RetrogeneDB ID: retro_mmus_1998

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:161287219..161287692(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081151
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Mphosph6
• Ensembl ID: ENSMUSG00000031843
• Aliases: Mphosph6, 1110001M01Rik, AA536809, C86426
• Description: M phase phosphoprotein 6 [Source:MGI Symbol;Acc:MGI:1915783]

Sequence

>retro_mmus_1998
ATGGCGTCGGAGCGCAAGATTAAGTTATCCAAGAACCTGCTGCGCATGAAGTTCATGCAAAGAGGCCTGGACTCGGAAAC
CAAGAAACAGCTAGAAGAGGAGGAGCGGAAGATGATCAGCGACGAGCACTGGTACCTGGATTTGCCGGAGTTGAAGGAGA
AAGAGAGCTTCATCATAGAGGAGCAGAGCTTCTCCCTGTGTGAAGATCTTCTCTACGGAAGGATGTCATTCAGAGGGTTT
AATCCTGAGGTTAATGCTTCAGATGAATTCTAAGAACCAAGCAGAGGCAGCAGAGGAAGACGAGACGGTAGAGGTCGATG
TGTCTGATGAAGAAATGGCAAGAAGATATGAGACTTTGGTGGGAACAATTGGAAAAAAAGTTTGTCAAGAAAAGGGACCG
AGCCAATTACGAAGAAGGTGAAAATGGAACTATAAAAGCCATAAAACCTAAGATGTTCTTAAAGCCCCAAGAC

Alignment

ORF - retro_mmus_1998 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.12 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASERKTKLSKNLLRMKFMQRGLDSETKKQLEEEERKMISDEHWYLDLPELKEKESFIVEEQSFSLCEDL
          MASERK.KLSKNLLRMKFMQRGLDSETKKQLEEEERKMISDEHWYLDLPELKEKESFI.EEQSFSLCEDL
Retrocopy MASERKIKLSKNLLRMKFMQRGLDSETKKQLEEEERKMISDEHWYLDLPELKEKESFIIEEQSFSLCEDL

Parental  LYGRMSFRGFNPEVEK-LMLQMNSKNRAEAAEEDETVEVDVSDEEMARRYETLVGTIG-KKFVKKRDRAN
          LYGRMSFRGFNPEV....M...N....AE..E...TVEVDVSDEEMARRYETLVGTIG.KKFVKKRDRAN
Retrocopy LYGRMSFRGFNPEVNA>QMNSKNQAEAAEEDE---TVEVDVSDEEMARRYETLVGTIG>KKFVKKRDRAN

Parental  YEEDENGTIKAIKPKKMFLKPQD
          YEE.ENGTIKAIKP.KMFLKPQD
Retrocopy YEEGENGTIKAIKP-KMFLKPQD

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	6.78 RPM
SRP007412_cerebellum	0.04 RPM	8.64 RPM
SRP007412_heart	0.00 RPM	3.80 RPM
SRP007412_kidney	0.02 RPM	6.39 RPM
SRP007412_liver	0.00 RPM	2.21 RPM
SRP007412_testis	0.05 RPM	8.28 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1998 was not detected

EST

No EST(s) were mapped for retro_mmus_1998 retrocopy.

TSS

No TSS is located nearby retro_mmus_1998 retrocopy 5' end.

Lab

retro_mmus_1998 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1998 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009746	1 retrocopy	retro_btau_591,
Choloepus hoffmanni	ENSCHOG00000000127	2 retrocopies	retro_chof_1602, retro_chof_740,
Callithrix jacchus	ENSCJAG00000016498	5 retrocopies	retro_cjac_1730, retro_cjac_2976, retro_cjac_3135, retro_cjac_3136, retro_cjac_3283,
Dipodomys ordii	ENSDORG00000011060	2 retrocopies	retro_dord_62, retro_dord_63,
Echinops telfairi	ENSETEG00000010276	6 retrocopies	retro_etel_1269, retro_etel_1300, retro_etel_1307, retro_etel_749, retro_etel_795, retro_etel_855,
Homo sapiens	ENSG00000135698	1 retrocopy	retro_hsap_353,
Gorilla gorilla	ENSGGOG00000001405	1 retrocopy	retro_ggor_367,
Macropus eugenii	ENSMEUG00000000580	1 retrocopy	retro_meug_726,
Myotis lucifugus	ENSMLUG00000000268	1 retrocopy	retro_mluc_78,
Macaca mulatta	ENSMMUG00000022575	2 retrocopies	retro_mmul_1786, retro_mmul_471,
Mus musculus	ENSMUSG00000031843	2 retrocopies	retro_mmus_1998 , retro_mmus_3662,
Nomascus leucogenys	ENSNLEG00000010725	1 retrocopy	retro_nleu_2264,
Oryctolagus cuniculus	ENSOCUG00000024341	2 retrocopies	retro_ocun_1042, retro_ocun_749,
Otolemur garnettii	ENSOGAG00000012532	3 retrocopies	retro_ogar_1288, retro_ogar_1382, retro_ogar_583,
Pongo abelii	ENSPPYG00000007592	1 retrocopy	retro_pabe_348,
Pan troglodytes	ENSPTRG00000008398	1 retrocopy	retro_ptro_277,
Rattus norvegicus	ENSRNOG00000050087	6 retrocopies	retro_rnor_1760, retro_rnor_2298, retro_rnor_2318, retro_rnor_2320, retro_rnor_2390, retro_rnor_2391,
Ictidomys tridecemlineatus	ENSSTOG00000019608	1 retrocopy	retro_itri_1186,
Tupaia belangeri	ENSTBEG00000013110	8 retrocopies	retro_tbel_1037, retro_tbel_1812, retro_tbel_3027, retro_tbel_32, retro_tbel_333, retro_tbel_4213, retro_tbel_4385, retro_tbel_4415,
Tarsius syrichta	ENSTSYG00000001928	2 retrocopies	retro_tsyr_1511, retro_tsyr_906,