RetrogeneDB ID: retro_mmus_759

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:6563382..6563681(-)
• Located in intron of: ENSMUSG00000000378

Retrocopy information

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

Parental gene information

• Parental gene symbol: 1810009A15Rik
• Ensembl ID: ENSMUSG00000071653
• Aliases: None
• Description: RIKEN cDNA 1810009A15 gene [Source:MGI Symbol;Acc:MGI:1913526]

Sequence

>retro_mmus_759
GAGAAGTTGTTCAAGCGCCGCAGGTCAGTCCTAAGCAGGAGTGGGAGATGGAAGCACCAGGCGATTGGGGCTGTGATATA
GCAGGGCTAACTACAAGATACCTCAAGAAGCGGGCATCCAGTACACATGCCAACATCACAGTATCTAAGAAGCACAGGAA
ACTCTTGAAAGAGATCCAACTTGCCCAGAAAGAAAAAGCAGCCATGGTAGTGGAAGCCCCCTCCAAGTTAACCAGGACTA
GTCAGCCACAGCCCAAACGACAAAAGAAGATAAAAGATCTCCAGGATGTGGATGTGGAG

Alignment

ORF - retro_mmus_759 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.84 %
• Parental protein coverage: 82.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KKLFKRRR-VLSRDRRRKRQVVGAVIDEG-LTTKHHLKKRASSARANITLSGKKRRKLLQQIRLAQKEKA
          .KLFKRRR.VLSR..R.K.Q..GAVI..G.LTT...LKKRASS..ANIT.S.KK.RKLL..I.LAQKEKA
Retrocopy EKLFKRRRSVLSRSGRWKHQAIGAVI*QG<LTTRY-LKKRASSTHANITVS-KKHRKLLKEIQLAQKEKA

Parental  AMEVEAPSKSTRTSQPQPKQQKKIKAPQDVAME
          AM.VEAPSK.TRTSQPQPK.QKKIK..QDV..E
Retrocopy AMVVEAPSKLTRTSQPQPKRQKKIKDLQDVDVE

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	0.05 RPM	7.01 RPM
SRP007412_cerebellum	0.00 RPM	8.51 RPM
SRP007412_heart	0.00 RPM	9.81 RPM
SRP007412_kidney	0.00 RPM	13.73 RPM
SRP007412_liver	0.00 RPM	11.55 RPM
SRP007412_testis	0.00 RPM	34.72 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_759 was not detected

EST

No EST(s) were mapped for retro_mmus_759 retrocopy.

TSS

No TSS is located nearby retro_mmus_759 retrocopy 5' end.

Lab

retro_mmus_759 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_759 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_1066

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006512	1 retrocopy	retro_amel_1386,
Bos taurus	ENSBTAG00000010465	2 retrocopies	retro_btau_1195, retro_btau_1799,
Canis familiaris	ENSCAFG00000015719	2 retrocopies	retro_cfam_1104, retro_cfam_757,
Felis catus	ENSFCAG00000025454	2 retrocopies	retro_fcat_1722, retro_fcat_773,
Macaca mulatta	ENSMMUG00000013949	4 retrocopies	retro_mmul_1186, retro_mmul_1541, retro_mmul_1785, retro_mmul_1981,
Mus musculus	ENSMUSG00000071653	2 retrocopies	retro_mmus_1809, retro_mmus_759 ,
Otolemur garnettii	ENSOGAG00000033103	1 retrocopy	retro_ogar_811,
Rattus norvegicus	ENSRNOG00000019701	4 retrocopies	retro_rnor_1066, retro_rnor_1955, retro_rnor_851, retro_rnor_883,
Sus scrofa	ENSSSCG00000023323	2 retrocopies	retro_sscr_1162, retro_sscr_1163,