RetrogeneDB ID: retro_mmus_2012

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:18249457..18249843(-)
• Located in intron of: ENSMUSG00000026740

Retrocopy information

• Ensembl ID: ENSMUSG00000083070
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Gar1
• Ensembl ID: ENSMUSG00000028010
• Aliases: Gar1, AA409823, AI326794, C430047J18Rik, Nola1
• Description: GAR1 ribonucleoprotein homolog (yeast) [Source:MGI Symbol;Acc:MGI:1930948]

Sequence

>retro_mmus_2012
GGATGAGGGGGTGGTCGTGGTGGCTTTAATAAATTTCAAGATCAAGGGCCTCCAGAACATGTCGTCTTGTTTGGAGAGTT
CATGCATCTCTGTGAAGATGACATCATTTGTAAATGTACCACAGAGGGAAACACGGTACCTTACTTCAATGCTCCTGTTT
ATTTAGAAAACAAAGAACAAATCAGGAAAGTGGATGGGATGTTTGGACAACTTAGAGATTTTTATTTTTCAGTTAAATTG
TCAAAAAACATGAAGGTATCTTCCTTTAAAAAGCTACAGAAGTTTTATATAACCCATATAAGCTGCTGCCACTGCAGAGG
TTTCTGCCTCGTCATACTGGTGAGAAAGGACCTCCCAGAGGTGGCAGTGGTGGCAGCAGGGGAGGT

Alignment

ORF - retro_mmus_2012 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.38 %
• Parental protein coverage: 55.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GRGGGRGGFNKFQDQGPPERVVLLGEFMHPCEDDIVCKCTTEENKVPYFNAPVYLENKEQVGKVDEIFGQ
          G.GGGRGGFNKFQDQGPPE.VVL.GEFMH.CEDDI.CKCTTE.N.VPYFNAPVYLENKEQ..KVD..FGQ
Retrocopy G*GGGRGGFNKFQDQGPPEHVVLFGEFMHLCEDDIICKCTTEGNTVPYFNAPVYLENKEQIRKVDGMFGQ

Parental  LRDFYFSVKLSENMKASSFKKLQKFYI-DPYKLLPLQRFLPRPPGEKGPPRGGGGGGRGG
          LRDFYFSVKLS.NMK.SSFKKLQKFYI..PYKLLPLQRFLPR..GEKGPPRGG.GG.RGG
Retrocopy LRDFYFSVKLSKNMKVSSFKKLQKFYI<NPYKLLPLQRFLPRHTGEKGPPRGGSGGSRGG

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	9.63 RPM
SRP007412_cerebellum	0.00 RPM	12.94 RPM
SRP007412_heart	0.00 RPM	9.09 RPM
SRP007412_kidney	0.00 RPM	13.38 RPM
SRP007412_liver	0.03 RPM	8.30 RPM
SRP007412_testis	0.00 RPM	33.48 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2012 was not detected

EST

No EST(s) were mapped for retro_mmus_2012 retrocopy.

TSS

No TSS is located nearby retro_mmus_2012 retrocopy 5' end.

Lab

retro_mmus_2012 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2012 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004605	2 retrocopies	retro_amel_1932, retro_amel_682,
Homo sapiens	ENSG00000109534	1 retrocopy	retro_hsap_3130,
Gorilla gorilla	ENSGGOG00000008681	1 retrocopy	retro_ggor_2144,
Myotis lucifugus	ENSMLUG00000003776	1 retrocopy	retro_mluc_1866,
Macaca mulatta	ENSMMUG00000021225	1 retrocopy	retro_mmul_1992,
Mustela putorius furo	ENSMPUG00000008615	2 retrocopies	retro_mputfur_1491, retro_mputfur_689,
Mus musculus	ENSMUSG00000028010	1 retrocopy	retro_mmus_2012 ,
Nomascus leucogenys	ENSNLEG00000016578	1 retrocopy	retro_nleu_2251,
Oryctolagus cuniculus	ENSOCUG00000003901	1 retrocopy	retro_ocun_414,
Otolemur garnettii	ENSOGAG00000004693	1 retrocopy	retro_ogar_1017,
Ochotona princeps	ENSOPRG00000012089	1 retrocopy	retro_opri_1168,
Pongo abelii	ENSPPYG00000014996	1 retrocopy	retro_pabe_2586,
Pan troglodytes	ENSPTRG00000016364	1 retrocopy	retro_ptro_2119,
Tarsius syrichta	ENSTSYG00000013668	2 retrocopies	retro_tsyr_355, retro_tsyr_613,
Tursiops truncatus	ENSTTRG00000016318	1 retrocopy	retro_ttru_1539,