RetrogeneDB ID: retro_zmay_8

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 7:174630923..174631610(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: GRMZM2G516421
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GRMZM2G007475
• Aliases: None
• Description: None

Sequence

>retro_zmay_8
ATGGACCTGGACATCATGGCGATGCCCACCACGCCCAAAGCCACCACCAGCAGCCCCGCCGCGTACTACGTCGCCAAGCC
TCCTCCTCCTCCTCCTCTGGGCTACGCGGTTCACAACAAGGCGGCGGCGGCGGCCTACGATTCCTACGACGGCCGACACG
GCGGCATGGTCGCCACCACCACCACCACCCGGTCGTCCTCCTCGGCGGCGCGCCACCACCACCACCACCACCACCACCAG
CAGCCGGCGGGAGCGCGGGCGCTGGACGGGGTCCTGCTGCTGCTGCGCGCGGCCGCGTCGGTCATGGCGTTCGTGGCCGT
CGCGCTCGTCGCGTCCTGCCGCCACGGCGACTGGATGGAGTTCGCGCGCTACCCGGAGTACCGGGGCCTCCTGGGGGCCT
CCGCGCTCGCCTGCGCCTACTCCGCCGCGCAGGCCACCCGTGGCTTCCGCCGGATGCGCGCCTCCGGGAGAGCGGGTGGC
GGCCTCGCGGATTTCGCCGGCGACCAGGTGGTGGCGTACCTGCTCATCACGGCGTCGGCGGCGGCTCTCCCCATCACCCT
CCGCATGAGATCCGCCGTACTCAACGTCTTCACGGACGCCATGACGGCCGCCATCAGCCTGGCTTTCATAGCCTTTGCGG
CGCTCGCCTTGTCCGCCGTGCTCTCCGCCGCCGCGCAACCATACTAG

Alignment

ORF - retro_zmay_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.87 %
• Parental protein coverage: 57.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LDKSPLALHAAAAVFAFVALVLVASNQHGDWMQFDRYQEYKYLLSIASLALLYSLAQAARHAHRMRGGVD
          LD...L.L.AAA.V.AFVA..LVAS..HGDWM.F.RY.EY..LL....LA..YS.AQA.R...RMR....
Retrocopy LDGVLLLLRAAASVMAFVAVALVASCRHGDWMEFARYPEYRGLLGASALACAYSAAQATRGFRRMRAS--

Parental  PISSASGRLLDFVGDQVVAYLLMSALSAAAPITNRMRSAVVNNFTDATAAAISMTFFAFAALALSAVVS
          ....A.G.L.DF.GDQVVAYLL..A..AA.PIT.RMRSAV.N.FTDA..AAIS..F.AFAALALSAV.S
Retrocopy --GRAGGGLADFAGDQVVAYLLITASAAALPITLRMRSAVLNVFTDAMTAAISLAFIAFAALALSAVLS

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_8 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	GRMZM2G007475	1 retrocopy	retro_zmay_8 ,
Leersia perrieri	LPERR03G12390	1 retrocopy	retro_lper_2,
Sorghum bicolor	Sb01g038100	1 retrocopy	retro_sbic_28,