RetrogeneDB ID: retro_mmus_85

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:126814067..126815480(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000058670
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Dmtf1
• Ensembl ID: ENSMUSG00000042508
• Aliases: Dmtf1, Dimp, Dmp1
• Description: cyclin D binding myb-like transcription factor 1 [Source:MGI Symbol;Acc:MGI:1344415]

Sequence

>retro_mmus_85
ATGAGCTCTGTCTTACTTAGTGAGGACTCAGACAGGAACCTCATGCTTTGCCTTCAGAATGAAGCTAATGAAATGGAAAA
TCCTACTGAACCTCTGAATAAGAGGCCTTGTTTGTCCTCTGAAGTTGATTCTACTTCGTATATGTCAGCTCTTGAATTCC
CACTACAAGAAATGGAGCAAAGTTTTGGTTTGGTCACAACCACAGCCACAGAGGTGGCTGAGGAAGAGTTTGGTGGGGAA
AATATGATGCAATTCGAGGTTTTAAAAGATGACAAACAATATGAAGTTTTCCCCTTGCCTAACAAGGAAGAGTCAGTAGT
TAGCCAAGCATGGTTCACAAGTAAGGAAGCTAAGGATGCTCTAACTCATCAAGGACAGAAATGGAAGCAGGGGATGTGGT
CCAAGGAAGAAACAGCTATTCTGATGAACAACATTGAAAGGTATATGAAGGACCATGGAGTAGAGAATCCTGCAGAAATC
ATTTTTAAGATGGCAAAAGGTAAAAGAAAAGATTTCTACAGGTCTGTATCATTGGGTCTGAATAGACCTTTGTTTTCAGT
TTATAGAAGAGTGGTCCGAATGTATGATGACAGAAACCATGTGGGTAAGTACAGCCCTGAGGAAATAGAGAAGCTCAAGG
AGCTCTGGCAGAAGCATGGCAATGACTGGATAACAATAGGGGCCGCCATGGGAAGAAGTCCATCTTCGGTCAAAGACCGG
TGCCGACTGATGAAGGATACTTGCAACACGGGGAAATGGACCGAAGAAGAAGAACAGCTTCTTGGCGATGTGGTTCATGA
ATTGACATGCACTGAGGTGGATGAGAAAGTTACCCATGGTGTGTGTTGGGCAACAGTGGCTCAACGAGTGGGTACTCGCT
CAGCAAAGCAGTGTCGTGCTAAATGGCTCAACTACTTGAACTGGAAACAGACTGGTGGTATTGAGTGGACAAGGAAAGAT
GAAGTCACTCTCATCCAAAGGCTAGTAGAGCTTGATGTATCCGATGAAAGTGAAATTCGCTGGGATGAATTAGCTAAAGG
ATGGGAAAGTGTTCGTTCACCACAATGGCTGCGAAATAAATGGTGGATCATCAAAAGGCAAATTACAAATCATAAAGATT
TTGCATTCCCAGTCCTAGTAAGATGTCTTCAACAAGAATATGAAAGCCAAAATGCCAGCCTCAGGTTTTGGGAGAATAAA
TCAGGATCTGAAGTACCAGATAGCAACCCTGATATCATTTTTCAACAAGTCCCCTTTGGAGTCACAAGTATAGAAAATAA
TAATGCATCCATCTGTACTGACCCCATGACAGGATTGCAAATTTCATTCCAGCTCATCCCCAGACCCACAACAGAATTAC
CTGATGCTGTTGTTGACTCTGAAACCATAACCCTGCCCACTGGACCACAGTAG

Alignment

ORF - retro_mmus_85 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.68 %
• Parental protein coverage: 55.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DATPCISVVALPLSENDQSFEVTMTATTEVADDELSEGTVTQIQILQNDQLDEISPLGTEEVSAVSQAWF
          D.T...S....PL.E..QSF....T..TEVA..E.......Q...L..D...E..PL...E.S.VSQAWF
Retrocopy DSTSYMSALEFPLQEMEQSFGLVTTTATEVAEEEFGGENMMQFEVLKDDKQYEVFPLPNKEESVVSQAWF

Parental  TTKEDKDSLTNKGHKWKQGMWSKEEIDILMNNIERYLKARGIKDATEIIFEMSKDERKDFYRTIAWGLNR
          T.KE.KD.LT..G.KWKQGMWSKEE..ILMNNIERY.K..G.....EIIF.M.K..RKDFYR....GLNR
Retrocopy TSKEAKDALTHQGQKWKQGMWSKEETAILMNNIERYMKDHGVENPAEIIFKMAKGKRKDFYRSVSLGLNR

Parental  PLFAVYRRVLRMYDDRNHVGKYTPEEIEKLKELRIKHGNDWATIGAALGRSASSVKDRCRLMKDTCNTGK
          PLF.VYRRV.RMYDDRNHVGKY.PEEIEKLKEL..KHGNDW.TIGAA.GRS.SSVKDRCRLMKDTCNTGK
Retrocopy PLFSVYRRVVRMYDDRNHVGKYSPEEIEKLKELWQKHGNDWITIGAAMGRSPSSVKDRCRLMKDTCNTGK

Parental  WTEEEEKRLAEVVHELTSTEPGDIVTQGVSWAAVAERVGTRSEKQCRSKWLNYLNWKQSGGTEWTKEDEI
          WTEEEE..L..VVHELT.TE....VT.GV.WA.VA.RVGTRS.KQCR.KWLNYLNWKQ.GG.EWT..DE.
Retrocopy WTEEEEQLLGDVVHELTCTEVDEKVTHGVCWATVAQRVGTRSAKQCRAKWLNYLNWKQTGGIEWTRKDEV

Parental  NLILRIAELDVADENDINWDLLAEGWSSVRSPQWLRSKWWTIKRQIANHKDVSFPVLIKGLKQLHENQKN
          .LI.R..ELDV.DE..I.WD.LA.GW.SVRSPQWLR.KWW.IKRQI.NHKD..FPVL...L.Q..E.Q..
Retrocopy TLIQRLVELDVSDESEIRWDELAKGWESVRSPQWLRNKWWIIKRQITNHKDFAFPVLVRCLQQEYESQNA

Parental  NPVLLENKSGSGVPNSNCNSSVQHVQIRVARLEDNTA-ISPSPMAALQIPVQITHVSSTDSPAASVDSET
          .....ENKSGS.VP.SN.....Q.V...V...E.N.A.I...PM..LQI..Q......T..P.A.VDSET
Retrocopy SLRFWENKSGSEVPDSNPDIIFQQVPFGVTSIENNNASICTDPMTGLQISFQLIPRPTTELPDAVVDSET

Parental  ITLNSG
          ITL..G
Retrocopy ITLPTG

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	59.74 RPM
SRP007412_cerebellum	0.00 RPM	71.60 RPM
SRP007412_heart	0.00 RPM	17.87 RPM
SRP007412_kidney	0.00 RPM	28.07 RPM
SRP007412_liver	0.00 RPM	19.80 RPM
SRP007412_testis	5.53 RPM	29.50 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_85 was not detected

EST

No EST(s) were mapped for retro_mmus_85 retrocopy.

TSS

No TSS is located nearby retro_mmus_85 retrocopy 5' end.

Lab

retro_mmus_85 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_85 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000042508	1 retrocopy	retro_mmus_85 ,
Rattus norvegicus	ENSRNOG00000005908	2 retrocopies	retro_rnor_1330, retro_rnor_2871,