00000007792	1 retrocopy	retro_cjac_261,
Echinops telfairi	ENSETEG00000001260	10 retrocopies	retro_etel_1194, retro_etel_1752, retro_etel_1839, retro_etel_229, retro_etel_590, retro_etel_704, retro_etel_717, retro_etel_721, retro_etel_838, retro_etel_979,
Felis catus	ENSFCAG00000022286	1 retrocopy	retro_fcat_1875,
Macaca mulatta	ENSMMUG00000012534	1 retrocopy	retro_mmul_269 ,
Mus musculus	ENSMUSG00000062248	4 retrocopies	retro_mmus_1356, retro_mmus_1470, retro_mmus_2392, retro_mmus_409,
Nomascus leucogenys	ENSNLEG00000008729	1 retrocopy	retro_nleu_1793,
Otolemur garnettii	ENSOGAG00000028843	1 retrocopy	retro_ogar_798,
Pongo abelii	ENSPPYG00000025843	1 retrocopy	retro_pabe_57,
Pteropus vampyrus	ENSPVAG00000011011	3 retrocopies	retro_pvam_1297, retro_pvam_1307, retro_pvam_605,
Rattus norvegicus	ENSRNOG00000014130	5 retrocopies	retro_rnor_1209, retro_rnor_1909, retro_rnor_2742, retro_rnor_279, retro_rnor_402,
Sus scrofa	ENSSSCG00000021161	2 retrocopies	retro_sscr_458, retro_sscr_675,
Ictidomys tridecemlineatus	ENSSTOG00000000048	7 retrocopies	retro_itri_1058, retro_itri_1306, retro_itri_1429, retro_itri_1632, retro_itri_269, retro_itri_585, retro_itri_774,