RetrogeneDB ID: retro_zmay_28

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 4:30460441..30461221(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: GRMZM2G444073
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GRMZM5G804893
• Aliases: None
• Description: None

Sequence

>retro_zmay_28
ATGAAGAACAGGAAGGGCTACGGGCACCAGGGCCACCTGCTGAGCCCCGTGGGCAGCCCGCTGTCGGACAACGAGTCCGG
CGCCGCGGCAGCGGCCGGCGGCGGCGGGTGCGGGAGCAGCGTGGGGTACTGCGGCGGCGGCGGCGGTGAGTCGCCGGCCA
AGGAGCAAGACCGGTTCCTGCCGATCGCCAACGTGTCGCGCATCATGAAGCGCTCCCTGCCGGCGAACGCCAAGATCTCC
AAGGAGGCCAAGGAGACGGTGCAGGAGTGCGTGTCCGAGTTCATCAGCTTCGTCACGGGGGAGGCCTCCGACAAGTGCCA
GCGCGAGAAGCGCAAGACCATCAACGGCGACGACCTGCTCTGGGCCATGACCACGCTCGGCTTCGAGGCCTACGTCGCCC
CGCTCAAGTCCTACCTCAACCGCTACCGCGAGGCCGAGGGCGAGAAGGCCGCCGTGCTCGGCGGCGGCGCGCGCCACGGC
GAAGGCGGCGGCGCGGCGGACGACGCCGGCCCACTCGCCGCGGGCGGCGGGGCCGGGGACGGTGTCGACCGCGCGGGCCA
CGACGACGACGCGCACGTCGGGCTCATGATGGGAGCCAGCAGCGTCGGGTTCGGCTCTGGCGGCGGGGCGGCGCCGTCGT
ACTACGCGGCGGCATCACGGAAGGCGTACGGCGCGGGGGAAGGGTCCAAGGTGATGGAGTTCGAAGGCGAGGAGGAGAAC
GGCGGCGTGCAGAGGGGGAGGGGATTTGCCAGCCACCTCCACGGCGCCGTGCAATGGTGA

Alignment

ORF - retro_zmay_28 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.24 %
• Parental protein coverage: 90.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  APASPGGGGGSHESGSPRGGGGGGSVREQDRFLPIANISRIMKKAIPANGKIAKDAKETVQECVSEFISF
          A.A..GGGG.....G...GGGG.....EQDRFLPIAN.SRIMK...PAN.KI.K.AKETVQECVSEFISF
Retrocopy AAAAAGGGGCGSSVGYCGGGGGESPAKEQDRFLPIANVSRIMKRSLPANAKISKEAKETVQECVSEFISF

Parental  ITSEASDKCQREKRKTINGDDLLWAMATLGFEDYIEPLKVYLQKYREVQGDSKLTAKSSDGSIKKDALGH
          .T.EASDKCQREKRKTINGDDLLWAM.TLGFE.Y..PLK.YL..YRE..G.....A....G.......G.
Retrocopy VTGEASDKCQREKRKTINGDDLLWAMTTLGFEAYVAPLKSYLNRYREAEGEK--AAVLGGGARHGEGGGA

Parental  VGASSSAAQGGAYNQGM
          .......A.GG....G.
Retrocopy ADDAGPLAAGGGAGDGV

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_28 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00080p00025480	1 retrocopy	retro_atri_9,
Zea mays	GRMZM5G804893	1 retrocopy	retro_zmay_28 ,