RetrogeneDB ID: retro_zmay_27

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 1:78371787..78373209(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AC199541.4_FG007
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AC199541.4_FG004
• Aliases: None
• Description: None

Sequence

>retro_zmay_27
ATGGAGAGCTCGAGCGCAGCAACGACGATGACCGGCTCCAGTTCCGGTCGAGAGCACGGTGGCGTCCACGTCCTGCTGGT
TCCCCTGCCGGCGCAGGGCCACATGAACCCGATGATCCAGTTCGGCCGCCGCCTCGCGTACCACGGCCTGATTCCCACGC
TGGTGACCACCAGGTACGTGATGTCCACCTCTCCTGCCGCCGGCGTGCCCTTCCCCTTGCTGGCCATCTCCGACGGCTTC
GACGAGGGCGGCATGGCCTCGTGCTCGGACCCCGTGGAGTGCTGCCGGCGGCTGGAGGCCGTGGGGTCGGAGACGCTGGC
GCGGGCCATCGACGCCGAGGCCCGGGCGGGGAGGGCGCCGGCCGTGATGGTGTACGACCCGCACATGCCGTGGGCGCAGC
GGGTGGCGAGCGCCGCGGGCGTCCCGACCGCCGTGTTCCTGCCGCAGTCCTGCGCCGTTGACCTCATCTACGGGGAAGCG
TGGGCGGGGCGCGCGCCGCTGCCGATGGCGGACGGGGGCGCGCTCCGGCGGCGGAGGGTGATCAGCGTGGACCTGGGAGC
GGAGGACCTGCCGCCCTTCGTGGTGGCGCCGGAGATCTACGCCCAGTACCTCAAGGTATCTATTGGTCAATTCGAGTTCC
TCGACGCCGCCGCCGACGTGTTCGTCAACTCGTTCCGCGACCTCGAGCCGCTGGAAGCAGAGTACATGGAGTCGACGTGG
CGCGCGAAGACGGTCGGCCCAGCCCTGCCGTCTTTCTATCTCGACGACGGCCGGATGCCGTCCAACTTGGCCTCCGGCGT
CAGCTTCTTCAGCAGCAGCGCGCCAACAATGGGATGGCTGGACAGGCAGCCCCCCTGCTCCGTGGTCCTTGCTTCCTACG
GGACCGTCTACAGCCTGGACGCCGACCAGCTCGGCGAGCTCGGCAACGGGCTGTGCGATTCCGGCTGGCCGTTCATCTGG
GTCGTGAGGCCCGACGAGGCGCAGAAGCTGCCTCAAGATCTCGAGGACGCCTGCAGGGAGAAGGAGAAGGGCCTCATCGT
GCAGTGGTGTCCTCAGCTAGAGGTCTTGTCGCACAAGGCCACGGGTTGTTTCATCACGCACTGCGGATGGAACTCGACGG
TGGAGGCGATCGTCGCCGGCGTGCCGATGGTGGGCATGCCGCGGTCGGCGGACCAGCCGACCAATGCGAGGTACGTGGAG
AGCGCGTGGGGGATCGGCCTGCGAATGCGGTTGGACCAGAATGGCTTGCTGAAGAGGGAGGAGGTGCAGAGGTGCATCCG
GCAAGTGATGGAAGGGGAGAGGAAGACAGAGTTCAGGCGGAATGCGGCGAAGTGGATGAGCAAGGCCAAGGAGGCGATGC
AGGAAGGTGGGAGCTCTGACAAGAACATTGCTGAATTTGCAGCAAAGTATTTGTCAGCTTAG

Alignment

ORF - retro_zmay_27 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.16 %
• Parental protein coverage: 96.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GDAHVLLLPFPGMQGHANPMLQLGRRLAFHGLRPTLVVSRHVLSTTSTSRSCPIPVAAISDGFDDGGISS
          G..HVLL.P.P..QGH.NPM.Q.GRRLA.HGL.PTLV..R.V.ST.S.....P.P..AISDGFD.GG..S
Retrocopy GGVHVLLVPLPA-QGHMNPMIQFGRRLAYHGLIPTLVTTRYVMST-SPAAGVPFPLLAISDGFDEGGMAS

Parental  CPDTAEYVRRMEAAGSETLAELLDAEARAGRSVRVLVYDSHLPWARRVARAAGVAAAAFMTQMCAVGLVY
          C.D..E..RR.EA.GSETLA...DAEARAGR...V.VYD.H.PWA.RVA.AAGV..A.F..Q.CAV.L.Y
Retrocopy CSDPVECCRRLEAVGSETLARAIDAEARAGRAPAVMVYDPHMPWAQRVASAAGVPTAVFLPQSCAVDLIY

Parental  GEAWAGRVALPLADGAALRGK--LAVELGPDDVPPFVAAPEWYPAFTESALSQFDGLEHADDVLVNSFRD
          GEAWAGR..LP.ADG.ALR......V.LG..D.PPFV.APE.Y.........QF..L..A.DV.VNSFRD
Retrocopy GEAWAGRAPLPMADGGALRRRRVISVDLGAEDLPPFVVAPEIYAQYLKVSIGQFEFLDAAADVFVNSFRD

Parental  LEPMEADYLESTWRAKTVGPTLPSFYLDDGRLPCDKTYGVDLFSSTDSEAAPCMTWLDKQEPCSVVLASY
          LEP.EA.Y.ESTWRAKTVGP.LPSFYLDDGR.P.....GV..FSS.....AP.M.WLD.Q.PCSVVLASY
Retrocopy LEPLEAEYMESTWRAKTVGPALPSFYLDDGRMPSNLASGVSFFSS----SAPTMGWLDRQPPCSVVLASY

Parental  GTVANLDKEQLDELGNGLCDSGKPFVWVLRSNEAEKLSRQLGGRC--KERGLIVPFCPQLEVLAHKATGC
          GTV..LD..QL.ELGNGLCDSG.PF.WV.R..EA.KL...L...C..KE.GLIV..CPQLEVL.HKATGC
Retrocopy GTVYSLDADQLGELGNGLCDSGWPFIWVVRPDEAQKLPQDLEDACREKEKGLIVQWCPQLEVLSHKATGC

Parental  FLTHCGWNSTIESIASGVPMVAMPQWADQPTTAKYVESAWGIGVRMR---KGSLVRKEVERCIREVMGGE
          F.THCGWNST.E.I..GVPMV.MP..ADQPT.A.YVESAWGIG.RMR....G.L.R.EV.RCIR.VM.GE
Retrocopy FITHCGWNSTVEAIVAGVPMVGMPRSADQPTNARYVESAWGIGLRMRLDQNGLLKREEVQRCIRQVMEGE

Parental  RKHVYGRNAARWMHKAKEAMQEGGSSDKNIAEFAAKYL
          RK....RNAA.WM.KAKEAMQEGGSSDKNIAEFAAKYL
Retrocopy RKTEFRRNAAKWMSKAKEAMQEGGSSDKNIAEFAAKYL

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_27 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Zea mays	AC199541.4_FG004	1 retrocopy	retro_zmay_27 ,