RetrogeneDB ID: retro_mmus_726

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:76514225..76514565(+)
• Located in intron of: ENSMUSG00000017631

Retrocopy information

• Ensembl ID: ENSMUSG00000080763
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rpl18
• Ensembl ID: ENSMUSG00000059070
• Aliases: Rpl18, L18, Rpl18a
• Description: ribosomal protein L18 [Source:MGI Symbol;Acc:MGI:98003]

Sequence

>retro_mmus_726
CCTGGCCGGGAGAACAAGACTGCTGTGGTTGTGGGGACGGTCACAGATGATGTGCAGATTCTGCAAGTTCCCAAGCTGAA
GGTGTGTGCACTGTGGGTGAGCAGCCGGGCCTGGAGTCGCATCCTCAAGGCTGGGGGTAAGATCCTCACCTTTGACCAGC
TGGCCCTGAAGTCTCCCAAGGGCCGGGGCACTGTGCTCCTGTCTGGTCCTCCGAAGGGCTGAGAGGCATTTTGGCAAGGC
CCCAGGAACCCCACACAGCCATACCAAACCCTATGTCCGTTCCAAGGGCCGGAAGTTTGAGCGCGCCAGAGGCCGAAGGG
CCAGCCGAGGCTACAAAAAC

Alignment

ORF - retro_mmus_726 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.47 %
• Parental protein coverage: 61.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PGRENKTAVVVGTVTDDVRILEVPKLKVCALRVSSRARSRILKAGGKILTFDQLALESPKGRGTVLLSGP
          PGRENKTAVVVGTVTDDV.IL.VPKLKVCAL.VSSRA.SRILKAGGKILTFDQLAL.SPKGRGTVLLSGP
Retrocopy PGRENKTAVVVGTVTDDVQILQVPKLKVCALWVSSRAWSRILKAGGKILTFDQLALKSPKGRGTVLLSGP

Parental  RKGREVYRHFGKAPGTP-HSHTKPYVRSKGRKFERARGRRASRGYKN
          .KG.E....F...P..P.HSHTKPYVRSKGRKFERARGRRASRGYKN
Retrocopy PKG*EA---FWQGPRNP>HSHTKPYVRSKGRKFERARGRRASRGYKN

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	0.02 RPM	16.59 RPM
SRP007412_cerebellum	0.09 RPM	13.11 RPM
SRP007412_heart	0.00 RPM	57.84 RPM
SRP007412_kidney	0.06 RPM	37.77 RPM
SRP007412_liver	0.03 RPM	37.99 RPM
SRP007412_testis	0.09 RPM	37.14 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_726 was not detected

EST

No EST(s) were mapped for retro_mmus_726 retrocopy.

TSS

No TSS is located nearby retro_mmus_726 retrocopy 5' end.

Lab

retro_mmus_726 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_726 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 98 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014872	3 retrocopies	retro_amel_1718, retro_amel_640, retro_amel_740,
Cavia porcellus	ENSCPOG00000026334	4 retrocopies	retro_cpor_1062, retro_cpor_1322, retro_cpor_703, retro_cpor_733,
Felis catus	ENSFCAG00000008652	4 retrocopies	retro_fcat_1055, retro_fcat_1268, retro_fcat_1596, retro_fcat_718,
Gorilla gorilla	ENSGGOG00000024878	7 retrocopies	retro_ggor_1038, retro_ggor_1280, retro_ggor_2200, retro_ggor_2550, retro_ggor_2624, retro_ggor_847, retro_ggor_937,
Macropus eugenii	ENSMEUG00000000640	1 retrocopy	retro_meug_1568,
Macaca mulatta	ENSMMUG00000022158	3 retrocopies	retro_mmul_32, retro_mmul_55, retro_mmul_92,
Monodelphis domestica	ENSMODG00000014099	1 retrocopy	retro_mdom_906,
Mustela putorius furo	ENSMPUG00000003891	4 retrocopies	retro_mputfur_135, retro_mputfur_1410, retro_mputfur_529, retro_mputfur_974,
Mus musculus	ENSMUSG00000059070	11 retrocopies	retro_mmus_1655, retro_mmus_2025, retro_mmus_2091, retro_mmus_2303, retro_mmus_2462, retro_mmus_2622, retro_mmus_2790, retro_mmus_3424, retro_mmus_3621, retro_mmus_726 , retro_mmus_740,
Nomascus leucogenys	ENSNLEG00000004537	11 retrocopies	retro_nleu_1124, retro_nleu_1136, retro_nleu_1410, retro_nleu_1799, retro_nleu_2006, retro_nleu_2380, retro_nleu_2464, retro_nleu_2597, retro_nleu_547, retro_nleu_577, retro_nleu_976,
Otolemur garnettii	ENSOGAG00000003562	16 retrocopies	retro_ogar_1167, retro_ogar_1474, retro_ogar_1563, retro_ogar_1753, retro_ogar_1978, retro_ogar_2394, retro_ogar_2419, retro_ogar_2527, retro_ogar_2613, retro_ogar_2833, retro_ogar_3319, retro_ogar_3456, retro_ogar_3458, retro_ogar_3459, retro_ogar_492, retro_ogar_996,
Oreochromis niloticus	ENSONIG00000006539	1 retrocopy	retro_onil_43,
Pongo abelii	ENSPPYG00000010206	6 retrocopies	retro_pabe_1003, retro_pabe_1337, retro_pabe_1402, retro_pabe_2681, retro_pabe_3100, retro_pabe_3176,
Rattus norvegicus	ENSRNOG00000021035	14 retrocopies	retro_rnor_1068, retro_rnor_1072, retro_rnor_1154, retro_rnor_1186, retro_rnor_1337, retro_rnor_1359, retro_rnor_2174, retro_rnor_2224, retro_rnor_2847, retro_rnor_2890, retro_rnor_516, retro_rnor_685, retro_rnor_856, retro_rnor_857,
Sarcophilus harrisii	ENSSHAG00000006564	2 retrocopies	retro_shar_571, retro_shar_659,
Sus scrofa	ENSSSCG00000025928	5 retrocopies	retro_sscr_1028, retro_sscr_118, retro_sscr_836, retro_sscr_864, retro_sscr_925,
Ictidomys tridecemlineatus	ENSSTOG00000012258	5 retrocopies	retro_itri_261, retro_itri_323, retro_itri_828, retro_itri_853, retro_itri_957,