RetrogeneDB ID: retro_zmay_41

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 1:226560273..226560881(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GRMZM2G017087
• Aliases: None
• Description: None

Sequence

>retro_zmay_41
GTTGGCGCAAGCAGCCACATCCACGGCCACGGCCAGCACCACTACCACCACCCGTGGGCATCCTCCCTTAGCACCGTCGT
AGCGCCGCTGCCGCTGCAACCGCCGGTCACAGGCCTGCCACTCACCTTGAACACGGTGGCGGCCACTGGGAACAGCGGCG
CTAGCAGCAACCCGGTAAACCCGGTGCTGCAGCTTGCCGACGGTGGCAACCTCCTCGACGCGTGTATCAAGGCGAAGGAG
CCCTCATCGTCGTCTCCCTATGTCGGGGCCATCAAGGCCAAGATCATCTCGCACCCACACTACTACTCGCTCCTCACTGC
CTACCTCGGGTGCAACAAGGTGGGGGCACCACCGGAGGTGTCGGCGAGGCTGACGGAGATAGCGCAGGAGGTGGAGGCGC
GGCAGCGCACGGCGCTCGGTGGCCTGGCCGTTGCGACGGAGCTGGAGCTGGGCCAGTTCGTGGAGGCGTACCACGAGATG
CTGGTAAAGTTCAGGGAGGAGCTAATGAGGCCGCTACAGGAGGCGATGGAGTTCATGCGGGGGTGGAGTCGCAGCTCAAC
TCGCTTTCCATCTCCGGAAGGTTGCTGCACGACATCCTTTCATCTGGG

Alignment

ORF - retro_zmay_41 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.36 %
• Parental protein coverage: 57.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VGASSHGHGHGQHHHHHHHHHPWASSLSAVVAPLPPQPPSAGLPLTLNTVAATGNSGGSGNPV---LQLA
          VGASSH.HGHGQ....HH.HHPWASSLS.VVAPLP.QPP..GLPLTLNTVAATGNSG.S.NPV...LQLA
Retrocopy VGASSHIHGHGQ----HHYHHPWASSLSTVVAPLPLQPPVTGLPLTLNTVAATGNSGASSNPVNPVLQLA

Parental  NGGGLLDACVKAKEPSSSSPYAGDVEAIKAKIISHPHYYSLLTAYLECNKVGAPPEVSARLTEIAQEVEA
          .GG.LLDAC.KAKEPSSSSPY.G...AIKAKIISHPHYYSLLTAYL.CNKVGAPPEVSARLTEIAQEVEA
Retrocopy DGGNLLDACIKAKEPSSSSPYVG---AIKAKIISHPHYYSLLTAYLGCNKVGAPPEVSARLTEIAQEVEA

Parental  RQRTALGGLAAATEPELDQFMEAYHEMLVKFREELTRPLQEAMEFMR-RVESQLNSLSISGRSLRNILSS
          RQRTALGGLA.ATE.EL.QF.EAYHEMLVKFREEL.RPLQEAMEFMR..VESQLNSLSISGR.L..ILSS
Retrocopy RQRTALGGLAVATELELGQFVEAYHEMLVKFREELMRPLQEAMEFMR<GVESQLNSLSISGRLLHDILSS

Parental  G
          G
Retrocopy G

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_41 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Zea mays	GRMZM2G017087	2 retrocopies	retro_zmay_41 , retro_zmay_57,