RetrogeneDB ID: retro_mmus_1023

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:64998992..64999372(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ctdnep1
• Ensembl ID: ENSMUSG00000018559
• Aliases: Ctdnep1, 2610507E10Rik, Dullard
• Description: CTD nuclear envelope phosphatase 1 [Source:MGI Symbol;Acc:MGI:1914431]

Sequence

>retro_mmus_1023
ATTTACCTTTTGCGGAGCAGATCCTCACGGTAATTCAGTATCTAACTGTTCAATATGATATCCTTCGCTTATCTCCCTTG
TCTGGGAATCTACTAGCCCAGGTGAAGAGGAAGATCCTGGTGTGGATATGGATGAAACCCTTATTTACTCTCACCACGAT
GGGGTCCTGAGGCCTACAGTGAGACCTGGAACACCTCCCCATTTCATCCTCAAGGTGGTAATAGACAAACATCCTGTCTG
GTTTTTTTGTACATAAGAGACTCCATGTGGATTTCTCCTTAGAAGTGGTAAACCAGTGGTATGAGCTTGTCATGTTCACA
GCAAGCATGGAAATTTATGGCTCTGCTGTGGCAGATAAACTGGACGATAGCAAAAGCATT

Alignment

ORF - retro_mmus_1023 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.85 %
• Parental protein coverage: 52.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IYLLR-RQIRTVIQYQTVRYDILPLSPLSRNRLAQVKRKILV-LDLDETLIHSHHDGVLRPTVRPGTPPD
          IYLLR..QI.TVIQY.TV.YDIL.LSPLS.N.LAQVKRKILV..D.DETLI.SHHDGVLRPTVRPGTPP.
Retrocopy IYLLR<EQILTVIQYLTVQYDILRLSPLSGNLLAQVKRKILV<VDMDETLIYSHHDGVLRPTVRPGTPPH

Parental  FILKVVIDKHPV-RFFVHKRPHVDFFLEVVSQWYELVVFTASMEIYGSAVADKLDNSRSI
          FILKVVIDKHPV..FFVHKR.HVDF.LEVV.QWYELV.FTASMEIYGSAVADKLD.S.SI
Retrocopy FILKVVIDKHPV>GFFVHKRLHVDFSLEVVNQWYELVMFTASMEIYGSAVADKLDDSKSI

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	44.02 RPM
SRP007412_cerebellum	0.00 RPM	37.86 RPM
SRP007412_heart	0.00 RPM	69.83 RPM
SRP007412_kidney	0.02 RPM	44.93 RPM
SRP007412_liver	0.00 RPM	28.37 RPM
SRP007412_testis	0.00 RPM	36.73 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1023 was not detected

EST

No EST(s) were mapped for retro_mmus_1023 retrocopy.

TSS

No TSS is located nearby retro_mmus_1023 retrocopy 5' end.

Lab

retro_mmus_1023 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1023 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019443	1 retrocopy	retro_btau_915,
Dasypus novemcinctus	ENSDNOG00000013673	2 retrocopies	retro_dnov_1802, retro_dnov_2494,
Echinops telfairi	ENSETEG00000004654	1 retrocopy	retro_etel_125,
Homo sapiens	ENSG00000175826	2 retrocopies	retro_hsap_2687, retro_hsap_3188,
Gorilla gorilla	ENSGGOG00000013777	2 retrocopies	retro_ggor_1338, retro_ggor_1874,
Macaca mulatta	ENSMMUG00000010547	1 retrocopy	retro_mmul_2011,
Mus musculus	ENSMUSG00000018559	1 retrocopy	retro_mmus_1023 ,
Otolemur garnettii	ENSOGAG00000004389	1 retrocopy	retro_ogar_1001,
Pongo abelii	ENSPPYG00000007902	2 retrocopies	retro_pabe_2294, retro_pabe_2645,
Pan troglodytes	ENSPTRG00000008668	2 retrocopies	retro_ptro_1814, retro_ptro_2256,
Drosophila melanogaster	FBgn0029067	1 retrocopy	retro_dmel_18,