RetrogeneDB ID: retro_mmus_2782

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:117997206..117997989(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082791
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Lasp1
• Ensembl ID: ENSMUSG00000038366
• Aliases: Lasp1, AA408629, Def-4, SH3P6, Tg(Col1a1-lacZ)1Ngma
• Description: LIM and SH3 protein 1 [Source:MGI Symbol;Acc:MGI:109656]

Sequence

>retro_mmus_2782
ATGAACCCTAAGTGTGCCCGGTGCGGCAAGATCGTGTACCCCACGGAGAAGGTGAACTGTTTAGATAAGTACTGGCATAA
AGCATGCTTTCACTGCGAGACCTGCAAGATGACCCTGAACATGAAGAACTACAAGGGTTATGAGAAGAAGCCTTACTGCA
ATGCACACTATCCCAAGCAGTCCTTCACCATAGTGGCCAACACTCCGGAAAACCTCCGCCTCAAGCAACAGAGCGAGCTG
CAGAGTCAGGTGCGCTACAAGGAGGAGTTTGAGAAGAATAAGGGCAAAGGTTTCAGCGTGGTGGCAGACACGCCCGAGCT
GCAGAGAATCAAGAAGATCCAGGACCAGATCAGCAATATCAAATACCATGAGGAGTTTGAGAAGAGCCGCAAGGGGCTCA
TTTGGGGTGAAGGGGTGGAACCAGAGCGCCGAGGAGCCCAGGACAGCAGCAGCTACCGGAGGCCCACAGAGCAGCCGCAG
CCTCACCATATCCCAACCAGTGCCCCCGTGTACCAGCAGCCCCAGCAGCAGCAGATGACCTCGTCCTATGGTGGATATAA
GGAGCCAGCAGCCCCTGTCTCCATACAGCGCAGTGCTCCAGGTGGCGGTGGGAAACGGTACCGTGCAGTGTATGATGACA
GCGCTGCCAATGAGGACGAGGTCTCCTTCCAGGATGGAGACACCATCGTCAATGTGCAGCAGATCGATGACGGCTGGATG
TACGGGACCGTAGAGCGCACCGGTGACTCGGGGATGCTGCCAGGCAACTACGCGGAGGCCATC

Alignment

ORF - retro_mmus_2782 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.92 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNPNCARCGKIVYPTEKVNCLDKYWHKACFHCETCKMTLNMKNYKGYEKKPYCNAHYPKQSFTMVADTPE
          MNP.CARCGKIVYPTEKVNCLDKYWHKACFHCETCKMTLNMKNYKGYEKKPYCNAHYPKQSFT.VA.TPE
Retrocopy MNPKCARCGKIVYPTEKVNCLDKYWHKACFHCETCKMTLNMKNYKGYEKKPYCNAHYPKQSFTIVANTPE

Parental  NLRLKQQSELQSQVRYKEEFEKNKGKGFSVVADTPELQRIKKTQDQISNIKYHEEFEKSRMGPSGGEGVE
          NLRLKQQSELQSQVRYKEEFEKNKGKGFSVVADTPELQRIKK.QDQISNIKYHEEFEKSR.G...GEGVE
Retrocopy NLRLKQQSELQSQVRYKEEFEKNKGKGFSVVADTPELQRIKKIQDQISNIKYHEEFEKSRKGLIWGEGVE

Parental  PERREAQDSSSYRRPTEQQQPQPHHIPTSAPVYQQPQQQQMTSSYGGYKEPAAPVSIQRSAPGGGGKRYR
          PERR.AQDSSSYRRPTE..QPQPHHIPTSAPVYQQPQQQQMTSSYGGYKEPAAPVSIQRSAPGGGGKRYR
Retrocopy PERRGAQDSSSYRRPTE--QPQPHHIPTSAPVYQQPQQQQMTSSYGGYKEPAAPVSIQRSAPGGGGKRYR

Parental  AVYDYSAADEDEVSFQDGDTIVNVQQIDDGWMYGTVERTGDTGMLPANYVEAI
          AVYD.SAA.EDEVSFQDGDTIVNVQQIDDGWMYGTVERTGD.GMLP.NY.EAI
Retrocopy AVYDDSAANEDEVSFQDGDTIVNVQQIDDGWMYGTVERTGDSGMLPGNYAEAI

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	0.56 RPM	122.09 RPM
SRP007412_cerebellum	1.78 RPM	110.16 RPM
SRP007412_heart	0.03 RPM	53.45 RPM
SRP007412_kidney	1.08 RPM	125.64 RPM
SRP007412_liver	0.66 RPM	77.72 RPM
SRP007412_testis	31.70 RPM	32.29 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2782 was not detected

EST

No EST(s) were mapped for retro_mmus_2782 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_117659	670 libraries	377 libraries	22 libraries	0 libraries	3 libraries

The graphical summary, for retro_mmus_2782 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_2782 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2782 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	ENSMUSG00000038366	1 retrocopy	retro_mmus_2782 ,
Rattus norvegicus	ENSRNOG00000004132	1 retrocopy	retro_rnor_946,