RetrogeneDB ID: retro_zmay_79

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 7:1971049..1971520(-)
• Located in intron of: None

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_79
ATGGGGTCCGTGTCCTTCGTCGGGAGGGTGCTCTTCGTCGCCGCTTTCCTCCTCTCCGCCTACCAGGAGTTGAATGAATT
CGGTGCTAATGGTGGACCAACATCTAAGGCCATTCAACCCAAATTCAACGTGTTTATCAAAAATGTCTCTGCTCATCTGG
GAGTAGCTGTGCCACACATTGAGTTGAAGCATGTGATTGCTGCTACAATTGGTCTTAAGGGTCTTGGAAGCCTCCTTTTT
ATTTTGAGCAGCTCTCTCGGTGCTTATCTCCTACTGCTGTACCTTGCTTTGATCACTCCTATCATCCATGACTTCTACAA
CTACGATATGGAGAAGGCAGAATTTGCAGGCCTCTTTGCGAAGTTCACCCAAGATTTGGCGCTGATCGGAGCTCTGCTCT
TCTTTCTGGGCATGAAGAACTCCATCCCGAAGCGGCAGGGGCGGCAAGAAGTCCCCAAGGCGAAGACGAAC

Alignment

ORF - retro_zmay_79 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.62 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGFVSFVGRVLFVAAFLLSAYQEFNEFGADGGPAAKALQPKFNVFVKNISAHLGVAVPHIELKHVIAATI
          MG.VSFVGRVLFVAAFLLSAYQE.NEFGA.GGP..KA.QPKFNVF.KN.SAHLGVAVPHIELKHVIAATI
Retrocopy MGSVSFVGRVLFVAAFLLSAYQELNEFGANGGPTSKAIQPKFNVFIKNVSAHLGVAVPHIELKHVIAATI

Parental  ALKGLGSLLFILSSSLGAYLLLLYLALITPIVHDFYNYDTEKEEFARLFAKFTQDVALVGALLVFLGMKN
          .LKGLGSLLFILSSSLGAYLLLLYLALITPI.HDFYNYD.EK.EFA.LFAKFTQD.AL.GALL.FLGMKN
Retrocopy GLKGLGSLLFILSSSLGAYLLLLYLALITPIIHDFYNYDMEKAEFAGLFAKFTQDLALIGALLFFLGMKN

Parental  SIPKRQGKKKAHKAKTN
          SIPKRQG.....KAKTN
Retrocopy SIPKRQGRQEVPKAKTN

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_79 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.

---

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,