RetrogeneDB ID: retro_zmay_21

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 4:2054554..2055724(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: GRMZM2G431856
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GRMZM2G382557
• Aliases: None
• Description: None

Sequence

>retro_zmay_21
ATGGCGCAGCGAGCGGTGGCCACGATGACGACTAATAAGCCCCTCCTCCTCCTCGCCCTGGCGTCCGCGCTCCTTGGTGC
GGCGCCGGCCGCCGCGAACGCGCCCGGCGGGGCGTTCAGCAACTGGGTGGCGATGAACCAGCAGAGCTACGCGCTGTACG
CGCAGAAGTCCGTCGGGGACGGGGGCAAGGAGCCCCTGGACAAGAAGCTGTCGGAGGCGGAGAAGAAGAAGGTCACGTAC
GTGGTGGACCCCAGCGGCAAGGGCGACTACACCAACATCACCGCGGCGCTGGAGGATATCCCGGTGAGCAACACCAAGCG
CGTGATCCTGGATCTCAAGCCCGGCGCTCAGTTCCGCGAGAAGCTGTTCCTGAACATCAGCAAGCCGTTCATCACGTTCC
GGTCGGACCCCAAGAAGCCCGCCGTCGTGGTCTGGAACGACACTGCGGCCACGAACGGCAAGGACGGCAAGCCGGTGGGC
ACGGTGGGGAGCGCCACGCTGGCGGTGGAGTCGGACTACTTCACGGCGTACGGCGTGGTGTTCCGGAACGACGCGCCGCT
GGCCAAGCCCGGCGCCAAGGGCGGCCAGGCGGTGGCGGTGCGGCTGTTCGGGACCAAGACGCAGATCTACAACTGCACCA
TCGACGGCGGACAGGACACGCTGTACGACCACAAGGGCCTGCACTACTTCAAGGGCTGCCTCATCCGGGGCAGCGTCGAC
TTCATCTTCGGCTTCGGCCGCAGCTTCTACGAGGACTGCCGCATCGAGTCGGTGGTCAAGGAGGTGGCGGTGCTGACGGC
GCAGCAGCGTTCCAAGTCCATCGAGGGCGCCATCGACACCGGCTTCTCGTTCAAGAACTGCAGCATCGGCGGCGTCAAGG
GCGGCCAGATCTACCTGGGCCGCGCCTGGGGGGACTCCTCCCGGGTCGTCTACTCGTACACGAAGATGGGGGAGGAGGTG
GTCCCCGTGGGCTGGGACGGCTGGCAGATCGCCAAGCCGGAGAGCAGCGGCATCTACTACGGCGAGTTCAAGTGCTTTGG
CCCCGGCGCTGACGCCAAGAAGAAGAAGAGGGTGGGGTGGGCGCTGGACCTCACCGAGGCGCAGGCCAAGCCATTCGTCG
GCACACACTACGTCCTCGGCGACACGTGGATCCAGCCACCGCCCAAGTAG

Alignment

ORF - retro_zmay_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.17 %
• Parental protein coverage: 87.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AVDGGAGSFVEFVTENVELYSNVSNEHMYGSAGKVWDPQLLVAQGMVVRYVVSPDGKGKFRTINEAVRAV
          A.....G.F...V..N...Y................D..L..A....V.YVV.P.GKG....I..A....
Retrocopy AANAPGGAFSNWVAMNQQSYALYAQKSVGDGGKEPLDKKLSEAEKKKVTYVVDPSGKGDYTNITAALEDI

Parental  PEGNKRRVILDIRT-ATYREKVLVPYTKPFITFLGNPKNPPVIMWDDRAATHGKDGKPVGTVGSATVAVE
          P..N..RVILD....A..REK......KPFITF...PK.P.V..W.D.AAT.GKDGKPVGTVGSAT.AVE
Retrocopy PVSNTKRVILDLKPGAQFREKLFLNISKPFITFRSDPKKPAVVVWNDTAATNGKDGKPVGTVGSATLAVE

Parental  SDYFMASGIVFRNHAPMAAPGQEGGQAVALRVFGTKAAFYDCTIEGGQDTLYDHKGLHYFKSCHIQGSVD
          SDYF.A.G.VFRN.AP.A.PG..GGQAVA.R.FGTK...Y.CTI.GGQDTLYDHKGLHYFK.C.I.GSVD
Retrocopy SDYFTAYGVVFRNDAPLAKPGAKGGQAVAVRLFGTKTQIYNCTIDGGQDTLYDHKGLHYFKGCLIRGSVD

Parental  FIFGFGRSLYEDCAIMSVTKQVAVVTAQQRTKSIAGAIESGFSFLRCRIAGTGAGQIYLGRAWGDSSRVV
          FIFGFGRS.YEDC.I.SV.K.VAV.TAQQR.KSI.GAI..GFSF..C.I.G...GQIYLGRAWGDSSRVV
Retrocopy FIFGFGRSFYEDCRIESVVKEVAVLTAQQRSKSIEGAIDTGFSFKNCSIGGVKGGQIYLGRAWGDSSRVV

Parental  YSYTTMGKEVVPVGWDGWRIERPEKSGIYYGEYMCSGPG--ALPHKRIGWSLVLNDAQAKPFTGIHFIFG
          YSYT.MG.EVVPVGWDGW.I..PE.SGIYYGE..C.GPG..A...KR.GW.L.L..AQAKPF.G.H...G
Retrocopy YSYTKMGEEVVPVGWDGWQIAKPESSGIYYGEFKCFGPGADAKKKKRVGWALDLTEAQAKPFVGTHYVLG

Parental  DSWILPPP
          D.WI.PPP
Retrocopy DTWIQPPP

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_21 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA036000	1 retrocopy	retro_oind_54,
Zea mays	GRMZM2G382557	1 retrocopy	retro_zmay_21 ,