RetrogeneDB ID: retro_zmay_33

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 1:224574692..224575015(+)
• Located in intron of: GRMZM2G063798

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_33
TCTGCTCATCTGGGAGTAGCTGTGCCACACATTGAGTTGAAGCATGTGGTTGCTGCTACAATTGGTCTTAAGGGTCTTGG
AAGCCTCCTTTTTATTTTGAGCAGCTCTCTCGGTGCTTATCTCCTACTGTTGTACCTTGCTTTGATCACTCCTATCATCC
ATGACTTCTACAACTACGATATGGAGAAGGCAGAATTTGCAGGCCTCTTTGCGAAGTTCACCCAAGATTTGGCGCTGATC
GGAGCTCTGCTCTTCTTTCTGGGCATGAAGAACTCCATCCCGAAGCGACAGGGCGGCAAGAAGTCCCCAAGGCGAAGACG
AAC

Alignment

ORF - retro_zmay_33 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.07 %
• Parental protein coverage: 68.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SAHLGVAVPHIELKHVIAATIALKGLGSLLFILSSSLGAYLLLLYLALITPIVHDFYNYDTEKEEFARLF
          SAHLGVAVPHIELKHV.AATI.LKGLGSLLFILSSSLGAYLLLLYLALITPI.HDFYNYD.EK.EFA.LF
Retrocopy SAHLGVAVPHIELKHVVAATIGLKGLGSLLFILSSSLGAYLLLLYLALITPIIHDFYNYDMEKAEFAGLF

Parental  AKFTQDVALVGALLVFLGMKNSIPKRQGKKKA-HKAKTN
          AKFTQD.AL.GALL.FLGMKNSIPKRQG.KK...KAKTN
Retrocopy AKFTQDLALIGALLFFLGMKNSIPKRQGGKKS<PKAKTN

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_33 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,