RetrogeneDB ID: retro_mmus_1654

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:65438127..65438697(-)
• Located in intron of: ENSMUSG00000045036

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Mrps10
• Ensembl ID: ENSMUSG00000034729
• Aliases: Mrps10, 1110038B19Rik, AW743084, Rpms10
• Description: mitochondrial ribosomal protein S10 [Source:MGI Symbol;Acc:MGI:1928139]

Sequence

>retro_mmus_1654
TGCCGGCGCCTGCAGCAGGAATTGAGGAATTCCTCTATAAATGGTTCTAAGAGCGGGACAACCAGAGCTGGTGGCCTCGC
GCTTGCTAGTATGAAGTGGGTGCCACTGTCAAACCTGCATGTGGACGTCCCAAAGGATGTGACCAGACCTACGATAACCA
CTTCCGATGAGCCAGACACGTTGTACAAACGCCTGTCCATCTTAGTGAAAGCCCATGACAGGGCTGTGTTAGACAGCTAT
GAGTACTTTGCCGTGCTCGCTGCTAAAGAACTTGGCATTTCTATTAAAGTACACGAGCCACCAAGGAAAATAGAGCGCTT
CACTCTTCTCAAGTCGGTGCACATCTTCAAGAAGCACAGAGTCCAGTATGAGATGAGGACACTCTACAGATGTTTGGAGT
TAAAACATTTGACTGGAAGCACAGCCAGTGTCTACCTGGAGTATATCCAGCGAAACTTGCCTGAAGGGGTGGCCATGGAA
GTGACAAAGACGCAGATACAGCAGTTGCCAGAACACATCAAGGAGCCGATGTGGGAAACGGTTCCCGAGGAGAAAGAAGA
AAGCAAGTCG

Alignment

ORF - retro_mmus_1654 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.95 %
• Parental protein coverage: 95. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CRRLQQELGNSSINGSKSRTTRAGGLALASMKWVPLSNLHVDVPKDVTRPTITTSDEPDTLYKRLSILVK
          CRRLQQEL.NSSINGSKS.TTRAGGLALASMKWVPLSNLHVDVPKDVTRPTITTSDEPDTLYKRLSILVK
Retrocopy CRRLQQELRNSSINGSKSGTTRAGGLALASMKWVPLSNLHVDVPKDVTRPTITTSDEPDTLYKRLSILVK

Parental  AHDRAVLDSYEYFAVLAAKELGISIKVHEPPRKIERFTLLKSVHIFKKHRVQYEMRTLYRCLELKHLTGS
          AHDRAVLDSYEYFAVLAAKELGISIKVHEPPRKIERFTLLKSVHIFKKHRVQYEMRTLYRCLELKHLTGS
Retrocopy AHDRAVLDSYEYFAVLAAKELGISIKVHEPPRKIERFTLLKSVHIFKKHRVQYEMRTLYRCLELKHLTGS

Parental  TASVYLEYIQRNLPEGVAMEVTKTQIQQLPEHIKEPMWETVPEEKEESKS
          TASVYLEYIQRNLPEGVAMEVTKTQIQQLPEHIKEPMWETVPEEKEESKS
Retrocopy TASVYLEYIQRNLPEGVAMEVTKTQIQQLPEHIKEPMWETVPEEKEESKS

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	0.12 RPM	14.20 RPM
SRP007412_cerebellum	0.52 RPM	14.11 RPM
SRP007412_heart	0.00 RPM	12.27 RPM
SRP007412_kidney	0.44 RPM	12.09 RPM
SRP007412_liver	0.44 RPM	16.11 RPM
SRP007412_testis	0.69 RPM	8.83 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1654 was not detected

EST

No EST(s) were mapped for retro_mmus_1654 retrocopy.

TSS

No TSS is located nearby retro_mmus_1654 retrocopy 5' end.

Lab

retro_mmus_1654 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1654 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001638	1 retrocopy	retro_cfam_598,
Choloepus hoffmanni	ENSCHOG00000006109	1 retrocopy	retro_chof_1964,
Dasypus novemcinctus	ENSDNOG00000006067	1 retrocopy	retro_dnov_2007,
Dipodomys ordii	ENSDORG00000002081	1 retrocopy	retro_dord_412,
Homo sapiens	ENSG00000048544	1 retrocopy	retro_hsap_4157,
Gorilla gorilla	ENSGGOG00000012808	1 retrocopy	retro_ggor_2532,
Microcebus murinus	ENSMICG00000011379	1 retrocopy	retro_mmur_321,
Macaca mulatta	ENSMMUG00000014661	1 retrocopy	retro_mmul_48,
Mus musculus	ENSMUSG00000034729	1 retrocopy	retro_mmus_1654 ,
Nomascus leucogenys	ENSNLEG00000004800	1 retrocopy	retro_nleu_1385,
Oryctolagus cuniculus	ENSOCUG00000016697	1 retrocopy	retro_ocun_1141,
Pongo abelii	ENSPPYG00000016613	1 retrocopy	retro_pabe_3456,
Pan troglodytes	ENSPTRG00000018169	1 retrocopy	retro_ptro_2826,
Rattus norvegicus	ENSRNOG00000022609	1 retrocopy	retro_rnor_2284,
Ictidomys tridecemlineatus	ENSSTOG00000027016	1 retrocopy	retro_itri_1183,
Tursiops truncatus	ENSTTRG00000014063	1 retrocopy	retro_ttru_1203,