RetrogeneDB ID: retro_zmay_66

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 5:20237460..20237845(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GRMZM5G821426
• Aliases: None
• Description: None

Sequence

>retro_zmay_66
AGGTATTTAGAGGAAACTTTGAGTGGATTGTTCTAGGCGGGTGGTAGCAGCGATTCGGTGTCATTTCTCCTTGAAGGCGA
TGCCCAAAATACCTTCAATTTGTGTGGTTGTCGGTGAAGTGGAGGCCTTTCGTCACTCCGCTCAGCTCAGTGGTCCTTGG
GCCTTTATCGCTCTGGGCGTCTGCTTGCTCCTGGTGCTCGACATTATGGCTCCAAACTCATTGGTGAAGAATCGGAGTTG
CCTCGTGTAGGGTGCGGCAAGGCTTTGAAACAATGGCGCACCATGGCCTTCCTCTGGTGTCGTTGTTTAGGTGTAGCCAT
CGTCGAGTTCCTTGGTCATTTTTTCAACCCATCTTGGGAAATCAGAGCTGCTCGTCCCTTGTCTT

Alignment

ORF - retro_zmay_66 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.06 %
• Parental protein coverage: 82.69 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RSSEETLLGLYQAGGDSFSTSFLLLEGAAQKTSSLCVRPCCGGSSSLCLARWCPGLCRFRRLLAPGVRRC
          R..EETL.GL..AGG.S.S.SFLL.EG.AQ.T..LC.....GG.SSL..A.W..GL.R..RLLAPG.R..
Retrocopy RYLEETLSGLF*AGGSSDSVSFLL-EGDAQNTFNLCGCR*SGGLSSLRSAQWSLGLYRSGRLLAPGARHY

Parental  GSLLV-VKNQSCLVWGVLRLVNDGTPW-SYSLRRCLDVSVVELLWQCV-AHLGKSELLVSCV
          GS.L..VKN.SCLV.G..RL.N.G.PW......RCL.V..VE.L......HLGKSELLV.C.
Retrocopy GSKLI>VKNRSCLV*GAARL*NNGAPW<AFLWCRCLGVAIVEFLGHFF>THLGKSELLVPCL

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_66 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Zea mays	GRMZM5G821426	3 retrocopies	retro_zmay_46, retro_zmay_55, retro_zmay_66 ,