RetrogeneDB ID: retro_mmus_2735

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:59942350..59942816(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Dck
• Ensembl ID: ENSMUSG00000029366
• Aliases: None
• Description: deoxycytidine kinase [Source:MGI Symbol;Acc:MGI:102726]

Sequence

>retro_mmus_2735
ATGACCACCCCACCTAAGAGACTCTGCCCTTTTCCATCCACCAGCTCTGAGGGGACCTGCATCAGGAAGGTCTCCATAGA
GGGGAACATCCCCGCCTGGAAGTCACCGTTTGTGAATATCCTAAAGCAAGTTTGTCAGGATTGGGAAGTGGTTCCTGAGC
CTGTCGCCAAGTGGTGCAATGTGCAGAATACTCAAGACAAATTTGAGGAATTGAAAAGGTCTCAGAAAAGCCATGGGGAT
GTTTGTCAGATGAGGAATGAGATACCTGGACGGTGTTTCTTTTAACTTCCAATCATATGCCTGTTTCAGCCGGATCCTAT
CTCAGTGTTCCTCTGTCAATGGCAAGCTCAAAGATGCAGAGAAACCTGTATTATTTTTTGAACCATCTGTGTATAGTGGC
AGGTGTGTTTTTCTATCTAATTTGTATGAATCCAACTGCATGAATAAAACAGAGTGGAGAATATAT

Alignment

ORF - retro_mmus_2735 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.08 %
• Parental protein coverage: 59.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MATPPKRFCPSPSTSSEGTRIKKISIEGNIAAGKSTFVNILKQASEDWEVVPEPVARWCNVQSTQEEFEE
          M.TPPKR.CP.PSTSSEGT.I.K.SIEGNI.A.KS.FVNILKQ...DWEVVPEPVA.WCNVQ.TQ..FEE
Retrocopy MTTPPKRLCPFPSTSSEGTCIRKVSIEGNIPAWKSPFVNILKQVCQDWEVVPEPVAKWCNVQNTQDKFEE

Parental  LTTSQKSGGNVLQMMYEKPERW-SFTFQSYACLSRIRAQLASLNGKLKDAEKPVLFFERSVYSDRYIFAS
          L..SQKS.G.V.QM..E.P.R..SF.FQSYAC.SRI..Q..S.NGKLKDAEKPVLFFE.SVYS.R..F.S
Retrocopy LKRSQKSHGDVCQMRNEIPGRC>SFNFQSYACFSRILSQCSSVNGKLKDAEKPVLFFEPSVYSGRCVFLS

Parental  NLYESDCMNETEWTIY
          NLYES.CMN.TEW.IY
Retrocopy NLYESNCMNKTEWRIY

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	17.64 RPM
SRP007412_cerebellum	0.00 RPM	12.38 RPM
SRP007412_heart	0.00 RPM	3.33 RPM
SRP007412_kidney	0.00 RPM	4.87 RPM
SRP007412_liver	0.00 RPM	4.18 RPM
SRP007412_testis	0.00 RPM	2.56 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2735 was not detected

EST

No EST(s) were mapped for retro_mmus_2735 retrocopy.

TSS

No TSS is located nearby retro_mmus_2735 retrocopy 5' end.

Lab

retro_mmus_2735 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2735 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000022606	1 retrocopy	retro_fcat_1830,
Myotis lucifugus	ENSMLUG00000005844	1 retrocopy	retro_mluc_2007,
Mus musculus	ENSMUSG00000029366	1 retrocopy	retro_mmus_2735 ,
Oryctolagus cuniculus	ENSOCUG00000001265	1 retrocopy	retro_ocun_1247,
Pan troglodytes	ENSPTRG00000016139	1 retrocopy	retro_ptro_427,
Pteropus vampyrus	ENSPVAG00000004341	1 retrocopy	retro_pvam_32,
Rattus norvegicus	ENSRNOG00000003296	1 retrocopy	retro_rnor_1026,
Xenopus tropicalis	ENSXETG00000018331	1 retrocopy	retro_xtro_9,