RetrogeneDB ID: retro_zmay_42

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 1:227228472..227228795(-)
• Located in intron of: GRMZM2G070392

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AC149475.2_FG002
• Aliases: None
• Description: None

Sequence

>retro_zmay_42
TCTACTCATCTGGGAGTAGCTGTGCCACACATTGAGTTGAAGCATGTGGTTGCTGCTACAATTGGTCTTAAGGGTCTTGG
AAGCCTCCTTTTTATTTTGAGTAGCTCTCTCGGTGCTTATCTCCTACTGTTGTACCTTGCTTTGATCACTCCTATCATCC
ATGACTTCTACAACTACGATATGGAGAAGACAGAATTTGCAGGCCTCTTTGCGAAGTTCACCCAAGATTTGGCGCTGATC
GGAGCTCTGCTCTTCTTTCTGGGCATGAAGAACTCCATCCCGAAGTGACAGGGCGGCAAGAAGCCCCCAAGGCGAAGACG
AAC

Alignment

ORF - retro_zmay_42 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.16 %
• Parental protein coverage: 68.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SAHLGVAVPHIELKHVIAATIALKGLGSLLFILSSSLGAYLLLLYLALITPIVHDFYNYDTEKEEFARLF
          S.HLGVAVPHIELKHV.AATI.LKGLGSLLFILSSSLGAYLLLLYLALITPI.HDFYNYD.EK.EFA.LF
Retrocopy STHLGVAVPHIELKHVVAATIGLKGLGSLLFILSSSLGAYLLLLYLALITPIIHDFYNYDMEKTEFAGLF

Parental  AKFTQDVALVGALLVFLGMKNSIPKRQGKKK-AHKAKTN
          AKFTQD.AL.GALL.FLGMKNSIPK.QG.KK.A.KAKTN
Retrocopy AKFTQDLALIGALLFFLGMKNSIPK*QGGKK<APKAKTN

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_42 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 2 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Zea mays	AC149475.2_FG002	4 retrocopies	retro_zmay_33, retro_zmay_42 , retro_zmay_61, retro_zmay_79,
Vitis vinifera	VIT_05s0049g00210	2 retrocopies	retro_vvin_165, retro_vvin_52,