RetrogeneDB ID: retro_zmay_7

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 4:77387711..77390084(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: GRMZM2G103186
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GRMZM2G063060
• Aliases: None
• Description: None

Sequence

>retro_zmay_7
ATGTCGAGAAAGATGGACGCCGACGGCAAGAAAGATTTTAGCACGGCGATCCTAGAGCGCAAGAAGGCGCCGAACCGCCT
CCTGGCGGACGACGGCGAGGGGGAGGTGGCCATAGACAACTCAATGGTGGCGCTCAGCCCCGCCACCGCGTTCCAGCTCG
AGATCTTCACGGGGGACCTGGTGCTGCTCCGCGGCAAGCGCCGCCGGGAGACCGTCTGCTACGCGGTGTTCGACGCCTCC
TGTCCCGACGGCAGGGTGCGCCTCAACCGCGCTGTGCGCGGCAACATCCGCGTCCACCTCGGGGACATCGTCTCTATCAA
CCGTATCGACGAGGTCCCGACCGGCGCGCGCGTCCAGATCACGCCGTTCGATGACACTGTCAACGGCATCTCCGGCAACC
TCTTCGACGTCTACCTAAAGCCCTACTTCGGCAACGACGCGCTGCGGCCGTTATGCAAGGGCGACCGCTTCATCGTGCAC
GGCAACATGCACGCCGTCGAGTTCAAGGTCGTCGACGCGGAACCCGCCGACCGCGTCGTCGTCCGGCCGGAGACGGCAAT
CTACTGCAGCGACCAGCCAGTCAAGCGGGAGGAAGAGGAGCGGCTCGACGGCCCTGGCTACGACGACGTGGGCGGCGTCC
GCAAGCAGCTGGCCCAGATCCGCGAGCTGGTCGAGCTGCCACTGCGCCACCCCAAGCTGTTCCAGACGCTCGGCGTCAAG
CCGCCCAAAGGGATCCTGCTTTACGGCCCGCCCGGCACCGGCAAGACGCTTCTGGCGCGCGCCATCGCGTCGGAGTCCGG
CGCACACTTCGTGGTTGTCAACGGCCCAGAGATTATGTCCATGATTGCCGGCCAGAGCGAGGCTAACCTGCGCAAGGTTT
TCGAGGACGCCGAAAAGTTCGCGCCTTCCGTCATCTTCATGGACGAGATCGACGCCATCGCCCCCAACCGCGACAAGACG
CACGGCGAGGTGGAGCGCCGCGTGGTCTCGCAGCTTCTCACGCTCATGGACGGCCTCCGGCCGCGCGCGCAGGTCGTGGT
GATCGGTGCAACCAACCGCCCCAACAGCCTGGACCCGGCGCTCCGGCGCTTTGGCCGTTTTGACCGGGAGCTTGACATCG
GCGTGCCCGACGAGGTCGGCCGCCTCGAGATCCTCCGCATCCACACCAAGGACATGCCGCTAGCCGAGGACGTCGACCTC
GAGCGCATCGGCAAGGACACTCACGGCTTCGTCGGCGCCGACCTCGCGGCGCTCTGCTCCGAGGCGGCCCTGCAGTTGAT
CCGCGAGAAGATGGACGTCATCGACGTGGAAGAAGACACTATCGACGTGGACGTGCTGGACTCGCTGTGCGTCTGCAACG
AGCACCTCAAGCACGCCATGGAGGTGACCAAGCCCTCGGCGCTGCGCGAGAGGGGGCTGGTGGAGGTGCCCAAGGTATCG
TGGGACGACATCGGCGGCCTGCAGAACGTCAAGCTGGAGCTCCAAGAGACGGTGCAGTACCCGGTGGAGCACCCAGAGAT
GTTCGAGATGTTTGGCATGTCGCCGTCGCGCGGCGTGCTCTTCTACGGCCCCCCAGGCTGCGGCAAGACGATGCTGGCCA
AGGCCATCGCTAAGGAGTGTAAGGCTAACTTCATCAGCGTCAAAGGCCCCGAACTGCTGACCATGTGGTACGGCGAGAGC
GAGTCCAACGTCCGTGACCTGTTTGACAAGGCGCGGTCGGCGGCTCCGTGCATCCTCTTCTTTGACGAGCTGGACTCGAT
CGCCGTGAAGCGCGGCAACAGCGTGGGCGACGTGGGCGGCACGTCCGACCGCGTGCTGAACCAGCTGCTAACGGAGATGG
ATGGCATCAACGCGAAGAAGACGGTGTTCGTAATCGGCGCCACCAACCGGCCTGACATTATCGACCCGGCAATGCTCCGG
CCGGGGAGGCTAGACCAGCTCATCTATATCCCGCTGCCTGACGAGCCCTCGCGGCTGCAGATCTTCAAGTCGTGCCTGCG
GCGGTCCCCAGTTTCCCGCCACGTCCACCTGCCAGCGCTGGCGCGCATCACGGCCGGGTTCAGCGGCGCCGACATCACGG
AGATTTGCCAGCGCGCGTGCAAGCTGGCGGTGCGCGACGTGATCCAGTGGAGCTTGAAGGTGGGCAAGGCCGAGGCCATG
CGCGGCGCGGAGATCGGAGTATGGCACCTCACGGAGGCCCTGAAACATGCGCGACGGAGCGTCAGCGACCTAGATGTTAT
GAAGTACGACTTCTTTGCTCAGCGACTCAAGGGAGGAGGCTTCGAGGACGAGACCATCATTGCTGCCCCGATGGGGACGC
AGCCGCTCACGATCACGGAGATAGAGGAGGAGGACGACAGCTCGCTCTACTGA

Alignment

ORF - retro_zmay_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.45 %
• Parental protein coverage: 86.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DPKGKKDYSTAILERKKSPNRLVVDEATND---DNSVVALHPDTMERLQLFRGDTVLIKGKKRKDTVCIV
          D..GKKD.STAILERKK.PNRL..D........DNS.VAL.P.T...L..F.GD.VL..GK.R..TVC..
Retrocopy DADGKKDFSTAILERKKAPNRLLADDGEGEVAIDNSMVALSPATAFQLEIFTGDLVLLRGKRRRETVCYA

Parental  LADETCEEPKVRMNKIVRKNLRVRLGDVVSVHQCPDVKYGKRVHILPIDDTIEGITGNLFDAFLKPYF-L
          ..D..C....VR.N..VR.N.RV.LGD.VS......V..G.RV.I.P.DDT..GI.GNLFD..LKPYF..
Retrocopy VFDASCPDGRVRLNRAVRGNIRVHLGDIVSINRIDEVPTGARVQITPFDDTVNGISGNLFDVYLKPYFGN

Parental  EAYRPLRKGDLFLVRGGMRSVEFKVIETDPAEYCIVAPDTEIFCEGEPIKREDEERLDEVGYDDVGGVRK
          .A.RPL.KGD.F.V.G.M..VEFKV....PA....V.P.T.I.C...P.KRE.EERLD..GYDDVGGVRK
Retrocopy DALRPLCKGDRFIVHGNMHAVEFKVVDAEPADRVVVRPETAIYCSDQPVKREEEERLDGPGYDDVGGVRK

Parental  QMAQIRELVELPLRHPQLFKSIGVKPPKGILLFGPPGSGKTLIARAVANETGAFFFLINGPEIMSKLAGE
          Q.AQIRELVELPLRHP.LF...GVKPPKGILL.GPPG.GKTL.ARA.A.E.GA.F...NGPEIMS..AG.
Retrocopy QLAQIRELVELPLRHPKLFQTLGVKPPKGILLYGPPGTGKTLLARAIASESGAHFVVVNGPEIMSMIAGQ

Parental  SESNLRKAFEEAEKNAPSIIFIDEIDSIAPKREKTHGEVERRIVSQLLTLMDGLKSRAHVIVMGATNRPN
          SE.NLRK.FE.AEK.APS.IF.DEID.IAP.R.KTHGEVERR.VSQLLTLMDGL..RA.V.V.GATNRPN
Retrocopy SEANLRKVFEDAEKFAPSVIFMDEIDAIAPNRDKTHGEVERRVVSQLLTLMDGLRPRAQVVVIGATNRPN

Parental  SIDPALRRFGRFDREIDIGVPDEVGRLEVLRIHTKNMKLAEDVDLELIAKDTHGYVGADLAALCTEAALQ
          S.DPALRRFGRFDRE.DIGVPDEVGRLE.LRIHTK.M.LAEDVDLE.I.KDTHG.VGADLAALC.EAALQ
Retrocopy SLDPALRRFGRFDRELDIGVPDEVGRLEILRIHTKDMPLAEDVDLERIGKDTHGFVGADLAALCSEAALQ

Parental  CIREKMDIIDLEDETIDAEILNSMAVSNDHFKTALGTSNPSALRET-VVEVPNVSWEDIGGLENVKRELQ
          .IREKMD.ID.E..TID...L.S..V.N.H.K.A.....PSALRE...VEVP.VSW.DIGGL.NVK.ELQ
Retrocopy LIREKMDVIDVEEDTIDVDVLDSLCVCNEHLKHAMEVTKPSALRERGLVEVPKVSWDDIGGLQNVKLELQ

Parental  ETVQYPVEHPDKFEKFGMSPSKGVLFYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGESEANVR
          ETVQYPVEHP..FE.FGMSPS.GVLFYGPPGCGKT.LAKAIA.EC.ANFISVKGPELLTMW.GESE.NVR
Retrocopy ETVQYPVEHPEMFEMFGMSPSRGVLFYGPPGCGKTMLAKAIAKECKANFISVKGPELLTMWYGESESNVR

Parental  EIFDKARQSAPCVLFFDELDSIATQRGSSVGDAGGAADRVLNQLLTEMDGMNAKKTVFIIGATNRPDIID
          ..FDKAR..APC.LFFDELDSIA..RG.SVGD.GG..DRVLNQLLTEMDG.NAKKTVF.IGATNRPDIID
Retrocopy DLFDKARSAAPCILFFDELDSIAVKRGNSVGDVGGTSDRVLNQLLTEMDGINAKKTVFVIGATNRPDIID

Parental  PALLRPGRLDQLIYIPLPDEQSRLQIFKACLRKSPVAKDVDLHALAKYTQGFSGADITEICQRACKYAIR
          PA.LRPGRLDQLIYIPLPDE.SRLQIFK.CLR.SPV...V.L.ALA..T.GFSGADITEICQRACK.A.R
Retrocopy PAMLRPGRLDQLIYIPLPDEPSRLQIFKSCLRRSPVSRHVHLPALARITAGFSGADITEICQRACKLAVR

Parental  ENIE
          ..I.
Retrocopy DVIQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Zea mays was not studied using RNA-Seq expression data.

ChIP-Seq

Zea mays was not studied using ChIP-Seq data.

EST

Zea mays was not studied using EST data.

TSS

Zea mays was not studied using FANTOM5 data.

Lab

retro_zmay_7 was not experimentally validated.

Homology

Retrocopy orthology:

Zea mays does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Zea mays	GRMZM2G063060	1 retrocopy	retro_zmay_7 ,
Oryza glaberrima	ORGLA06G0255900	1 retrocopy	retro_ogla_73,
Populus trichocarpa	POPTR_0006s12740	1 retrocopy	retro_ptri_3,
Sorghum bicolor	Sb01g046840	1 retrocopy	retro_sbic_42,