RetrogeneDB ID: retro_mmul_1079

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 14:87959532..87962197(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDON
• Ensembl ID: ENSMMUG00000007628
• Aliases: None
• Description: None

Sequence

>retro_mmul_1079
TTGCATCCAGATCTTGGCCTTTTATGGACACTGTATGTTACTCTTATGATTCCCTGCTCTTCTATTAGTTCAGACGTGGC
ACCTTATTTCATTTCTGAGCCACTCTCTGCCGTCCAGAAACTTAGTGGACCTATAGAACTCTATTGTTCTGCTAAACCTG
TGACCACTCATATCTCAAGGTCGCATAATGTAAAAAATAGAAGAGAAACATGGAATATATTAAGATTCATCAGGGGACTT
TGGCAATTTTTTTCTCTTAACTCCTCCCTTTTGGGTTACTACCAATGCGTTTTCAACGATAGGTCGATGTTGTTGTAAGT
GGCCCTGTAACAGTATCCACAGCAGTTCTTGGTGATTTTGGTTCACCCACAAAGCATGTTATTACAGCAGAAGAAAAAAG
TGCTGTTTTCATTGGCTGCAGTGAACCAGAGAGTAACCCCAAAGCTGAGGTGTGCTCTAAAATCCAGGGAAAGTGGCTGA
AGCATTCCACAAAGAATTACTTAATCCTTCCATCAAGACATCTTTAAATTTTGAACGTATCCTTAGAGGACAAGAAATCA
TACAAATATGCGGCTTATAATCCTGTCACACATGAATTAAAAGTTGAACCCATTGGCCAAAAGCTCCTTGTGAGTCACCT
TTCTTCAGATGATTTTGACATTCTTCATCCTGCTTGTTCACAGGTATTAGTTGTTTTTTCACATATTCCTCTAACATTGG
AGTGTGTGGTTAGTGGGGTCTCAGCTCCTCAAGTGTGTTGGCTAAAGGACAAGCAGGATATTGCCCCAGGAAGCAACTGG
AGAAGGTTGTATTCTTATGTTGCCACAGATAGCATTGACCCAGTGGACTCTGGAAACTATTCCTGCATGGTGGGAAACAA
GACTGGAGATGTGAAATATGTAACATACATGGTTAATGTGCTTGAATATGCTCCCATTTCTAAAGGACTACAGGATCAGG
TAGTGTCTCTGGTGCACAGTACATGTTACCTGTCATATTCATGGAAACCCACCTGCCAACCGTACCTGGTTTTATATTGC
ACAGCCTATTCATCCTTCCCCATGACATCTAATTGCAAGAAATTGACTGAAAGTCAGTGGGGTTATTATGGAAGATACTG
GGCTGTATCAGTGTTTAGCAGATAATAGGATTGGATTTATGCAGTCTACTGGAAGACTTGAAATTGAAAAAGACAATGGA
TTCAAACCAGTTATAATCATGGCACCAGCAAGTGCAAAGGTGATAGGTGGAGACTTTGTCATTCTGTCCTGCCATGCCAG
TGGGCTGCCAGTTTCGGTCATTCCTTGGTTATGACAGCTATGGGTTAATATCCAGCCATCTTGCGTAAGTCCTTAGACCT
AAGTCCCAAAAGTCACACTTATCAAGGTCTGCAATCTTGGACCTGAAGCCTGGCTACTTCCTCATGTCCCAAGTTGACTC
AAGCTCTCTCCATATTTAGGATGTGACTCAGAAACATGTGGGGAAACACATACAGGAAGCTCCAGATGGACACAGTACCA
GGCAGGGAGAAGCATCTCTCATGGTCGTTCCTTCTGAAACAAATACAGAAGTGGAAACAGTCATACTTTCTGCTGCTACT
CAGAATGATGAAAGAAATAAAAGGGATGGTTCAGAAACTGGATTGAGCTCATGTCCAGTTAAGGTACATCCCAGTGCAGT
GGAATCAGCATCAGAGAAAAATGTTAATGGCATCGCTGTTCCTGTCGCCCGCATCATACTGATCCCCTGACAGACCCACA
CACCAGATACGTACAAGCTGATGTGGAGGGCAGGTGGGAATGGTGGGCTATCCATTAATGGGTATTTTATGACATATCAA
AAGCTGAACAATGGGGTTGGTTTAGTAGGAATTTAACATACAGTTCAAGTCCCAGGGAGTGAAAATGAGCTCCATTTAGC
TGAACTAGGGCCATCTAGTCTTTACAAAGTCTTGCTGGTAGCAAGAAGTGGAGCAGGTGAAGGACAAACTGTCATGCTTA
CCTTCTGAACCAGCAAAGAAAAAAGAGCATTGACAAAAAACACCCAGGCATTCTCTCCACCCATGGGCATCCCTAAGTAT
CCTGTTGTTTCAGAAGCTGCAAACAATTTTGGAGTGGTACTTACAGATTCTTGAAGGCACAGCGAAGTTCCAGAGGCACC
AGATGGCCTTGCTATCTCCAATGCATCAGAGACATTGGTCTATGTCACTTGGATTCTTCTGGAAAATTGGGTTTCTCCAA
TCACTGCCTTCAAAGTTAAATATAAAAGGATGAGGACCAGTGATTGACTAGTGGCAACTGAAGATATCCTTGCTTCCAAA
ATATCCATGGAAGTTCATAGTTTAGAAACGGGTTCAACATACAAATTGAAAGTCATTGCTATCCATCATTAGGAAGGGAG
TTTTAGGAGTCCAGAGTCTTGTCCTTATCAGTTGGCTGGGTTCCCCAGTCATTTTTTCAACCATCCAGTAATGGAACTCA
CATTGCATACACAGAGGCTGTCAGTGTTACCCAGATAGTGCTAAAGTGGACATACATTCCATGAAGTAACAGTAACACTT
CCATTCTTTTATATCTATTGCCGACCATCAGATAGTGACAATGACAGTGATTACAAGAGGGATGTAGTAGGAGACTCAAA
GGAGTGGCACATGATTGGCCATCTG

Alignment

ORF - retro_mmul_1079 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.4 %
• Parental protein coverage: 69.41 %
• Number of stop codons detected: 13
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  MHPDLGALCTLLYVTLTALCSSVSSDLAPYFTSEPLSTVQKLGGPVVLHCSAKPGTTHISWLHNGK-KLD
          .HPDLG.L.TL.YVTL...CSS.SSD.APYF.SEPLS.VQKL.GP..L.CSAKP.TTHIS..HN.K.K..
Retrocopy LHPDLGLLWTL-YVTLMIPCSSISSDVAPYFISEPLSAVQKLSGPIELYCSAKPVTTHISRSHNVK<K*K

Parental  GNMEHTKIHQGTLTIL-SLNSSLLGYYQCLANNS-IGAIVSGPATVSVAVLGDFGSSTKHVITAEENSAG
          .NME..KIHQGTL.I..SLNSSLLGYYQC..N.......VSGP.TVS.AVLGDFGS.TKHVITAEE.SA.
Retrocopy RNMEYIKIHQGTLAIF>SLNSSLLGYYQCVFNDR<VDVVVSGPVTVSTAVLGDFGSPTKHVITAEEKSAV

Parental  FIGCRVPESNPRAEVRYKIRGKWLKHSTENYLILPSGNLQILNVSLEDKGSYKCAAYNPVTHQLKVEPIG
          FIGC..PESNP.AEV..KI.GKWLKHST.NYLILPS..L.ILNVSLEDK.SYK.AAYNPVTH.LKVEPIG
Retrocopy FIGCSEPESNPKAEVCSKIQGKWLKHSTKNYLILPSRHL*ILNVSLEDKKSYKYAAYNPVTHELKVEPIG

Parental  RKLLVSRPSSDDFHILHPTHSQALAVLSRSPVILECVVSGVPAPPVYWLKDGQDIAPGSSWRRLYSHLAT
          .KLLVS..SSDDF.ILHP..SQ.L.V.S..P..LECVVSGV.AP.V.WLKD.QDIAPGS.WRRLYS..AT
Retrocopy QKLLVSHLSSDDFDILHPACSQVLVVFSHIPLTLECVVSGVSAPQVCWLKDKQDIAPGSNWRRLYSYVAT

Parental  DSIDPADSGNYSCMVGNKSGDVKYVTYMVNVLEHASISKGLQDQTVSL-GA-TVHFTCDVRGNPAPNCTW
          DSIDP.DSGNYSCMVGNK.GDVKYVTYMVNVLE.A.ISKGLQDQ.VSL.GA.TVH.TC...GNP..N.TW
Retrocopy DSIDPVDSGNYSCMVGNKTGDVKYVTYMVNVLEYAPISKGLQDQVVSL<GA<TVHVTCHIHGNPPANRTW

Parental  FHNAQPIHPSARRLTAGNGLKISGVTVEDAGMYQCVADNGIGFMQSTGRLEIENDSGFKPVIITAPASAK
          F..AQPIHPS...L.A.N.LK.SGV..ED.G.YQC.ADN.IGFMQSTGRLEIE.D.GFKPVII.APASAK
Retrocopy FYIAQPIHPSP*HLIARN*LKVSGVIMEDTGLYQCLADNRIGFMQSTGRLEIEKDNGFKPVIIMAPASAK

Parental  VADGGFVTLSCNASGMPVPVIRW-YDSHGLITSHPSQVLRSKSRKSQLSRPEGLNLEPVYFVMSQAGASS
          V..G.FV.LSC.ASG.PV.VI.W.YDS.GLI.SH...VLR.KS.KS.LSR...L.L.P.YF.MSQ...SS
Retrocopy VIGGDFVILSCHASGLPVSVIPW>YDSYGLISSHLA*VLRPKSQKSHLSRSAILDLKPGYFLMSQVDSSS

Parental  LHIQAVTQEHAGRYICEATNEHGSTQAEASLMVVPFETNTKAETVTLPDAAQNDERNKRDGSETGLLSSF
          LHI..VTQ.H.G..I.EA...H...Q.EASLMVVP.ETNT..ETV.L..A.QNDERNKRDGSETGL.SS.
Retrocopy LHI*DVTQKHVGKHIQEAPDGHSTRQGEASLMVVPSETNTEVETVILSAATQNDERNKRDGSETGL-SSC

Parental  PVKVHPSAVETAPEKNASGISVPDAPIILSPPQTHTPDTYNLLWRAGKDGGLPINAYFVKYRKLDDGVGM
          PVKVHPSAVE.A.EKN..GI.VP.A.IIL.P.QTHTPDTY.L.WRAG..GGL.IN.YF..Y.KL..GVG.
Retrocopy PVKVHPSAVESASEKNVNGIAVPVARIILIP*QTHTPDTYKLMWRAGGNGGLSINGYFMTYQKLNNGVGL

Parental  VGSWHTVRVPGSENELHLAELEPSSLYEVLMVARSAAGEGQPAMLTFRTSKEKTASSKNTQASSPPVGIP
          VG..HTV.VPGSENELHLAEL.PSSLY.VL.VARS.AGEGQ..MLTF.TSKEK.A..KNTQA.SPP.GIP
Retrocopy VGI*HTVQVPGSENELHLAELGPSSLYKVLLVARSGAGEGQTVMLTF*TSKEKRALTKNTQAFSPPMGIP

Parental  KYPVVSEAANNNFGVVLTDSSRHSGVPEAPDRPTISTASETSVYVTWIPRANGGSPITAFKVEYKQMRTS
          KYPVVSEAANN.FGVVLTDS.RHS.VPEAPD...IS.ASET.VYVTWI...N..SPITAFKV.YK.MRTS
Retrocopy KYPVVSEAANN-FGVVLTDS*RHSEVPEAPDGLAISNASETLVYVTWILLENWVSPITAFKVKYKRMRTS

Parental  DWLVAAEDIPPSKLSVEVRSLEPGSTYKFRVIAINHYGESFRSSASRPYQVAGFPSRFSNRPV-TGPHIA
          D.LVA.EDI..SK.S.EV.SLE.GSTYK..VIAI.H...SFRS..S.PYQ.AGFPS.F.N.PV..G.HIA
Retrocopy D*LVATEDILASKISMEVHSLETGSTYKLKVIAIHH*EGSFRSPESCPYQLAGFPSHFFNHPV<NGTHIA

Parental  YTEAVSDTQIMLKWTYIPSSNNNT-PIQGFYIYYRPTDSDNDSDYKRDVVEGKMQWHDLGSL
          YTEAVS.TQI.LKWTYIP.SN.NT.P....Y......D.D..SDYKRDVV.....WH..G.L
Retrocopy YTEAVSVTQIVLKWTYIP*SNSNT>PFFYIYCRPSDSDND--SDYKRDVVGDSKEWHMIGHL

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	11.09 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	10.00 RPM
SRP007412_cerebellum	0.00 RPM	42.43 RPM
SRP007412_heart	0.00 RPM	12.90 RPM
SRP007412_kidney	0.00 RPM	7.86 RPM
SRP007412_liver	0.00 RPM	3.09 RPM
SRP007412_testis	0.04 RPM	4.49 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1079 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1079 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1079 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000064309	1 retrocopy	retro_hsap_872,
Macaca mulatta	ENSMMUG00000007628	1 retrocopy	retro_mmul_1079 ,
Pongo abelii	ENSPPYG00000004042	1 retrocopy	retro_pabe_723,
Pan troglodytes	ENSPTRG00000004452	1 retrocopy	retro_ptro_607,