RetrogeneDB ID: retro_mmus_1546

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:12962767..12963190(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000089695
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Mrps18c
• Ensembl ID: ENSMUSG00000016833
• Aliases: None
• Description: mitochondrial ribosomal protein S18C [Source:MGI Symbol;Acc:MGI:1915985]

Sequence

>retro_mmus_1546
GCTCTGGTTGCTCTGTGCAGTGGTATAGGGAGGAAGAACTTGAGAACCGCGACTGGCTGCTTCATGGATCTCGGAACTCA
CGCAGTTTCTGTACTGTGGAGAAGAAGTTTTTCACAGTCTGAACAGGTAACCAGCAATGAGGACCTGCCAATCCCAATGG
AAAAGCCCTATAAGGAGCCTCTTAAGAAGTGTGTCTTGTGCGAGAAACATGTAGATTACAAGAATGTGCAGCTTTTGTCC
CAGTTTATTTCTCCATTTACCGGATGCATTTACAGAAGGCACATAACAGGACTTTGTGGAAAGAAACAGAGGGAAATAAC
TAAAGCCACTAAGAGAACTCAGAAAATGGGGTTTATGCCAGTTACATACAAGGATCCTGCATATCTCAAAGACCCTAGAG
TTTGTAACATCAGATACCGAGAA

Alignment

ORF - retro_mmus_1546 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.07 %
• Parental protein coverage: 98.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ALVALCSGIGRKNLTTAAGCFTDRGTQAVSVIWRRCFSQFEQVTSNEDLPVPMENPYKEPLKKCVLCEKR
          ALVALCSGIGRKNL.TA.GCF.D.GT.AVSV.WRR.FSQ.EQVTSNEDLP.PME.PYKEPLKKCVLCEK.
Retrocopy ALVALCSGIGRKNLRTATGCFMDLGTHAVSVLWRRSFSQSEQVTSNEDLPIPMEKPYKEPLKKCVLCEKH

Parental  VDYKNVQLLSQFISPFTGCIYGRHITGLCGKKQREITKAIKRAQKMGFMPVTYKDPAYLKDPRVCNIRYR
          VDYKNVQLLSQFISPFTGCIY.RHITGLCGKKQREITKA.KR.QKMGFMPVTYKDPAYLKDPRVCNIRYR
Retrocopy VDYKNVQLLSQFISPFTGCIYRRHITGLCGKKQREITKATKRTQKMGFMPVTYKDPAYLKDPRVCNIRYR

Parental  E
          E
Retrocopy E

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	0.14 RPM	11.28 RPM
SRP007412_cerebellum	0.13 RPM	7.95 RPM
SRP007412_heart	0.00 RPM	12.30 RPM
SRP007412_kidney	0.06 RPM	18.42 RPM
SRP007412_liver	0.03 RPM	15.02 RPM
SRP007412_testis	0.05 RPM	17.29 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1546 was not detected

EST

No EST(s) were mapped for retro_mmus_1546 retrocopy.

TSS

No TSS is located nearby retro_mmus_1546 retrocopy 5' end.

Lab

retro_mmus_1546 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1546 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018155	3 retrocopies	retro_btau_1386, retro_btau_309, retro_btau_502,
Callithrix jacchus	ENSCJAG00000005286	3 retrocopies	retro_cjac_1419, retro_cjac_234, retro_cjac_3970,
Cavia porcellus	ENSCPOG00000009198	1 retrocopy	retro_cpor_178,
Dasypus novemcinctus	ENSDNOG00000018326	2 retrocopies	retro_dnov_1030, retro_dnov_152,
Homo sapiens	ENSG00000163319	5 retrocopies	retro_hsap_1540, retro_hsap_2597, retro_hsap_4019, retro_hsap_4684, retro_hsap_969,
Gorilla gorilla	ENSGGOG00000008603	2 retrocopies	retro_ggor_1173, retro_ggor_2908,
Macropus eugenii	ENSMEUG00000010972	2 retrocopies	retro_meug_104, retro_meug_1113,
Myotis lucifugus	ENSMLUG00000017057	1 retrocopy	retro_mluc_2360,
Macaca mulatta	ENSMMUG00000015353	4 retrocopies	retro_mmul_2203, retro_mmul_2494, retro_mmul_655, retro_mmul_793,
Mus musculus	ENSMUSG00000016833	2 retrocopies	retro_mmus_1546 , retro_mmus_2127,
Nomascus leucogenys	ENSNLEG00000009119	4 retrocopies	retro_nleu_111, retro_nleu_1614, retro_nleu_2722, retro_nleu_3010,
Ochotona princeps	ENSOPRG00000004113	2 retrocopies	retro_opri_1041, retro_opri_966,
Pongo abelii	ENSPPYG00000025867	2 retrocopies	retro_pabe_1276, retro_pabe_70,
Pan troglodytes	ENSPTRG00000016233	3 retrocopies	retro_ptro_1039, retro_ptro_1521, retro_ptro_3113,
Pteropus vampyrus	ENSPVAG00000006439	2 retrocopies	retro_pvam_1326, retro_pvam_1412,
Rattus norvegicus	ENSRNOG00000002178	3 retrocopies	retro_rnor_2264, retro_rnor_2265, retro_rnor_477,
Sarcophilus harrisii	ENSSHAG00000007084	1 retrocopy	retro_shar_718,
Ictidomys tridecemlineatus	ENSSTOG00000007989	1 retrocopy	retro_itri_1231,
Tupaia belangeri	ENSTBEG00000012505	3 retrocopies	retro_tbel_1755, retro_tbel_4724, retro_tbel_508,
Tarsius syrichta	ENSTSYG00000012924	1 retrocopy	retro_tsyr_649,
Tursiops truncatus	ENSTTRG00000004897	2 retrocopies	retro_ttru_144, retro_ttru_1721,