RetrogeneDB ID: retro_mmus_1744

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:86914816..86915563(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Dmap1
• Ensembl ID: ENSMUSG00000009640
• Aliases: Dmap1, 1500016M21Rik, DNMAP1, DNMTAP1, Dmtap1, mKIAA1425
• Description: DNA methyltransferase 1-associated protein 1 [Source:MGI Symbol;Acc:MGI:1913483]

Sequence

>retro_mmus_1744
ATCAAAATACCAGTATTTGATGCCGGGCATAAGAAATGTCAGAAGGAATATCTGGATCAGTTTTACAACCAGACCCCAAA
GCAAGTGGCAAAGGAGGAGTACCTGCTACAGGAGCTACATAAGATTGAGGCCTGGAAAAAAGAGCGGGAAAAGATCAGCC
AAGACCTGCAGAAGCTGATTACAGCAGCAGATACTGCGGAGTACACAGAACACAAGTCTCCCAAGAAGCTACCCCAGAAG
GAGGCCGAAAAGCAGGATGTTCCTGAGACTGCAGACATCAAGTTTCCAGATTTTTAAGTCAGCAGGTGTAACACCACAGA
GCCAGGGGATGAAGCTAACCAGCCTTGTGAGTCAGAAGATCGAAGCTTCTGGAATAGATTCTGCTGGAACTTGGTGTGGA
CCTGAGCTCTAGTCCTTCAGAGGAGCTGGTGCATATGTTCAGTGAGTTGCAGAGTGACCTAGTGTTGCTCTCTGAGCTCA
AGCAGGCCTTTGCCAACTGTGAATATGAGCTACAGATGCTGCTACACAGGCATGAGACCCTGGTTCAGGCAAGAGCCCTG
CGGCCCTGACATACCAGCAGTGGGACCAAACCAGGCTTCTGCTGAGTCAACAGTGTCTGAATATGGACTTGGTTTTGACC
TCACCAAGGACAGTATCCATGATGTAGTGGGAGCGCCCATCATACCCAATGCACAGAAACGACAGAAACTAACGTCCAGC
TCATCTTCTGTGAAGAAAGTAAAAAAA

Alignment

ORF - retro_mmus_1744 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.38 %
• Parental protein coverage: 54.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LKIPVFDAGHERRRKEQLERLYNRTPEQVAEEEYLLQELRKIEARKKEREKRSQDLQKLITAADTTAEQR
          .KIPVFDAGH....KE.L...YN.TP.QVA.EEYLLQEL.KIEA.KKEREK.SQDLQKLITAADT.....
Retrocopy IKIPVFDAGHKKCQKEYLDQFYNQTPKQVAKEEYLLQELHKIEAWKKEREKISQDLQKLITAADTA---E

Parental  RTERKAPKKKLPQKKEAEKPAVPETAGIKFPD-FKSAGVTLRSQRMKLPSSVGQKKIKA-LEQMLLELGV
          .TE.K.P.KKLPQ.KEAEK..VPETA.IKFPD.FKSAGVT..SQ.MKL.S.V.Q.KI.A.LE..LLELGV
Retrocopy YTEHKSP-KKLPQ-KEAEKQDVPETADIKFPD>FKSAGVTPQSQGMKLTSLVSQ-KIEA>LE*ILLELGV

Parental  ELSPTPTEELVHMFNELRSDLVLLYELKQACANCEYELQMLRHRHEALARAGVLGAPAAAAVGPTP-ASA
          .LS..P.EELVHMF.EL.SDLVLL.ELKQA.ANCEYELQML.HRHE.L..A..L..P.....G..P.ASA
Retrocopy DLSSSPSEELVHMFSELQSDLVLLSELKQAFANCEYELQMLLHRHETLVQARAL-RP*HTSSGTKP>ASA

Parental  EPTVSESGLGLDPTKDTIIDVVGAPLTPNSRKRRESASSSSSVKKAKK
          E.TVSE.GLG.D.TKD.I.DVVGAP..PN..KR....SSSSSVKK.KK
Retrocopy ESTVSEYGLGFDLTKDSIHDVVGAPIIPNAQKRQKLTSSSSSVKKVKK

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	18.48 RPM
SRP007412_cerebellum	0.00 RPM	18.45 RPM
SRP007412_heart	0.00 RPM	12.33 RPM
SRP007412_kidney	0.00 RPM	10.91 RPM
SRP007412_liver	0.00 RPM	6.72 RPM
SRP007412_testis	0.00 RPM	41.58 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1744 was not detected

EST

No EST(s) were mapped for retro_mmus_1744 retrocopy.

TSS

No TSS is located nearby retro_mmus_1744 retrocopy 5' end.

Lab

retro_mmus_1744 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1744 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003922	1 retrocopy	retro_cjac_2754,
Mus musculus	ENSMUSG00000009640	1 retrocopy	retro_mmus_1744 ,
Rattus norvegicus	ENSRNOG00000019407	4 retrocopies	retro_rnor_2428, retro_rnor_2504, retro_rnor_2507, retro_rnor_2940,