RetrogeneDB ID: retro_zmay_46

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 2:224398090..224398478(+)
• 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_46
AGGTCTTCGGAGGAAACTTTGCTTGGTTTGTACCAGGTGGGCGGCGACGGCTTTTCGAGATCGTTTCTCCTTCTTGAAGG
CGCGGCCCAGAAGACCTCCAGTTTGTGTGTTCGTCCGTGTTGTGGAGGCTCTTCGTCACTCCGCTTGGCTCGATGGTGTC
CGGGCCTTTGTCGCTTTAGGTGTCTGCTCGCTCCCGGAGTTCGGCGTTGTGGATCTTTTTGCTCGTAGTGAAGAATCGGA
GCTGCCTCATGTGGGTGTGCTGAGGCTTGGCAACGATGGCGCGCCGCGGTCTTATTCCTTGCGTCGGTGTCTGGATGTAA
GCGTCGTCGAGTTGCTTTGGCAGTGTGCAGCTCGTCTTGGGAAGTCGGAGCTGCTCGTCTCTTGTGTT

Alignment

ORF - retro_zmay_46 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.12 %
• Parental protein coverage: 82.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RSSEETLLGLYQAGGDSFSTSFLLLEGAAQKTSSLCVRPCCGGSSSLCLARWCPGLCRFRRLLAPGVRRC
          RSSEETLLGLYQ.GGD.FS.SFLLLEGAAQKTSSLCVRPCCGGSSSL.LARWCPGLCRFR.LLAPGVRRC
Retrocopy RSSEETLLGLYQVGGDGFSRSFLLLEGAAQKTSSLCVRPCCGGSSSLRLARWCPGLCRFRCLLAPGVRRC

Parental  GS-LLVV-KNQSCLVW-GVLRLVNDGTPWSYSLRRCLDVSVVELLWQCVAHLGKSELLVSCV
          GS..L.V.KN.SCL.W.GVLRL.NDG.P.SYSLRRCLDVSVVELLWQC.A.LGKSELLVSCV
Retrocopy GS<FLLVVKNRSCLMW<GVLRLGNDGAPRSYSLRRCLDVSVVELLWQCAARLGKSELLVSCV

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_46 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.

---

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,