RetrogeneDB ID: retro_zmay_15

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 10:29229697..29230849(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: GRMZM2G420407
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GRMZM2G066358
• Aliases: None
• Description: None

Sequence

>retro_zmay_15
ATGTCCCCCACGGAAGAAGCCGCTGGTGGTGGTGGCGACGACTATGACCGCTTGAGCGAGCTGAAGGCGTTCGACGACAG
CAAGGCCGGCGTCAAGGGCCTCGTGGACGCTGGCGTCACGACCATCCCTGCCATCTTCCGCGGCCATCTCCTTCAGGAAG
GGCCGAAGGTATCGTCCTCTAGCAGTAGCAGCAGTACTAGTCTTAGCATTATCCCGGTCATCGACCTCTCGGCGGCGGAC
GCAGTCGCACGGGAGGAGGTGGTCGCCCAGTTGAAGGCTGCAGCCGAGACGGTGGGGTTCTTCCAGCTGGTGAACCACGG
CGTTCCCAGCGAGCTCCTGTGCGAGATGCTGCCGTCGGTGAGGCGGTTCAACGAGGAGCCCCACGAGGTGAAGCGGCCCT
ACTACACGCGGGACGCACGTCGCAAGGTGCGGTTCAACTCCAACTTCGATCTGTTCCAGTCGCCGGCGGCCAACTGGCGC
GACACGCTCTTCTGCGAGGCAGCGCCGGAGCCGCCGCGGGCGGAGGAGCTGCCGGTCGCCGTCAGGCACGTGATGCTGGA
GTACGGCGGCGCGGTGCGGGAGGTGGCGGCGCGCGTGCTGGGGCTGCTCTCGGAGGCCCTGGGGCTGAGCCCCGGGCACC
TCGCAGGGATGGGGTGCGCGGAGGGCCTCAGCCTGGTGTGCAACTACTACCCGCCGTGCCCGGAACCGGACCTCACCCTG
GGCTGCAGCAGGCACTCGGACCCCAGCTTCCTGACCGTGCTGCTGCAGGACTCGCATGCGCAGGGCGGCCTGCAGGCGCT
CCTCGCATCCAGGTGGCTGGACGTGCCTCCGGTGGCCGGCGCGCTCCTGGTGAACGTCGGAGACCTTCTCCAGCTGGTCA
GCAACGGGCGGTTCAAGAGCGTGGAGCACCGGGTGGTGGCTAACCGGAGCAGGGACACGGCGAGAGTGTCAGTGGCGTGC
TTCTGCAACGCGGACATCGCGAGATCCACGAGGCTGTATGGACCCATCGCGGAGCTCATCGCCGCGGACGACAGCGACGG
CGCGGGAAGGGCGCTGTACAGGAACGTGACGGTCCCGGAGTTCCTAGCGCACTACGACAAGAAAGGCCTCGACGGTCGCC
CGGCGCTCCACCGCTTCCAGCTGCTTCAATAA

Alignment

ORF - retro_zmay_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.5 %
• Parental protein coverage: 94.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LAGVRRFNEQQAEAKRRFYTRDTARKVRFTSNYDLFQSAAASWRDTLFCELAPDPPRPEELPEAVRGAML
          L..VRRFNE...E.KR..YTRD..RKVRF.SN.DLFQS.AA.WRDTLFCE.AP.PPR.EELP.AVR..ML
Retrocopy LPSVRRFNEEPHEVKRPYYTRDARRKVRFNSNFDLFQSPAANWRDTLFCEAAPEPPRAEELPVAVRHVML

Parental  EYGDAATELALRVLELLSESLGLPSDHLREMGCARSLNVASHYYPPCPEPHLTLGTSRHADATFLTVLLQ
          EYG.A..E.A.RVL.LLSE.LGL...HL..MGCA..L.....YYPPCPEP.LTLG.SRH.D..FLTVLLQ
Retrocopy EYGGAVREVAARVLGLLSEALGLSPGHLAGMGCAEGLSLVCNYYPPCPEPDLTLGCSRHSDPSFLTVLLQ

Parental  D--AMGGLQVLLDRGGWVDVPPLPGALIVNIGDILQLVSNDRFRSVEHRVLANKSKDTPRVSVACFFNAD
          D..A.GGLQ.LL....W.DVPP..GAL.VN.GD.LQLVSN.RF.SVEHRV.AN.S.DT.RVSVACF.NAD
Retrocopy DSHAQGGLQALL-ASRWLDVPPVAGALLVNVGDLLQLVSNGRFKSVEHRVVANRSRDTARVSVACFCNAD

Parental  VKRSTRLYGPI----ITDGGGSSSPPLYKSVTAREFVGYSYSKGLDGRPLEH
          ..RSTRLYGPI......D........LY..VT..EF......KGLDGRP..H
Retrocopy IARSTRLYGPIAELIAADDSDGAGRALYRNVTVPEFLAHYDKKGLDGRPALH

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_15 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Zea mays	AC148152.3_FG005	1 retrocopy	retro_zmay_1,
Zea mays	GRMZM2G066358	1 retrocopy	retro_zmay_15 ,
Sorghum bicolor	Sb10g006910	1 retrocopy	retro_sbic_29,