RetrogeneDB ID: retro_mmul_221

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 10:37543304..37543652(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000031189
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MMU.1655
• Ensembl ID: ENSMMUG00000020627
• Aliases: None
• Description: 60S acidic ribosomal protein P2 [Source:RefSeq peptide;Acc:NP_001180505]

Sequence

>retro_mmul_221
ATGCACTACATCGCCTCCTACCTGCTGGCTGCCCTCAGGGGTAACTCTTCCCCCAGCGTCAAGGACATCAAGAAGATCTT
GGACAGTGTGGGCATCGAGGCGGACGACGACCGGCTCAACAAGGTTATTAGTGAGCTGAATGGAAAAAACATTGAAGATG
TCATTGCCCAGGGTATTGGCAAGCTTGCCAGTGTACCTGCCGGTGGGGCTGTGGCCGTCTCCGCTGCCCCAGGCTCTGCA
GCGTCTGCTGCTGGCTCCGCGCCTGCTGCAGCAGAGGAGAAGAAAGATGAGAAGAAGAAGGAGTCTGAAGAGTCAGACGA
TGACATGGGATTTGGCCTCTTTGATTAA

Alignment

ORF - retro_mmul_221 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.78 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRYVASYLLAALGGNSSPSAKDIKKILDSVGIEADDDRLNKVISELNGKNIEDVIAQGIGKLASVPAGGA
          M.Y.ASYLLAAL.GNSSPS.KDIKKILDSVGIEADDDRLNKVISELNGKNIEDVIAQGIGKLASVPAGGA
Retrocopy MHYIASYLLAALRGNSSPSVKDIKKILDSVGIEADDDRLNKVISELNGKNIEDVIAQGIGKLASVPAGGA

Parental  VAVSAAPGSAAPAAGSAPAAAEEKKDEKKEESEESDDDMGFGLFD
          VAVSAAPGSAA.AAGSAPAAAEEKKDEKK.ESEESDDDMGFGLFD
Retrocopy VAVSAAPGSAASAAGSAPAAAEEKKDEKKKESEESDDDMGFGLFD

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	4.82 RPM
SRP007412_brain_prefrontal_cortex	0.48 RPM	41.49 RPM
SRP007412_cerebellum	0.13 RPM	5.10 RPM
SRP007412_heart	0.18 RPM	9.60 RPM
SRP007412_kidney	0.00 RPM	8.22 RPM
SRP007412_liver	0.04 RPM	119.54 RPM
SRP007412_testis	0.08 RPM	5.20 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_221 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_221 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_221 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006935	1 retrocopy	retro_amel_197,
Bos taurus	ENSBTAG00000001777	2 retrocopies	retro_btau_117, retro_btau_1399,
Canis familiaris	ENSCAFG00000009523	1 retrocopy	retro_cfam_18,
Ciona intestinalis	ENSCING00000000626	1 retrocopy	retro_cint_34,
Callithrix jacchus	ENSCJAG00000011838	6 retrocopies	retro_cjac_2399, retro_cjac_2497, retro_cjac_2539, retro_cjac_2745, retro_cjac_3097, retro_cjac_3859,
Dasypus novemcinctus	ENSDNOG00000011513	12 retrocopies	retro_dnov_143, retro_dnov_1464, retro_dnov_1498, retro_dnov_1522, retro_dnov_1655, retro_dnov_1693, retro_dnov_1768, retro_dnov_200, retro_dnov_2104, retro_dnov_2293, retro_dnov_335, retro_dnov_366,
Dipodomys ordii	ENSDORG00000016458	3 retrocopies	retro_dord_705, retro_dord_706, retro_dord_707,
Echinops telfairi	ENSETEG00000010240	4 retrocopies	retro_etel_1206, retro_etel_1458, retro_etel_1640, retro_etel_455,
Felis catus	ENSFCAG00000008417	1 retrocopy	retro_fcat_860,
Macaca mulatta	ENSMMUG00000020627	2 retrocopies	retro_mmul_221 , retro_mmul_311,
Mustela putorius furo	ENSMPUG00000009049	1 retrocopy	retro_mputfur_254,
Mus musculus	ENSMUSG00000025508	4 retrocopies	retro_mmus_1364, retro_mmus_2111, retro_mmus_2282, retro_mmus_330,
Otolemur garnettii	ENSOGAG00000016296	2 retrocopies	retro_ogar_156, retro_ogar_275,
Petromyzon marinus	ENSPMAG00000009576	1 retrocopy	retro_pmar_15,
Rattus norvegicus	ENSRNOG00000002116	3 retrocopies	retro_rnor_257, retro_rnor_320, retro_rnor_388,
Sarcophilus harrisii	ENSSHAG00000001056	1 retrocopy	retro_shar_321,
Sus scrofa	ENSSSCG00000012842	1 retrocopy	retro_sscr_54,
Tursiops truncatus	ENSTTRG00000012450	1 retrocopy	retro_ttru_1420,