RetrogeneDB ID: retro_mmus_3225

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:83477473..83478710(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Pes1
• Ensembl ID: ENSMUSG00000020430
• Aliases: None
• Description: pescadillo homolog 1, containing BRCT domain (zebrafish) [Source:MGI Symbol;Acc:MGI:1890613]

Sequence

>retro_mmus_3225
GCCCTACGTCATCACTGCCCAAGCCCTGCCCTGTCCAATAAAGGCATTTATTATCAGGCTGAAGTGCTGGGTCAGCTCAT
CGTATGGATTGCACCCTATGCTTTCTCCCATGATCATCCGACAGATGTGGACTACAGGGTCATGGCCACCTTCACTGAGT
TCTATACCATGCTCCTGGGCTTCGTCAACTTCCATCTCTACCAGTCACTCAACCTTCACTACCCACCAAAGCTTGAAGGT
CAAGCCCAAGCAGAGACAAAGATCAGCGAGGACACATATGCATTGGACTCTGAGAGCTCTATGGAGAAACTGGCTGCCCT
CAGTGCCAGCCTGGCCCGAGTGGTGGTGCCTGCTCTAGAGGAGGCTGAGGCTGATGAATTCCCTACTGATAGGGAGGTGA
CAGCACAGGAGGAAGATCGGAGGAAAGAGCTGGAGGCACAGGAAAAGCACAAGAAACTCTTTGAAGGCCCGAAGTTCTTT
CTGAACCGAGAGGTGCCCCGTGAAGCATTGGCCTTCATCATCAGGAGTTTTGGTGGGGATGTATCCTGGGACAAGTCTCT
GTGTATTGGAGCCACCTATGACGTCACAGACTCATGCATCACCCACCAGTTTGTTGACCGGCCGGGGCAGCAAACCCCCA
TCATTGGCAGGTACTATGTACAGCCCCAGTGGGTCTTTGACTGTGTGAATGCCCGGCTCCTCCTCCCTATGGCAGAGTAC
TTCCCCAGGGTTGCAGCTGCCCCCACATCTTTCACCCTTCGTATCTGAGAAGGAAGGAGATTACATTCTCCCTGAGAAGC
TGAAGCTCCTGGCTCTGCAGTGGGGAGAAGACCCAGGAAACTTGGAAAAGGAGGAGGAGGAGGATGAAGATGATGACAAC
GAACGTGATGTTGCATGGGAAAATGAGGAGGAGGAAGATATGGAAGTTGAATCGGAGGAAGAGGAGGAGGAGGTGCACCT
GTTGGCCTTGGAGCAGCACAGGCTGGAAGAGAAGAAACCCCAGGTTATGGCCGGCACTGTGAAGCTGGAAGACAAGCAGC
GGCTGGCCCAGGAGGAAGAGAGTGAGGCTAAGCGCTTGGCCATCATGATGAAGAAAAAGCGAGAGAAGTACCTTTACCAA
AAGATCATGTTTGGCAAATGGCGCAAAATCCGAGAGGCCAACAAGCTGGCAGAGAAGAGGAAAGCCCATGATGATGCTGT
GAGGTCTGAGAAAAAGGCCAAGAGGACAAGGCCCGTG

Alignment

ORF - retro_mmus_3225 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.75 %
• Parental protein coverage: 70.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ALRKLPPQVFLSIKGIYYQAEVLGQPIVWIAPYAFSHDHPTDVDYRVMATFTEFYTTLLGFVNFRLYQSL
          ALR...P...LS.KGIYYQAEVLGQ.IVWIAPYAFSHDHPTDVDYRVMATFTEFYT.LLGFVNF.LYQSL
Retrocopy ALRHHCPSPALSNKGIYYQAEVLGQLIVWIAPYAFSHDHPTDVDYRVMATFTEFYTMLLGFVNFHLYQSL

Parental  NLHYPPKLEGQAQAETKISEDTYALDSESSMEKLAALSASLARVVVPAIEEAEADEFPTDGEVTAQEEDR
          NLHYPPKLEGQAQAETKISEDTYALDSESSMEKLAALSASLARVVVPA.EEAEADEFPTD.EVTAQEEDR
Retrocopy NLHYPPKLEGQAQAETKISEDTYALDSESSMEKLAALSASLARVVVPALEEAEADEFPTDREVTAQEEDR

Parental  KKELEAQEKHKKLFEGLKFFLNREVPREALAFIIRSFGGDVSWDKSLCIGATYDVTDSCITHQIVDRPGQ
          .KELEAQEKHKKLFEG.KFFLNREVPREALAFIIRSFGGDVSWDKSLCIGATYDVTDSCITHQ.VDRPGQ
Retrocopy RKELEAQEKHKKLFEGPKFFLNREVPREALAFIIRSFGGDVSWDKSLCIGATYDVTDSCITHQFVDRPGQ

Parental  QTPIIGRYYVQPQWVFDCVNARLLLPVAEYF-PGMQLPPHLSPFVSEKEGDYIPPEKLKLLALQRGEDPG
          QTPIIGRYYVQPQWVFDCVNARLLLP.AEYF.PG.QLPPHLSPFVSEKEGDYI.PEKLKLLALQ.GEDPG
Retrocopy QTPIIGRYYVQPQWVFDCVNARLLLPMAEYF>PGLQLPPHLSPFVSEKEGDYILPEKLKLLALQWGEDPG

Parental  HLEEEEEEDEDDDNEGDVAAEN-EEEDVEVESEEEEEEEVHLSALEQHRLEEKKPQVMAGTVKLEDKQRL
          .LE.EEEEDEDDDNE.DVA.EN.EEED.EVES.EEEEEEVHL.ALEQHRLEEKKPQVMAGTVKLEDKQRL
Retrocopy NLEKEEEEDEDDDNERDVAWENEEEEDMEVES-EEEEEEVHLLALEQHRLEEKKPQVMAGTVKLEDKQRL

Parental  AQEEESEAKRLAIMMMKKREKYLYQKIMFGKRRKIREANKLAEKRKAHDDAVRSEKKAKRTRPV
          AQEEESEAKRLAIMM.KKREKYLYQKIMFGK.RKIREANKLAEKRKAHDDAVRSEKKAKRTRPV
Retrocopy AQEEESEAKRLAIMMKKKREKYLYQKIMFGKWRKIREANKLAEKRKAHDDAVRSEKKAKRTRPV

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	27.31 RPM
SRP007412_cerebellum	0.09 RPM	27.36 RPM
SRP007412_heart	0.06 RPM	25.56 RPM
SRP007412_kidney	0.08 RPM	38.44 RPM
SRP007412_liver	0.00 RPM	25.23 RPM
SRP007412_testis	0.14 RPM	54.84 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3225 was not detected

EST

No EST(s) were mapped for retro_mmus_3225 retrocopy.

TSS

No TSS is located nearby retro_mmus_3225 retrocopy 5' end.

Lab

retro_mmus_3225 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3225 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000003565	1 retrocopy	retro_cpor_986,
Mus musculus	ENSMUSG00000020430	2 retrocopies	retro_mmus_1393, retro_mmus_3225 ,
Rattus norvegicus	ENSRNOG00000004515	2 retrocopies	retro_rnor_2953, retro_rnor_824,