RetrogeneDB ID: retro_mmus_1073

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:12259815..12260271(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Dazap2
• Ensembl ID: ENSMUSG00000000346
• Aliases: Dazap2, AI314727, Brbp, Gcap28, Prtb, gt6-12, mKIAA0058
• Description: DAZ associated protein 2 [Source:MGI Symbol;Acc:MGI:1344344]

Sequence

>retro_mmus_1073
CCAACACAGCCTACCTACCCTGTGCAACCTCCTGGGAATCCAGTATATCCTCAGACCTTACATCTTCCTCAGGCTCCACC
CTATACTGATGCTCCACCTGCATATTCAGAGCTCTATCGTCCAAGCTTTGTTCATCCAGGGGCTGCCACAGTCCCCACCA
TGTCAGCTGCATTTCCTGGCGCCTCATTGTATCTGCCTATGGCCCAGTCTGTGGCTGTTGGGCCTCTAGGTTCCACAATA
CCCATGGCTTATTATGCAGTTGGTCCCAACTATTCACCTGGCTCAGCAGTGTTGGTGGAAGGAGGGCATGATGCAGGTGC
CAGATTTGGAGCTGGTGCCACCGCTGGCAACATTCCTCCTCCACCTCCTGGATGCCCTCCCAACACTGCTCAGCTCGCAG
TCATGCAGGGAGCAAATGTCCCTGTAACTCAGCTCAAGGGAAACTTCTTCATGGGT

Alignment

ORF - retro_mmus_1073 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.39 %
• Parental protein coverage: 90.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PTQPTYPVQPPGNPVYPQTLHLPQAPPYTDAPPAYSELYRPSFVHPGAATVPTMSAAFPGASLYLPMAQS
          PTQPTYPVQPPGNPVYPQTLHLPQAPPYTDAPPAYSELYRPSFVHPGAATVPTMSAAFPGASLYLPMAQS
Retrocopy PTQPTYPVQPPGNPVYPQTLHLPQAPPYTDAPPAYSELYRPSFVHPGAATVPTMSAAFPGASLYLPMAQS

Parental  VAVGPLGSTIPMAYYPVGPIYPPGSAVLVEGGYDAGARFGAGATAGNIPPPPPGCPPNAAQLAVMQGANV
          VAVGPLGSTIPMAYY.VGP.Y.PGSAVLVEGG.DAGARFGAGATAGNIPPPPPGCPPN.AQLAVMQGANV
Retrocopy VAVGPLGSTIPMAYYAVGPNYSPGSAVLVEGGHDAGARFGAGATAGNIPPPPPGCPPNTAQLAVMQGANV

Parental  LVTQRKGNFFMG
          .VTQ.KGNFFMG
Retrocopy PVTQLKGNFFMG

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	0.21 RPM	87.19 RPM
SRP007412_cerebellum	0.39 RPM	93.92 RPM
SRP007412_heart	0.06 RPM	140.55 RPM
SRP007412_kidney	0.77 RPM	194.46 RPM
SRP007412_liver	0.36 RPM	90.04 RPM
SRP007412_testis	0.55 RPM	76.48 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1073 was not detected

EST

No EST(s) were mapped for retro_mmus_1073 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_27055	412 libraries	507 libraries	151 libraries	2 libraries	0 libraries

The graphical summary, for retro_mmus_1073 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_1073 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1073 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000298	1 retrocopy	retro_chof_85,
Dasypus novemcinctus	ENSDNOG00000009306	1 retrocopy	retro_dnov_1772,
Equus caballus	ENSECAG00000007313	1 retrocopy	retro_ecab_286,
Myotis lucifugus	ENSMLUG00000009959	1 retrocopy	retro_mluc_351,
Mus musculus	ENSMUSG00000000346	1 retrocopy	retro_mmus_1073 ,
Sorex araneus	ENSSARG00000003823	1 retrocopy	retro_sara_632,
Tupaia belangeri	ENSTBEG00000013232	1 retrocopy	retro_tbel_3228,
Vicugna pacos	ENSVPAG00000001156	2 retrocopies	retro_vpac_314, retro_vpac_568,