RetrogeneDB ID: retro_mmus_1525

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 16:65195843..65196450(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gmnn
• Ensembl ID: ENSMUSG00000006715
• Aliases: Gmnn, AW546347, Gem
• Description: geminin [Source:MGI Symbol;Acc:MGI:1927344]

Sequence

>retro_mmus_1525
AATCCCTGTATGAAGCAGAAACAGGAAGAAGCCCAAGAGAAGGTGAAGAATAGTCCTGTTCCAAGGAGAATGCTGAAGAT
GATTCAGCTCTCTGCAGCTGGGTCTCTTGCTGGCAGAGAAAAAAGTTGCCAAAGGGCTTGTCCAAAACGAAGCTTTAGGA
TAACCAGCTAACACCTAAGACTCTGAGCTGTGGTCCAGAAGCAAAAGAAAATAAAGATGTAGGAGACGTCATCTAGGAAG
CATTTGATCTTATGATTAAAGAAAAATCCTCTTCTTGGTATTGGAAAGAAGTGGTAGAAAAATGGAGGAAAGCTCTCTAT
GAAACACTTAAGGAGAATGAGAAACATTATAAAGACATTAAACAAAGGGACAGTGAAATGCCTGTGTGAAATGGGCGAGT
GAAGACTTGGCAGAAGTATCGGAATATACACAGTACAAAGCAGAGGTGATGGAGAGGGTAAGTAATGACCCACGGGATAA
TGCTGAGTCACTGCATAGCCAGGAATTTGATTCTGCAGAGGAACCTGTTGAGTATTATGAAGTGGAAGACTCAGAAACTG
GGTCGTGTGCTGAAGAGAGTGTGTCTTCCTCCACAGAAGCCAAGCCA

Alignment

ORF - retro_mmus_1525 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.32 %
• Parental protein coverage: 98.54 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NLSMKQKQEGAQENVKNSPVPRRTLKMIQPSADGSLVGREN-ELPKGLFKRKLWDDQLASQTSSCGPEAN
          N..MKQKQE.AQE.VKNSPVPRR.LKMIQ.SA.GSL.GRE...LPKGL.K.KL.D.QL...T.SCGPEA.
Retrocopy NPCMKQKQEEAQEKVKNSPVPRRMLKMIQLSAAGSLAGREK<KLPKGLSKTKL*DNQLTPKTLSCGPEAK

Parental  ENKDVGDLTQEAFDLISKENPSSQYWKEVAEQRRKALYEALKENEKLHKEIEQKDSEI-ARLRKENKDLA
          ENKDVGD...EAFDL..KE..SS.YWKEV.E..RKALYE.LKENEK..K.I.Q.DSE..A.......DLA
Retrocopy ENKDVGDVI*EAFDLMIKEKSSSWYWKEVVEKWRKALYETLKENEKHYKDIKQRDSEM<ACVKWASEDLA

Parental  EVAEHVQYMAEVIERLSNEPLDNFESPDSQEFDSEEEAVEYSELEDSGAGTCAEETVSSSTDARP
          EV.E..QY.AEV.ER.SN.P.DN.ES..SQEFDS.EE.VEY.E.EDS..G.CAEE.VSSST.A.P
Retrocopy EVSEYTQYKAEVMERVSNDPRDNAESLHSQEFDSAEEPVEYYEVEDSETGSCAEESVSSSTEAKP

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	1.89 RPM
SRP007412_cerebellum	0.00 RPM	1.17 RPM
SRP007412_heart	0.00 RPM	21.67 RPM
SRP007412_kidney	0.00 RPM	10.66 RPM
SRP007412_liver	0.00 RPM	5.87 RPM
SRP007412_testis	0.00 RPM	23.24 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1525 was not detected

EST

No EST(s) were mapped for retro_mmus_1525 retrocopy.

TSS

No TSS is located nearby retro_mmus_1525 retrocopy 5' end.

Lab

retro_mmus_1525 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1525 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006161	1 retrocopy	retro_cjac_1012,
Microcebus murinus	ENSMICG00000014010	1 retrocopy	retro_mmur_594,
Myotis lucifugus	ENSMLUG00000014849	2 retrocopies	retro_mluc_1589, retro_mluc_743,
Monodelphis domestica	ENSMODG00000011682	1 retrocopy	retro_mdom_1800,
Mus musculus	ENSMUSG00000006715	2 retrocopies	retro_mmus_1525 , retro_mmus_2213,
Oryctolagus cuniculus	ENSOCUG00000000728	1 retrocopy	retro_ocun_613,
Otolemur garnettii	ENSOGAG00000004982	1 retrocopy	retro_ogar_1726,
Ochotona princeps	ENSOPRG00000007969	1 retrocopy	retro_opri_439,
Rattus norvegicus	ENSRNOG00000018782	1 retrocopy	retro_rnor_820,
Sarcophilus harrisii	ENSSHAG00000004058	2 retrocopies	retro_shar_581, retro_shar_769,
Tupaia belangeri	ENSTBEG00000010502	2 retrocopies	retro_tbel_1028, retro_tbel_353,