RetrogeneDB ID: retro_zmay_24

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 7:725315..726404(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: GRMZM2G177104
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GRMZM2G006964
• Aliases: None
• Description: None

Sequence

>retro_zmay_24
ATGCAACAATCCTCGGCCGCCTCGATGGCAATGGAGGAAGACGACGACTACGAGCCGCCGTTGATGGCCACGTACAAGCA
TCTGTTGGACAGTCACCCGCACCGACAACTGGGCGCCGGCGCCGCGCAAGACGACGAGGATTGCTTCCTCCTCCCGGTGA
TCGACCTTTCCAGCCTCCTGCCGCCGGTGCATCATCGCAAGCAGTCATCATCAGCAGCAGCTGCAGAGCAGTGCCGGGCG
TCCATCGTGCGCGCCGCCTCCGAGTGGGGCTTCTTCCAGGTGACCAACCACGGCGTGCCGCAGGTTCTGCTGGACGAGCT
GCACCAGGCGCAGGCCGGCGTCTTCCGCCGGCCCTTCCAACTCAAGGCGCACCAGCCGCTGCTGGACTTCTCGCCGGAGA
GCTACCGCTGGGGCACGCCCACCGCCACGTGCCTGGAGCAGCTCTCGTGGTCCGAGGCCTACCACATCCCCACAACGACG
ACCACGACCGGTAACGACGACAAGACCCGGCTAGTGGTCGAGGAGGTGTCGACGGCGATGTCGAAGCTGGCGCAGCGGCT
GGCGGGGATCCTCGTCGCGGAGCTGGGCGAAGACAGCGCGGCGGCGGTGGTGTCGCGGTGCACGCGGAGCACCTGCTTCC
TGCGGCTGAACCGGTACCCGCCGTGCGCGGCGGCGGCCAGCGGCGTCGTCTACGGGCTGTGCCCACACTCGGACAGCGAC
TTCCTGACCATACTCCACCAGGACGGCGTCGGCGGCCTCCAGCTCGTCAAGGACGGGCAGTGGGTAGCCGTGAAGCCCAG
CCCCGGCGCGCTCATCGTCAATGTGGGCGACCTCCTGCAGGCGTGGAGCAACGACCGGTACCGGAGCGTCGAGCACCGGG
TGATGGCCAGCGCCACGAGGGAGCGGTTCTCCGCCGCCTTCTTCCTGTGCCCCAGCTACGACACGCTCATCCGGCCGCGC
TGCGGCGCCGGCGGACCTCCTCCTCGCTATGAGAGCTTCACCTTCGGGGAGTACCGGAACCAGATCAGGGAGGACGTCAG
GCTCACGGGCCGAAAGCTCGGCCTGCAACGCTTCCGCAAAGCAGAGTAG

Alignment

ORF - retro_zmay_24 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.8 %
• Parental protein coverage: 55.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ISGTACDFGELSSLRDVVQEVADAMSRVAKTVAVALAGSLLGHDEAAAFPAGCGETTCYLRLNRYPACPF
          I..T....G.....R.VV.EV..AMS..A...A..L...L.G.D.AAA....C...TC.LRLNRYP.C..
Retrocopy IPTTTTTTGNDDKTRLVVEEVSTAMSKLAQRLAGILVAEL-GEDSAAAVVSRCTRSTCFLRLNRYPPCAA

Parental  AAN--TFGLVPHTDSDFLTVLSQDQVGGLQLMTDAGWVAVKPRPDALIVNIGDLFQAWSNNLYKSVEHKV
          AA.....GL.PH.DSDFLT.L.QD.VGGLQL..D..WVAVKP.P.ALIVN.GDL.QAWSN..Y.SVEH.V
Retrocopy AASGVVYGLCPHSDSDFLTILHQDGVGGLQLVKDGQWVAVKPSPGALIVNVGDLLQAWSNDRYRSVEHRV

Parental  VANAAAERFSAAYFLCPSYDSLV----GTCGEPSPYRDFTFGEYRRKVQEDVKRTGRKIGLPNFLK
          .A.A..ERFSAA.FLCPSYD.L.....G..G.P..Y..FTFGEYR....EDV..TGRK.GL..F.K
Retrocopy MASATRERFSAAFFLCPSYDTLIRPRCGAGGPPPRYESFTFGEYRNQIREDVRLTGRKLGLQRFRK

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_24 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	GRMZM2G006964	1 retrocopy	retro_zmay_24 ,
Sorghum bicolor	Sb06g022880	1 retrocopy	retro_sbic_13,
Setaria italica	Si012266m.g	1 retrocopy	retro_sita_32,