RetrogeneDB ID: retro_zmay_59

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 4:235981600..235981989(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GRMZM2G358405
• Aliases: None
• Description: None

Sequence

>retro_zmay_59
CAGACGTTTATGCAGCTCCGACTAACGAAATCCATGCGTGCAGGTAGGCAGGTACCTGTTGAGGGCGAGGGTGGCGGCGA
TGTGGCTAGGGCGCACTCCGCGATCGACGAGGCCGGTGGCAAGGCTCTGCACGCCCCCGCCGAACTCCGCGCTGGTGAGG
CATCGACCGCCTGGGCCGGCAGCGACGACGACAGTGACAAGTGATAAGGGCTGCTGGGCTGAGGCGGTGCGAGGCAAGAA
GCCTGCTAGTCGCGCCTCGAGAGGGGCAGCGGTGGGGACCGATATCTGGGGTTGTGATGGGAGAAGAAACTGAGGAGAGG
CCGAAAGCGGACGGGGCGAGAAGGTTGGTGTGGGAGGGAGAGGAGGAAGCGGACTGCAGAGGTGTTGCC

Alignment

ORF - retro_zmay_59 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.28 %
• Parental protein coverage: 68.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KVFRSQVISSNTHSSRQLPVEGEGGDDVARAHSTIGEAGGKALHAASNLRAGEASTDWAGS-DDDG-FDK
          ..F............RQ.PVEGEGG.DVARAHS.I.EAGGKALHA...LRAGEAST.WAGS.DD....DK
Retrocopy QTFMQLRLTKSMRAGRQVPVEGEGGGDVARAHSAIDEAGGKALHAPAELRAGEASTAWAGSDDDSD>SDK

Parental  GCWAEAVRGKEPARRASRG-QRRGPGSGVVMGEEIEERLEADGARRLVWEGEEEADCRGVA
          GCWAEAVRGK.PA.RASRG.QR.GP.SGVVMGEE.EER..ADGARRLVWEGEEEADCRGVA
Retrocopy GCWAEAVRGKKPASRASRG>QRWGPISGVVMGEETEERPKADGARRLVWEGEEEADCRGVA

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_59 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	GRMZM2G358405	3 retrocopies	retro_zmay_39, retro_zmay_59 , retro_zmay_60,