RetrogeneDB ID: retro_zmay_1

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 4:1252740..1253862(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: GRMZM6G617209
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AC148152.3_FG005
• Aliases: None
• Description: None

Sequence

>retro_zmay_1
ATGGCTCCAACGACCGCCACCAAGGACGACAGTGGCTACGGCGACGAGCGCCGGCGCGAGCTGCAGGCGTTCGACGACAC
GAAGCTGGGGGTGAAAGGTCTGGTGGACTCCGGCGTCAAGTCCATCCCGTCCATCTTCCACCACCCGCCGGAAGCCCTGA
GCGACATAATTTCTCCGGCGCCTCTGCCGTCGTCGCCACCCTCCGGCGCCGCCATCCCGGTGGTGGACCTCTCGGTGACG
CGGCGCGAGGACCTAGTCGAGCAGGTGAGGCACGCGGCCGGGACGGTGGGCTTCTTCTGGCTGGTGAACCACGGCGTGGC
GGAGGAGCTGATGGGCGGCATGCTCCGCGGGGTGCGCCAGTTCAACGAGGGCCCCGTGGAGGCGAAGCAGGCGCTCTACT
CCAGGGACCTGGCTCGCAACCTGCGCTTCGCCTCCAACTTCGACCTCTTCAAGGCCGCTGCGGCCGACTGGCGCGACACG
CTCTTCTGCGAGGTGGCTCCGAACCCGCCGCCGCGGGAGGAGCTGCCGGAGCCACTGAGGAACGTGATGCTGGAGTACGG
CGCGGCGGTGACGAAGCTGGCGCGGTTCGTGTTCGAGCTGCTGTCCGAGTCCCTCGGCATGCCCAGCGACCACCTGTACG
AGATGGAGTGCATGCAGAACCTGAACGTGGTGTGCCAGTACTACCCGCCGTGCCCGGAGCCGCACCGCACCGTGGGCGTC
AAGAGGCACACGGACCCTGGCTTCTTCACCATCCTCCTGCAGGACGGCATGGGCGGCCTGCAGGTGCGCCTCGGCAACAA
CGGGCAGAGCGGCGGCTGCTGGGTGGACATCGCTCCCCGGCCTGGGGCGCTCATGGTCAACATCGGTGATCTTCTGCAGC
TCGTGACCAATGACCGGTTCAGGAGCGTGGAGCACCGGGTGCCAGCCAACAAGAGCAGCGACACGGCGAGGGTCTCCGTG
GCGTCCTTCTTCAACACGGACGTGAGGAGGTCCGAGAGGATGTACGGCCCCATTCCAGACCCCAGCAAGCCCCCGCTGTA
CAGGAGCGTCAGGGCCCGAGACTTCATCGCAAAGTTCAACACCATAGGACTCGATGGCCGCGCGCTCGACCACTTCAGGC
TC

Alignment

ORF - retro_zmay_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.2 %
• Parental protein coverage: 96.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAPTAAK--DSGSAD-RWREVQAFEDSKLGVKGLVDSGVKSIPAMFHHPPESLKDVISPPALPSSDDA-P
          MAPT.A...DSG..D.R.RE.QAF.D.KLGVKGLVDSGVKSIP..FHHPPE.L.D.ISP..LPSS.....
Retrocopy MAPTTATKDDSGYGDERRRELQAFDDTKLGVKGLVDSGVKSIPSIFHHPPEALSDIISPAPLPSSPPSGA

Parental  AIPVVDLSVARREDLVAQVKHAAGTVGFFWVVNHGVPEELMASMLSGVRQFNEGSLEAKQALYSRDPARN
          AIPVVDLSV.RREDLV.QV.HAAGTVGFFW.VNHGV.EELM..ML.GVRQFNEG..EAKQALYSRD.ARN
Retrocopy AIPVVDLSVTRREDLVEQVRHAAGTVGFFWLVNHGVAEELMGGMLRGVRQFNEGPVEAKQALYSRDLARN

Parental  VRFASNFDLFESAAADWRDTLYCKIAPDPAPRELVPEPLRNVMMEYGEELTKLARSMFELLSESLGMPSD
          .RFASNFDLF..AAADWRDTL.C..AP.P.PRE..PEPLRNVM.EYG...TKLAR..FELLSESLGMPSD
Retrocopy LRFASNFDLFKAAAADWRDTLFCEVAPNPPPREELPEPLRNVMLEYGAAVTKLARFVFELLSESLGMPSD

Parental  HLHKMECMQQLHIVCQYYPPCPEPHLTIGVRKHSDTGFFTILLQDGMGGLQV-LVDRGGGRQTWVDVTPR
          HL..MECMQ.L..VCQYYPPCPEPH.T.GV..H.D.GFFTILLQDGMGGLQV.L...G.....WVD..PR
Retrocopy HLYEMECMQNLNVVCQYYPPCPEPHRTVGVKRHTDPGFFTILLQDGMGGLQVRLGNNGQSGGCWVDIAPR

Parental  PGALMVNMGSFLQLVTNDRYKSVDHRVPANKSSDTARVSVAAFFNPDEKRTERLYGPIPDPSKPPLYRSV
          PGALMVN.G..LQLVTNDR..SV.HRVPANKSSDTARVSVA.FFN.D..R.ER.YGPIPDPSKPPLYRSV
Retrocopy PGALMVNIGDLLQLVTNDRFRSVEHRVPANKSSDTARVSVASFFNTDVRRSERMYGPIPDPSKPPLYRSV

Parental  TFPDFIAKFNSIGLDGRVLDHFRL
          ...DFIAKFN.IGLDGR.LDHFRL
Retrocopy RARDFIAKFNTIGLDGRALDHFRL

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_1 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Zea mays	AC148152.3_FG005	1 retrocopy	retro_zmay_1 ,
Zea mays	GRMZM2G066358	1 retrocopy	retro_zmay_15,
Setaria italica	Si010340m.g	1 retrocopy	retro_sita_15,