RetrogeneDB ID: retro_zmay_26

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 5:159951529..159953125(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: GRMZM2G028677
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GRMZM2G010468
• Aliases: None
• Description: None

Sequence

>retro_zmay_26
ATGGCGGTGTCCGCGGCCAAGATGGCCGTCGCCACGGCCGTCTCCTTAGCCGTGCACTGGCTCCTCCGGTCCTTCCTCCA
GGCGCAGCACCCTGCGCTGGGCCTGCTCCTCCCGACCGTCGTCTTCATCGGCATTGCCGCGTCTGGCAATGCCGCAGGCG
CTGCCAACGACGCGCCGCCGGGGCCGCCGGCCGTGCCGGTGTTCGGCAACTGGCTGCAGGTGGGCAACGACCTGAACCAC
CGGTTCCTGGCGCGCCTGTCCGCGCGGTACGGGCCCGTCTTTCGCCTCCGCCTCGGCGTGCGCAACCTGGTGGTCGTCTC
CGACCCGCGCCTCGCCACGGAGGTGCTGCACACGCAGGGGGTGGAGTTCGGCTCCCGCCCCCGCAACGTCGTCTTCGACA
TCTTCACCGCCAACGGCGCCGACATGGTGTTCACCGAGTACGGCGACCACTGGCGCCGCATGCGCCGCGTCATGACGCTG
CCCTTCTTCACCGCGCGCGTCGTGCAGCAGTACAGGGGCATGTGGGAGGCCGAGATGGACGCCGCCGTCTCCGACGTCGC
CTCCGCGGCCCAGCGCGCCGCCGGCCTCGTCGTGCGGCGCAGGCTGCAGCTCATGCTCTACAACATCATGTACGGGATGA
TGTTCGACGCGCGCTTCGGCTCCGTCGACGACCCCATGTTCGTGGAGGCCACCAGGTTCAACTCCGAGCGAAGCCGCCTC
GCGCAGAGCTTCGACTACAACTACGGCGACTTCATCCCCGTCCTGCGCCCATTCCTGCGCGGCTACCTCGCCAGGTGCAA
GGACCTGCAGGCCAGGCGGCTCGCCTTCTTCAACAGCAACTACGTCGAGAAGAGGAGGAAGGTCATGGACGCGCCGGGGG
ACAAGGGCAAGCTCAGGTGCGCCATCGACCACGTCCTCCAGGCGGAGAAGAGCGGCGAGATCACCCCGGAGAACGTCATC
TACATCGTCGAGAACATCAACGTCGCCGCCATCGAGACCACGCTCTGGTCCATCGAGTGGGCGCTCGCGGAGGTCGTCAA
CCACCCGGCGGTGCAGCGCAAGGTCCGCGACGAGATCAAGGCCGTCGTCGCCGACCACGAGCCCATCACGGAGTCCACCA
TCCACCGCCTCCCCTACCTGCAGGCCGTCATCAAGGAGACGCTGCGCCTCCACTCCCCGATCCCGCTCCTCGTCCCGCAC
ATGAACCTCGAGGAGGCCAAGCTCGGCGGCTACACCATCCCCAAGGGCTCCAAGGTGGTGGTCAACGCGTGGTGGCTGGC
CAACAATCCGGAGCTGTGGGACAAGCCCGAGGAGTTCCGGCCGGAGCGGTTCCTAGGCGAGGAGAAGAGCGTGGACGCCA
CCGTTGGCGGGAAGGTGGACTTCCGCTTCCTGCCGTTCGGCGTGGGCCGCCGCAGCTGCCCCGGGATCATCCTCGCGCTG
CCCATCCTCGCGCTCATCGTCGGCAAGCTCGTGCGCAGCTTCGAGATGGTACCACCGCCCGGCGTGGAGAAGCTCGACGT
CAGCGAGAAAGGAGGACAGTTCAGCCTGCACATTGCCAACCACTCCGTCATCGCCTTCCACCCCGTCTCTGCATGA

Alignment

ORF - retro_zmay_26 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.49 %
• Parental protein coverage: 96.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VMVAIAVS-KIRGRKLRLPPGPVPVPVFGNWLQVGDDLNHRNLAALSRKFGDVFLLRMGQRNLVVVSSPP
          V...IA.S....G.....PPGP..VPVFGNWLQVG.DLNHR.LA.LS...G.VF.LR.G.RNLVVVS.P.
Retrocopy VFIGIAASGNAAGAANDAPPGPPAVPVFGNWLQVGNDLNHRFLARLSARYGPVFRLRLGVRNLVVVSDPR

Parental  LAREVLHTQGVEFGSRTRNVVFDIFTDKGQDMVFTVYGDHWRKMRRIMTVPFFTNKVVQQYRHGWEAEAA
          LA.EVLHTQGVEFGSR.RNVVFDIFT..G.DMVFT.YGDHWR.MRR.MT.PFFT..VVQQYR..WEAE..
Retrocopy LATEVLHTQGVEFGSRPRNVVFDIFTANGADMVFTEYGDHWRRMRRVMTLPFFTARVVQQYRGMWEAEMD

Parental  AVVDDVRLDPKAATDGIVLRRRLQLMMYNNIYRIMFDRRFESMDDPLFLRLRALNGERSRLAQSFEYNYG
          A.V.DV......A..G.V.RRRLQLM.YN..Y..MFD.RF.S.DDP.F......N.ERSRLAQSF.YNYG
Retrocopy AAVSDVASAAQRAA-GLVVRRRLQLMLYNIMYGMMFDARFGSVDDPMFVEATRFNSERSRLAQSFDYNYG

Parental  DFIPILRPFLRGYLRVCKEVKETRLKLFKDFFLEERKKLASTKATDSNGLKCAIDHILEAQQKGEINEDN
          DFIP.LRPFLRGYL..CK.....RL..F.....E.R.K.......D...L.CAIDH.L.A...GEI...N
Retrocopy DFIPVLRPFLRGYLARCKDLQARRLAFFNSNYVEKRRKVMDAPG-DKGKLRCAIDHVLQAEKSGEITPEN

Parental  VLFIVENINVAAIETTLWSIEWAVAELVNHPEIQQKLRQELDTVLGPGHQITEPDTHNLPYLQAVIKETL
          V..IVENINVAAIETTLWSIEWA.AE.VNHP..Q.K.R.E...V......ITE...H.LPYLQAVIKETL
Retrocopy VIYIVENINVAAIETTLWSIEWALAEVVNHPAVQRKVRDEIKAVVADHEPITESTIHRLPYLQAVIKETL

Parental  RLRMAIPLLVPHMNLHDAKLGGYDIPAESKILVNAWYLANNPDSWRRPEEFRPERFLEEEKHVEANGN--
          RL...IPLLVPHMNL..AKLGGY.IP..SK..VNAW.LANNP..W..PEEFRPERFL.EEK.V.A.....
Retrocopy RLHSPIPLLVPHMNLEEAKLGGYTIPKGSKVVVNAWWLANNPELWDKPEEFRPERFLGEEKSVDATVGGK

Parental  -DFRYLPFGVGRRSCPGIILALPILGITIGRLVQNFELLPPPGQDKVDTTEKGGQFSLHILKHSTIVCKP
          .DFR.LPFGVGRRSCPGIILALPIL....G.LV..FE..PPPG..K.D..EKGGQFSLHI..HS.I...P
Retrocopy VDFRFLPFGVGRRSCPGIILALPILALIVGKLVRSFEMVPPPGVEKLDVSEKGGQFSLHIANHSVIAFHP

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_26 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Zea mays	GRMZM2G010468	1 retrocopy	retro_zmay_26 ,
Hordeum vulgare	MLOC_4708	1 retrocopy	retro_hvul_35,
Sorghum bicolor	Sb03g038160	1 retrocopy	retro_sbic_33,