RetrogeneDB ID: retro_zmay_57

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 4:127299069..127299669(+)
• 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_57
GTTGGCGCAAGCAACCACGGCCACAACCACGGCCAGCACCACTACCACCGCCTGTGGGCATCCTCCCTCAGCGTCGTTGT
AGCGCAGCTGCCGCCGCAACCGCCGGGCACAGGCCTGCCGCTAACCCTGAACATGGTGGTGTCCACTGGGAACAACAGTG
CTAGCGGCAACCCGGTGCTGCAGCTTGCCAACAGCGGCGGCCTCCTCGATGCGTGCGTCAAGGCGAAGGAGCCCTCATCG
TTGTCTCCCTACGGAGGCGACGTCGTGGCCATCAAAGCCAAGATCGTCTCGCGCCCACACTACTACTCGCTCCTCACTGC
CTACCTCACGTGGAACAAGGTGGGGGCACCACCGGAGGTGTCGGCGAAGCTGACAAAGATAGTGCAGGAGGTGGAGGCGC
GGCAACACACGGCGCTCGGCGGCCTGGCCGCTGCGACGGAGCTAGACCAGTTCATGGAGGCGTACCACGAGATGCTGGTG
AAGTTCAGGGAGGAGTTGACGAGGCTGCTGCAGGAGGCGATGGAGTTCATACGAAGGGTGGAGTCACAGCTCAACTCGCT
TTCCATCTCTGGAAGGTCGCTGCGCAACATCCTTTCATCT

Alignment

ORF - retro_zmay_57 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.01 %
• Parental protein coverage: 57.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VGASSHGHGHGQHHHHHHHHHPWASSLSAVVAPLPPQPPSAGLPLTLNTVAATGNSGGSGNPVLQLANGG
          VGAS.HGH.HGQ....HH.H..WASSLS.VVA.LPPQPP..GLPLTLN.V..TGN...SGNPVLQLAN.G
Retrocopy VGASNHGHNHGQ----HHYHRLWASSLSVVVAQLPPQPPGTGLPLTLNMVVSTGNNSASGNPVLQLANSG

Parental  GLLDACVKAKEPSSSSPYAGDVEAIKAKIISHPHYYSLLTAYLECNKVGAPPEVSARLTEIAQEVEARQR
          GLLDACVKAKEPSS.SPY.GDV.AIKAKI.S.PHYYSLLTAYL..NKVGAPPEVSA.LT.I.QEVEARQ.
Retrocopy GLLDACVKAKEPSSLSPYGGDVVAIKAKIVSRPHYYSLLTAYLTWNKVGAPPEVSAKLTKIVQEVEARQH

Parental  TALGGLAAATEPELDQFMEAYHEMLVKFREELTRPLQEAMEFMRRVESQLNSLSISGRSLRNILSS
          TALGGLAAAT..ELDQFMEAYHEMLVKFREELTR.LQEAMEF.RRVESQLNSLSISGRSLRNILSS
Retrocopy TALGGLAAAT--ELDQFMEAYHEMLVKFREELTRLLQEAMEFIRRVESQLNSLSISGRSLRNILSS

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_57 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 ,