RetrogeneDB ID: retro_mmus_1056

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:103356501..103357701(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000047643
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Etv1
• Ensembl ID: ENSMUSG00000004151
• Aliases: Etv1, ER81, Etsrp81
• Description: ets variant gene 1 [Source:MGI Symbol;Acc:MGI:99254]

Sequence

>retro_mmus_1056
TTAGTGGCTTTTCATGGCCTCCCACTGAAAATCAAGAAAGAACCCCACAGCCCATGTTCAGAACTCGGGTCTGCTTGCAG
TCAAGAGCAGCCCTTTAAATTCAGCTATGGAGAAAAGTGCCTGTGCAATGTCAGTGCCTATGATCAGAAGCCACAAGTGG
GAATGAGGCCCTCCAATCCCCCGACACCATCCAGCACTCCAGTGTCCCCACTACACCATGCATCTCCAAACACAGCTCAT
ACTCCGAAACCTGACCGGGCCTTCCCAGCTCACCTCCCTCCTTCTCAGTCCATACCAGACAGCACCTACCCCATGGACCA
CAGATTTCGCCGCCAGCTTTCTGAACCCTGTAATTCTTTTCCTCCTTTGCCGACAATGCCAAGGGAAGGGCGTCCTATGT
ACCAACGCCAGATGTCTGAGCCAAACATCCCCTTCCCACCACAAGGCTTTAAGCAGGAGTACCACGACCCAGTCTATGAA
CATACCACCATGGTTGGCGGTGCAGCCAGCCAAAGCTTCCCCCCTCCTTTGATGATCAAACAGGAACCCAGAGATTTTGC
ATATGACTCAGAAGTGCCTAGCTGCCACTCCATTTATATGAGGCAAGAAGGCTTCCTGGCTCATCCAAGCAGAACAGAAG
GCTGCATGTTTGAGAAGGGTCCCAGGCAGTTCTATGATGACACCTGTGTGGTCCCGGAGAAGTTCGATGGGGACATTAAG
CAAGAGCCTGGAATGTACCGGGAAGGACCCATGTACCAGTGGCGAGGATCCCTCCAGCTCTGGCAGTTTTTGGTAGCTCT
TCTGGATGACCCTTCAAATTCTCATTTCATTGCCTGGACTGGACGAGGCATGGAATTTAAACTGATTGAGCCCGAAGAGG
TGGCCCGGCGTTGGGGCATTCAGAAGAACAGGCCGGCGATGAACTATGACAAACTTAGTCGTTCTCTCCGCTATTATTAT
GAGAAGGGAATCATGCAAAAGGTGGCTGGAGAAAGATACGTGTACAAATTTGTGTGTGACCCGGAAGCCCTTTTCTCTAT
GGCCTTTCCGGATAACCAGCGCCCACTGCTGAAGACGGACATGGAACGTCACATCAACGAAGAGGACACAGTTCCTCTGT
CTCACTTTGATGAGAGCATGACCTACATGCCTGAAGGGGGCTGCTGCAACCCTCACCCCTACAACGAAGGATACGTGTAC

Alignment

ORF - retro_mmus_1056 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.25 %
• Parental protein coverage: 95.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LVAFHGLPLKIKKEPHSPCSELGSACSQEQPFKFSYGEKCLYNVSAYDQKPQVGMRPSNPPTPSSTPVSP
          LVAFHGLPLKIKKEPHSPCSELGSACSQEQPFKFSYGEKCL.NVSAYDQKPQVGMRPSNPPTPSSTPVSP
Retrocopy LVAFHGLPLKIKKEPHSPCSELGSACSQEQPFKFSYGEKCLCNVSAYDQKPQVGMRPSNPPTPSSTPVSP

Parental  LHHASPNTAHTPKPDRAFPAHLPPSQSIPDSTYPMDHRFRRQLSEPCNSFPPLPTMPREGRPMYQRQMSE
          LHHASPNTAHTPKPDRAFPAHLPPSQSIPDSTYPMDHRFRRQLSEPCNSFPPLPTMPREGRPMYQRQMSE
Retrocopy LHHASPNTAHTPKPDRAFPAHLPPSQSIPDSTYPMDHRFRRQLSEPCNSFPPLPTMPREGRPMYQRQMSE

Parental  PNIPFPPQGFKQEYHDPVYEHTTMVGGAASQSFPPPLMIKQEPRDFAYDSEVPSCHSIYMRQEGFLAHPS
          PNIPFPPQGFKQEYHDPVYEHTTMVGGAASQSFPPPLMIKQEPRDFAYDSEVPSCHSIYMRQEGFLAHPS
Retrocopy PNIPFPPQGFKQEYHDPVYEHTTMVGGAASQSFPPPLMIKQEPRDFAYDSEVPSCHSIYMRQEGFLAHPS

Parental  RTEGCMFEKGPRQFYDDTCVVPEKFDGDIKQEPGMYREGPTYQRRGSLQLWQFLVALLDDPSNSHFIAWT
          RTEGCMFEKGPRQFYDDTCVVPEKFDGDIKQEPGMYREGP.YQ.RGSLQLWQFLVALLDDPSNSHFIAWT
Retrocopy RTEGCMFEKGPRQFYDDTCVVPEKFDGDIKQEPGMYREGPMYQWRGSLQLWQFLVALLDDPSNSHFIAWT

Parental  GRGMEFKLIEPEEVARRWGIQKNRPAMNYDKLSRSLRYYYEKGIMQKVAGERYVYKFVCDPEALFSMAFP
          GRGMEFKLIEPEEVARRWGIQKNRPAMNYDKLSRSLRYYYEKGIMQKVAGERYVYKFVCDPEALFSMAFP
Retrocopy GRGMEFKLIEPEEVARRWGIQKNRPAMNYDKLSRSLRYYYEKGIMQKVAGERYVYKFVCDPEALFSMAFP

Parental  DNQRPLLKTDMERHINEEDTVPLSHFDESMTYMPEGGCCNPHPYNEGYVY
          DNQRPLLKTDMERHINEEDTVPLSHFDESMTYMPEGGCCNPHPYNEGYVY
Retrocopy DNQRPLLKTDMERHINEEDTVPLSHFDESMTYMPEGGCCNPHPYNEGYVY

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	1.38 RPM	38.67 RPM
SRP007412_cerebellum	2.17 RPM	133.69 RPM
SRP007412_heart	0.22 RPM	6.32 RPM
SRP007412_kidney	0.38 RPM	11.57 RPM
SRP007412_liver	0.03 RPM	0.52 RPM
SRP007412_testis	0.00 RPM	2.84 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1056 was not detected

EST

4 EST(s) were mapped to retro_mmus_1056 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AW125172	103356700	103356999	100	299	0	299
BE649667	103356682	103357237	99.9	554	1	553
DT908720	103356634	103357219	100	581	0	577
DT914351	103356634	103357064	98.2	422	8	414

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_26286	929 libraries	108 libraries	30 libraries	5 libraries	0 libraries

The graphical summary, for retro_mmus_1056 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_1056 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1056 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000004151	1 retrocopy	retro_mmus_1056 ,
Mus musculus	ENSMUSG00000013089	1 retrocopy	retro_mmus_572,