RetrogeneDB ID: retro_mmus_3281

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:57846467..57847091(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mnd1
• Ensembl ID: ENSMUSG00000033752
• Aliases: Mnd1, 2610034E18Rik, AI591601, Gaj
• Description: meiotic nuclear divisions 1 homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1924165]

Sequence

>retro_mmus_3281
ATGTTAAAGAAAAAAAGGCCGAGTGGGGAGGAAAAGAGAACCCGGATGATGGAGATTTTTTTTTTTTTTGAGACAAAAGA
TGTATTTCAACGGAAAGACCTGGAGGAGCTTGCTCCCAAAGAGAAAGGCATCACTGCCGTGTCAGTGAAGGAAGTCCTTC
AGAGCTTGGTGGGTGATGGTATGACTGACTGCGAGAGGATTGGGACGTCCAATTCCTATTGGGCTTTTCAAAGCAAGGCT
CTTCATGCCAGGAAGTGCAAGTTAGAGGCTCAGAACTCTCAGCTGTCAGAGGGAAGCCAGAAGCAACGCAGACTTAGAGA
AGAGCATTGAGAAAGCTGGAGTTGGCCAGCAAGAGATGGAAGAATGAGCCATGCTTGCAAAAGAACTTAATTCATTTCAA
GACCAAAGGGAACAACTTAAGGCAGAAGCAGAAAAATGCAGAGCATGTGACCCACAGGTTGTGGGAGGAGATATGTCAAG
CAAACAAAGTAGCCAAAGACTCCGTCAATCGATGGACTGGTAACATATCTGCAATAAAATCCTGGGCCAAAAGAAAATTG
GGGTTTGAAGAAAGTAAAAATTGATAAAAACTTTGGAATTCCAGCAGACTTTGACTACATAGAG

Alignment

ORF - retro_mmus_3281 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.52 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSKKRGLSGEEKRTRMMEIFF--ETKDVFQLKDLEKLAPKEKGITAMSVKEVLQSLVDDGMVDCERIGTS
          M.KK...SGEEKRTRMME.....ETKDVFQ.KDLE.LAPKEKGITA.SVKEVLQSLV.DGM.DCERIGTS
Retrocopy MLKKKRPSGEEKRTRMMEXXXXXETKDVFQRKDLEELAPKEKGITAVSVKEVLQSLVGDGMTDCERIGTS

Parental  NYYWAFPSKALHARKRKLEALNSQLSEGSQK-HADLQKSIEKARVGRQETEERAMLAKELSSFRDQRQQL
          N.YWAF.SKALHARK.KLEA.NSQLSEGSQK..ADL.KSIEKA.VG.QE.EE.AMLAKEL.SF.DQR.QL
Retrocopy NSYWAFQSKALHARKCKLEAQNSQLSEGSQK>NADLEKSIEKAGVGQQEMEE*AMLAKELNSFQDQREQL

Parental  KAEVEKYRECDPQVV-EEIREANKVAKEAANRWTDNIFAIKSWAKRKFGFEES-KIDKNFGIPEDFDYID
          KAE.EK.R.CDPQVV.EEI..ANKVAK...NRWT.NI.AIKSWAKRK.GFEES.KIDKNFGIP.DFDYI.
Retrocopy KAEAEKCRACDPQVV>EEICQANKVAKDSVNRWTGNISAIKSWAKRKLGFEES>KIDKNFGIPADFDYIE

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	0.14 RPM
SRP007412_cerebellum	0.00 RPM	0.17 RPM
SRP007412_heart	0.00 RPM	0.72 RPM
SRP007412_kidney	0.00 RPM	0.60 RPM
SRP007412_liver	0.00 RPM	2.27 RPM
SRP007412_testis	0.00 RPM	5.40 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3281 was not detected

EST

No EST(s) were mapped for retro_mmus_3281 retrocopy.

TSS

No TSS is located nearby retro_mmus_3281 retrocopy 5' end.

Lab

retro_mmus_3281 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3281 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018446	1 retrocopy	retro_amel_1745,
Callithrix jacchus	ENSCJAG00000001993	5 retrocopies	retro_cjac_1495, retro_cjac_1907, retro_cjac_2624, retro_cjac_2946, retro_cjac_3979,
Dipodomys ordii	ENSDORG00000004514	1 retrocopy	retro_dord_99,
Felis catus	ENSFCAG00000022084	1 retrocopy	retro_fcat_1833,
Macaca mulatta	ENSMMUG00000004937	1 retrocopy	retro_mmul_395,
Mus musculus	ENSMUSG00000033752	2 retrocopies	retro_mmus_1172, retro_mmus_3281 ,
Nomascus leucogenys	ENSNLEG00000005936	1 retrocopy	retro_nleu_998,
Oryctolagus cuniculus	ENSOCUG00000004594	2 retrocopies	retro_ocun_1865, retro_ocun_360,
Ochotona princeps	ENSOPRG00000015738	1 retrocopy	retro_opri_1121,
Sorex araneus	ENSSARG00000011001	1 retrocopy	retro_sara_417,
Tupaia belangeri	ENSTBEG00000004475	1 retrocopy	retro_tbel_1734,