RetrogeneDB ID: retro_mmus_947

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:71754163..71754385(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: 3110009E18Rik
• Ensembl ID: ENSMUSG00000026388
• Aliases: None
• Description: RIKEN cDNA 3110009E18 gene [Source:MGI Symbol;Acc:MGI:1920353]

Sequence

>retro_mmus_947
ATGGCTGCTGAGGAGGCTACCACTACAGTTCACCTCATCCATTCATTTGAGCGTCAAAATTTCAAACCTATAGTAGATCA
TGGAGTTAATTTGCCTCAAACTATGTAGGAATTTATACGATTCCTAAAGCAAGATGTCCTTGTGAGGACCACCCTGCTGC
CACCACTCACAAATTACAAATATGATACACTAAAGATTCTTCATCAAGCTCACAAGGCAAAG

Alignment

ORF - retro_mmus_947 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.38 %
• Parental protein coverage: 61.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAEEATLTVRLIRSFEHRNFKPVVYHGVNLHQTVKEFIIFLKQDVPLRTSLPPPLRNYKYDTLKILHQA
          MAAEEAT.TV.LI.SFE..NFKP.V.HGVNL.QT..EFI.FLKQDV..RT.L.PPL.NYKYDTLKILHQA
Retrocopy MAAEEATTTVHLIHSFERQNFKPIVDHGVNLPQTM*EFIRFLKQDVLVRTTLLPPLTNYKYDTLKILHQA

Parental  HKAK
          HKAK
Retrocopy HKAK

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	1.17 RPM
SRP007412_cerebellum	0.00 RPM	0.52 RPM
SRP007412_heart	0.00 RPM	0.90 RPM
SRP007412_kidney	0.00 RPM	1.04 RPM
SRP007412_liver	0.00 RPM	0.19 RPM
SRP007412_testis	0.00 RPM	3.20 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_947 was not detected

EST

No EST(s) were mapped for retro_mmus_947 retrocopy.

TSS

No TSS is located nearby retro_mmus_947 retrocopy 5' end.

Lab

retro_mmus_947 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_947 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008507	2 retrocopies	retro_amel_1062, retro_amel_1693,
Bos taurus	ENSBTAG00000010599	1 retrocopy	retro_btau_965,
Canis familiaris	ENSCAFG00000004896	2 retrocopies	retro_cfam_1119, retro_cfam_1727,
Equus caballus	ENSECAG00000002063	1 retrocopy	retro_ecab_384,
Myotis lucifugus	ENSMLUG00000004031	1 retrocopy	retro_mluc_1204,
Mustela putorius furo	ENSMPUG00000000943	1 retrocopy	retro_mputfur_726,
Mus musculus	ENSMUSG00000026388	1 retrocopy	retro_mmus_947 ,
Pteropus vampyrus	ENSPVAG00000011615	1 retrocopy	retro_pvam_337,
Sus scrofa	ENSSSCG00000015718	1 retrocopy	retro_sscr_311,