RetrogeneDB ID: retro_mmus_2036

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:59564270..59564693(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081157
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Mrps18b
• Ensembl ID: ENSMUSG00000024436
• Aliases: Mrps18b, 2400002C15Rik
• Description: mitochondrial ribosomal protein S18B [Source:MGI Symbol;Acc:MGI:1914223]

Sequence

>retro_mmus_2036
ATTGAGAAGAATGTGAAGCTCTTGGAACAGTTTGTCTGTGCACACACGGGTATCATCTTTCACGCCCCATACACAGGGGT
CTGTATGAAGCAGCACAAGAAGCTGACCCAGGCCATCCAGAAAGCCAGGGAGTGTGGTCTTCTCAGTTACTACGTCCCCC
AGGTTGAGCCCCGGGATGCTGACTTTCGTACTGTGCATGGAGCTGTCAGTGTGACTCCACCAGCCCCCACACTGTTGTCA
GGTGAACCTTGGTACCCATGGTACAGCTGGCAACAGCCACCAGAGAGAGAGCTGTCTCGCCTTCGCCGACTCTATCAAGG
AAATCTCCTAGAAGAAAGTGGCCCGCCACCTGAGTCGATGCCAGAGATGCCCACTACACCACCAGCAGAATCCTCCATTG
AGCAGCCAGGCTCCCAGAGTGCT

Alignment

ORF - retro_mmus_2036 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.16 %
• Parental protein coverage: 87.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VAQNVKLLEQFVCAHTGIIFHAPYTGVCMKQHKKLTQAIQKARECGLLSYYVPQVEPRDADFGTVHGAVS
          ...NVKLLEQFVCAHTGIIFHAPYTGVCMKQHKKLTQAIQKARECGLLSYYVPQVEPRDADF.TVHGAVS
Retrocopy IEKNVKLLEQFVCAHTGIIFHAPYTGVCMKQHKKLTQAIQKARECGLLSYYVPQVEPRDADFRTVHGAVS

Parental  VTPPAPTLLSGEPWYPWYSWQQPPERELSRLRRLYQGNLLEESGPPPESMPEMPTTPPAESSIEQPGSQS
          VTPPAPTLLSGEPWYPWYSWQQPPERELSRLRRLYQGNLLEESGPPPESMPEMPTTPPAESSIEQPGSQS
Retrocopy VTPPAPTLLSGEPWYPWYSWQQPPERELSRLRRLYQGNLLEESGPPPESMPEMPTTPPAESSIEQPGSQS

Parental  A
          A
Retrocopy A

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	6.38 RPM
SRP007412_cerebellum	0.04 RPM	4.65 RPM
SRP007412_heart	0.09 RPM	8.09 RPM
SRP007412_kidney	0.06 RPM	7.89 RPM
SRP007412_liver	0.22 RPM	8.60 RPM
SRP007412_testis	0.32 RPM	10.93 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2036 was not detected

EST

No EST(s) were mapped for retro_mmus_2036 retrocopy.

TSS

No TSS is located nearby retro_mmus_2036 retrocopy 5' end.

Lab

retro_mmus_2036 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2036 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005581	1 retrocopy	retro_chof_505,
Macropus eugenii	ENSMEUG00000012457	10 retrocopies	retro_meug_1183, retro_meug_2004, retro_meug_2124, retro_meug_215, retro_meug_610, retro_meug_648, retro_meug_696, retro_meug_712, retro_meug_717, retro_meug_734,
Macaca mulatta	ENSMMUG00000006525	1 retrocopy	retro_mmul_900,
Monodelphis domestica	ENSMODG00000015933	1 retrocopy	retro_mdom_426,
Mus musculus	ENSMUSG00000024436	1 retrocopy	retro_mmus_2036 ,
Nomascus leucogenys	ENSNLEG00000005224	1 retrocopy	retro_nleu_1811,
Oryctolagus cuniculus	ENSOCUG00000002149	2 retrocopies	retro_ocun_1307, retro_ocun_1641,
Pongo abelii	ENSPPYG00000016412	1 retrocopy	retro_pabe_2050,
Pan troglodytes	ENSPTRG00000017932	1 retrocopy	retro_ptro_1648,
Rattus norvegicus	ENSRNOG00000000804	1 retrocopy	retro_rnor_1328,
Ictidomys tridecemlineatus	ENSSTOG00000011853	1 retrocopy	retro_itri_254,
Tarsius syrichta	ENSTSYG00000003333	1 retrocopy	retro_tsyr_1769,