RetrogeneDB ID: retro_mmus_330

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:65552680..65552997(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082774
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rplp2
• Ensembl ID: ENSMUSG00000025508
• Aliases: Rplp2, 2700049I22Rik
• Description: ribosomal protein, large P2 [Source:MGI Symbol;Acc:MGI:1914436]

Sequence

>retro_mmus_330
GTTGCCTCCTACCTGCTGGCCGCCCGCGGGGCAACTCCTCTCCTAGCGCCAAAGACATCAAGAAAATACTAGACAGTGTG
GGCATCTAGGTGGACAATGACCGGCTCAACATGATCATCAGTGAGCTGAATGGAAAGTACGTTGAGGATGTCATCGCTCA
GGGTGTTGGCAAGCTGGCCAGTGTGTCTGCTGGTGGGGCTGTGGCTGTTTCTGCTGCCCCTGGCTCTGCAGCTCCTGCTG
CTGCAGAGGAGAAGAAAGATGAGAAGAAGGAGGAGTCTGAGGAGTAGGATGACGACATGGGATTTGGCTTGTTTGAT

Alignment

ORF - retro_mmus_330 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.65 %
• Parental protein coverage: 97.39 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VASYLLAALG-GNSSPSAKDIKKILDSVGIEADDDRLNKVISELNGKNIEDVIAQGVGKLASVPAGGAVA
          VASYLLAA.G.GNSSPSAKDIKKILDSVGI..D.DRLN..ISELNGK..EDVIAQGVGKLASV.AGGAVA
Retrocopy VASYLLAARG<GNSSPSAKDIKKILDSVGI*VDNDRLNMIISELNGKYVEDVIAQGVGKLASVSAGGAVA

Parental  VSAAPGSAAPAAGSAPAAAEEKKDEKKEESEESDDDMGFGLFD
          VSAAPGSAAPAA..A.....EKK.E....SEE.DDDMGFGLFD
Retrocopy VSAAPGSAAPAA--AEEKKDEKKEE----SEE*DDDMGFGLFD

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	57.64 RPM
SRP007412_cerebellum	0.00 RPM	42.16 RPM
SRP007412_heart	0.09 RPM	94.82 RPM
SRP007412_kidney	0.04 RPM	60.89 RPM
SRP007412_liver	0.03 RPM	54.48 RPM
SRP007412_testis	0.05 RPM	45.19 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_330 was not detected

EST

No EST(s) were mapped for retro_mmus_330 retrocopy.

TSS

No TSS is located nearby retro_mmus_330 retrocopy 5' end.

Lab

retro_mmus_330 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_330 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
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,
Dipodomys ordii	ENSDORG00000016458	3 retrocopies	retro_dord_705, retro_dord_706, retro_dord_707,
Felis catus	ENSFCAG00000008417	1 retrocopy	retro_fcat_860,
Homo sapiens	ENSG00000177600	5 retrocopies	retro_hsap_1777, retro_hsap_3395, retro_hsap_3440, retro_hsap_821, retro_hsap_982,
Gorilla gorilla	ENSGGOG00000010789	5 retrocopies	retro_ggor_2238, retro_ggor_2298, retro_ggor_2323, retro_ggor_672, retro_ggor_784,
Macaca mulatta	ENSMMUG00000020627	2 retrocopies	retro_mmul_221, retro_mmul_311,
Mus musculus	ENSMUSG00000025508	4 retrocopies	retro_mmus_1364, retro_mmus_2111, retro_mmus_2282, retro_mmus_330 ,
Nomascus leucogenys	ENSNLEG00000026860	5 retrocopies	retro_nleu_1948, retro_nleu_2144, retro_nleu_2296, retro_nleu_2762, retro_nleu_85,
Otolemur garnettii	ENSOGAG00000016296	2 retrocopies	retro_ogar_156, retro_ogar_275,
Pongo abelii	ENSPPYG00000002885	6 retrocopies	retro_pabe_1537, retro_pabe_1543, retro_pabe_2789, retro_pabe_2844, retro_pabe_732, retro_pabe_830,
Pan troglodytes	ENSPTRG00000003137	5 retrocopies	retro_ptro_1189, retro_ptro_2307, retro_ptro_2332, retro_ptro_572, retro_ptro_764,
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,