RetrogeneDB ID: retro_mmus_1051

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:97609533..97609817(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Plac8
• Ensembl ID: ENSMUSG00000029322
• Aliases: Plac8, C15, D5Wsu111e
• Description: placenta-specific 8 [Source:MGI Symbol;Acc:MGI:2445289]

Sequence

>retro_mmus_1051
CCCAAGGTCATCATGACTCAATTTGGGTTTGTTCAAGTGTCCAGCTGGCAGGCAACCCATGTGATTGCCTCCATGACGGC
GGAGTCTGAATCAGTCATACATTTTGTTTTATGTGTCTTGAGTGTCAAGTGGCATCTCACATGAATGAATGTTGTTTGTG
GGGAATAACTGCAGCAATGGGGACTGTCCACCAACCCTGATCTGGCAATCCCAGGTCTGTTTGTGATAACCACACTGCTG
TCCACTGCTGTCCTGTTTTCTCTCTGTGCCAAATCAAGCAGGAG

Alignment

ORF - retro_mmus_1051 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.52 %
• Parental protein coverage: 87.5 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PTVIVTQPGFVRAPQNSNWQTSL-CDCFSDCGVCLCGTFCFTCLGCQVAADMNECCLCGTTVAMRTLYRT
          P.VI.TQ.GFV...Q.S.WQ....CDC..D.GV....TFCF.CL.CQVA..MNECCL.G.T.AM.T....
Retrocopy PKVIMTQFGFV---QVSSWQATH<CDCLHDGGV*ISHTFCFMCLECQVASHMNECCLWGITAAMGTVHQP

Parental  RYGIPGSICDDYMVTLFCPVCSVCQLKRD
          ..G.P.S.CD.......CPV.S.CQ.K..
Retrocopy *SGNPRSVCDNHTAVHCCPVFSLCQIKQE

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	0.30 RPM
SRP007412_cerebellum	0.00 RPM	1.22 RPM
SRP007412_heart	0.00 RPM	0.50 RPM
SRP007412_kidney	0.00 RPM	11.38 RPM
SRP007412_liver	0.00 RPM	12.26 RPM
SRP007412_testis	0.14 RPM	19.39 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1051 was not detected

EST

No EST(s) were mapped for retro_mmus_1051 retrocopy.

TSS

No TSS is located nearby retro_mmus_1051 retrocopy 5' end.

Lab

retro_mmus_1051 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1051 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000145287	1 retrocopy	retro_hsap_1165,
Gorilla gorilla	ENSGGOG00000007464	1 retrocopy	retro_ggor_910,
Monodelphis domestica	ENSMODG00000019309	1 retrocopy	retro_mdom_950,
Mus musculus	ENSMUSG00000029322	1 retrocopy	retro_mmus_1051 ,
Otolemur garnettii	ENSOGAG00000017232	1 retrocopy	retro_ogar_714,
Pan troglodytes	ENSPTRG00000016226	1 retrocopy	retro_ptro_800,
Rattus norvegicus	ENSRNOG00000002217	2 retrocopies	retro_rnor_1489, retro_rnor_1878,