RetrogeneDB ID: retro_zmay_11

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 6:48567057..48568056(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: GRMZM2G327051
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GRMZM2G075290
• Aliases: None
• Description: None

Sequence

>retro_zmay_11
ATGGCGCGCGCGCGTGACGCCGCCCTCCACCTCCTCCTCCTGGCAGCGGGCGCACTCCTACTTCTAGCCGTGGTGTCTCA
GGCCACCGTGGTGCCGCCGAGCGTTCCGGCGGGCGCCCCCGAGGACCCGCGGTGCCGCGCGCTGGCGCCGCGGCGTGGCG
CGCTGGCGGTGTACCCGAGCGACATGGAGCAACTGCAGTTCCTTCTCAACGCCAAGTTCGTGGAGGCGGAGTGGTTCCTG
CACGCGGCGCTGGGACGTGGCGTGGACTTCCTGGACCGCAACCTGTCCGGCGGCGGGCCTCGGCCGTCCGGGGCCAGGAA
GGCGGACCTGGACTTCCGCACAACCGAGGTCGCCGCCGAGCTCGGGTACCAGGAGGTGGGCCACATCCGCGCCATCAGGC
AGGCCGTGGGCGGGTTCCCGCGGCCGCCCATCGACCTCGGCGCCGACCGCTTCGCCATGGTCATGGACGACGCCATGGGC
GTCCGTCTGGACCCGCCGTTCGACCCGTACGCCGGGCCCGTCAACTTCCTGCTCGCCTCCTACGTGTTCCCGCACGTCAC
CGCCGCCGCCGCCATGGGCATCGGCCCCAGCCTCATGGGCTACGCCTCCAAGCGCCTCCAGGCGAGCATCCTGGCGGTGG
AGGCCGGGCAGGACGCGGTGATCCGGCTGCTGCTGTACCAGCGCGCCGACGATGCCGTCCCACCGTACCAGGGCCACACC
GTGGCCGACTTCACGCGCCGGATCTCCGACTGGCGCAACCGGATGTCCGGGTGCGGCGCCAAGGACGAAGGGGTCAAGGT
GCTGGACCGGCGGCAGGGCGCCGAGCGCCGCACCATAAGCAACATCCTCGGCGCCGGCGAGGACTCGCTCGGGTTCCAAC
GCACGCCTGCGGAGGTGCTCCGCATCCTCTACGGCTCGCGCAACGAGCAGATCCCCGGTGGGTTCCTCCCCAGGGGTGCC
AATGGAACCATCGCTAGAGGTTTCTTCCAGCTCGCGTAG

Alignment

ORF - retro_zmay_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.49 %
• Parental protein coverage: 84.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AVAAVSSAESSYVEPRRCQPPAPHI-AVAVFPYDVDPMQFALNLEYTEAEFFLHGAYGVGLDHLAPRLAL
          A.....S......E..RC...AP...A.AV.P.D....QF.LN....EAE.FLH.A.G.G.D.L...L..
Retrocopy ATVVPPSVPAGAPEDPRCRALAPRRGALAVYPSDMEQLQFLLNAKFVEAEWFLHAALGRGVDFLDRNLSG

Parental  GGPPPVGARKANLDEVTRRIVAEFGLQEVGHIRAIQRTVGGIPRPLIDLSAHNFARVMDEAFGTRLDPPF
          GGP.P.GARKA.LD..T....AE.G.QEVGHIRAI...VGG.PRP.IDL.A..FA.VMD.A.G.RLDPPF
Retrocopy GGPRPSGARKADLDFRTTEVAAELGYQEVGHIRAIRQAVGGFPRPPIDLGADRFAMVMDDAMGVRLDPPF

Parental  DPYVNSLNFLLASYVIPYLGINGYVGTNPIVDGYQTKKLLAGLLGVEAAQDAVFRARLFERLGEAVPPYG
          DPY....NFLLASYV.P........G..P...GY..K.L.A..L.VEA.QDAV.R..L..R...AVPPY.
Retrocopy DPYAGPVNFLLASYVFPHVTAAAAMGIGPSLMGYASKRLQASILAVEAGQDAVIRLLLYQRADDAVPPYQ

Parental  NITVAEFTDRVSALRNRLGRCGVKDEGLTV-PRRLGAEGAICTNVLSADRDSLSYARTPAELLSILYLTG
          ..TVA.FT.R.S..RNR...CG.KDEG..V..RR.GAE.....N.L.A..DSL...RTPAE.L.ILY...
Retrocopy GHTVADFTRRISDWRNRMSGCGAKDEGVKVLDRRQGAERRTISNILGAGEDSLGFQRTPAEVLRILYGSR

Parental  DERVPGGFYPEGANGRIARSF
          .E..PGGF.P.GANG.IAR.F
Retrocopy NEQIPGGFLPRGANGTIARGF

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_11 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	GRMZM2G075290	1 retrocopy	retro_zmay_11 ,