RetrogeneDB ID: retro_zmay_31

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 1:60743858..60744674(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GRMZM2G068506
• Aliases: None
• Description: None

Sequence

>retro_zmay_31
GTTCCTGGAATCATTCTCGGAGGTGGTGCTGAGACTAGATTGTACCTCTTGACAAAGAAATGTGCCAAGCCTGCAGTGAC
ATTGGGTGCCAACTATAGGCTGATTAATATTCCTATCAGCAATTGTCTCAACAACAACATATCCAAGATCTATGTGCTAA
CACAATTTAACTCTGCTTCCCTCAACCATCACCTCTCAACTACCTACGGGAGCAACATTGGAGGGTACACGAATGAAGGG
TTTTTTGAAGTCTTAGCTGCACAGCAGAGCCCAGATAATCCAAACTGGTTTCAGGGTACTACAGACGATGTAAGGCAGTA
CTTGTGGTTGTTTGAGGAGCATAATGTGATGGAGTTTCTAATTCTTGCTGGTGATCGTCTATACCGGATGGACTACGAAA
AGTTCATTTAGGCACATAGAGAAATATATGCTGATATTTGTGTTGTGGCCCTACCAATGGATGAGAAACGTACAACTGCA
TTTGGACTCATGCAAATCGATGAAGAATGGAGGATCATTGAGTTTGCTAAGAAACCGAAAGGAGAGCAGTTGAACGAAAT
GATAGTTGACACCACCATACTTGGCCTTGATGACGTGAGGGCAAAGGCAATGCTTTATATTGCTAGCATGGATATCTATG
TTTTTAGCCAAGATGTAATGCTTCAGCTCCTCCGTGAACAATTTCCTAGAGCCAATGACTTGGGAAGTGAGGTTATTCCA
GGTGCAACCAGCATTGGAAAGAGGGTTCACGCTTATCTGTATGATGGTTACTTGGAAGATATTGGTACCATTAACACATT
TTATAATGCAAACTTG

Alignment

ORF - retro_zmay_31 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.03 %
• Parental protein coverage: 57.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VLGIILGGGAGTRLYPLTKKRAKPAVPLGANYRLIDIPVSNCLNSNISKIYVLTQFNSASLNRHLSRAYG
          V.GIILGGGA.TRLY.LTKK.AKPAV.LGANYRLI.IP.SNCLN.NISKIYVLTQFNSASLN.HLS..YG
Retrocopy VPGIILGGGAETRLYLLTKKCAKPAVTLGANYRLINIPISNCLNNNISKIYVLTQFNSASLNHHLSTTYG

Parental  SNIGGYKNEGFVEVLAAQQSPDNPNWFQGTADAVRQYLWLFEEHNVMEFLILAGDHLYRMDYEKFIQAHR
          SNIGGY.NEGF.EVLAAQQSPDNPNWFQGT.D.VRQYLWLFEEHNVMEFLILAGD.LYRMDYEKFI.AHR
Retrocopy SNIGGYTNEGFFEVLAAQQSPDNPNWFQGTTDDVRQYLWLFEEHNVMEFLILAGDRLYRMDYEKFI*AHR

Parental  ETNADITVAALPMDEKRATAFGLMKIDEEGRIIEFAEKPKGEQLKAMMVDTTILGLDDVRAKEMPYIASM
          E..ADI.V.ALPMDEKR.TAFGLM.IDEE.RIIEFA.KPKGEQL..M.VDTTILGLDDVRAK.M.YIASM
Retrocopy EIYADICVVALPMDEKRTTAFGLMQIDEEWRIIEFAKKPKGEQLNEMIVDTTILGLDDVRAKAMLYIASM

Parental  GIYVFSKDVMLQLLREQFPEANDFGSEVIPGATSIGKRVQAYLYDGYWEDIGTIAAFYNANL
          .IYVFS.DVMLQLLREQFP.AND.GSEVIPGATSIGKRV.AYLYDGY.EDIGTI..FYNANL
Retrocopy DIYVFSQDVMLQLLREQFPRANDLGSEVIPGATSIGKRVHAYLYDGYLEDIGTINTFYNANL

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_31 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Zea mays	GRMZM2G068506	1 retrocopy	retro_zmay_31 ,