RetrogeneDB ID: retro_zmay_25

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 4:79784734..79785688(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: GRMZM2G172834
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GRMZM2G009136
• Aliases: None
• Description: None

Sequence

>retro_zmay_25
ATGGCGAGCCTGACCATGCCGCCGGTGCCGGCGTGGCCGCGGCAGGACGCCATCGACCTCCACAAAGCATTCAGAGGGTT
CGGTTGCGACAGCACGACGGTGACCAACATCCTGGCGCACCGCGACGCGACGCAGCGCTCGCTGATCCAGCAGGAGTACC
GGGCCGTGTTCAACCAGGACCTGGCCCGGCGCATCGCGTCCGAGCTGAGCGGCCACCACAAGCGGGCGATGCTGCTGTGG
ATCCTGGACCCGGCCACCCGCGACGCCACCATCCTGAAGCAGGCGCTCACGGGCGACATCACCAACCTGCGGGCGGCCAC
GGAGATCGTCTGCTCCCGGACGCCGTCGCAGCTGCAGATCATGCGCCAGACGTACCGCGCCAGGTTCGGCTGCTACGTCG
AGCACGACGTCACCGAACGCACGTCCGGCGACCACCAGCGCCTCCTGCTCGCGTACCTGGCCATCCCGCGCGCCGAGGGC
CACGAGGTCGACCCGTCGACGGTGACGCTGGACGCGCGCGACCTCTACAAGGCCGGCGAGCGGCGGCTGGGCACCGACGA
GCGCGCCTTCATCCGAATCTTCAGCCAGCGGAGCTGGGCGCACATGGCGGCCGTTGCCCGGGCGTACCACCACATGTACG
ACCGCCCCCTGGAGCGCGCCGTCAAGAGCGAGACGTCGGGCAACTTCGGTTTCGGTCTCCTCACCGTGCTCCGCTGCGCC
GACAGCCCCGCCAGGTACTTCGCCAAGGAGCTGCACAGGGCCATGAAGGGGCTGGGCACCAGCGACTCGGTGCTCATCCG
GGTGGTGGTCACCAGGGCGGAGATCGACATGCAGTACATCAAGGCGGAGTACCACAGCATGTACAAGCGCTCGCTCGCCG
ACGCCATCCACGCCGAGACGTCCGGCAACTACCGCACCTTCCTCCTCTCCCTCGTCGGCCGCGACCGCACCTAG

Alignment

ORF - retro_zmay_25 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.8 %
• Parental protein coverage: 99.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASLTLPPAPPNPRQDAIDLHKAFKGFGCDSTTVINILTHRDSVQRGLIQQEYRAMYHEELSHRISSELS
          MASLT.PP.P..PRQDAIDLHKAF.GFGCDSTTV.NIL.HRD..QR.LIQQEYRA.....L..RI.SELS
Retrocopy MASLTMPPVPAWPRQDAIDLHKAFRGFGCDSTTVTNILAHRDATQRSLIQQEYRAVFNQDLARRIASELS

Parental  GNHKKAMSLWILDPAGRDATVLREALNGDTMDLRAATEIICSRTPSQLQIMKQTYYARFGTYLEHDIAHH
          G.HK.AM.LWILDPA.RDAT.L..AL.GD...LRAATEI.CSRTPSQLQIM.QTY.ARFG.Y.EHD....
Retrocopy GHHKRAMLLWILDPATRDATILKQALTGDITNLRAATEIVCSRTPSQLQIMRQTYRARFGCYVEHDVTER

Parental  TSGDHQKLLLAYMGIPRYEGPEVDPTIVTHDAKDLYKAGEKRLGTDEKIFIRVFTERSWAHLASVSSAYH
          TSGDHQ.LLLAY..IPR.EG.EVDP..VT.DA.DLYKAGE.RLGTDE..FIR.F..RSWAH.A.V..AYH
Retrocopy TSGDHQRLLLAYLAIPRAEGHEVDPSTVTLDARDLYKAGERRLGTDERAFIRIFSQRSWAHMAAVARAYH

Parental  HMYDRKLEKVIKSETSGNFEFALLTILRCAENPAKYFAKLLRKAMKGLGTDDMTLIRVVVTRTEIDMQYI
          HMYDR.LE...KSETSGNF.F.LLT.LRCA..PA.YFAK.L..AMKGLGT.D..LIRVVVTR.EIDMQYI
Retrocopy HMYDRPLERAVKSETSGNFGFGLLTVLRCADSPARYFAKELHRAMKGLGTSDSVLIRVVVTRAEIDMQYI

Parental  KAEYLKKYKKPLAEAINSETSGNYRTFLLSLVG
          KAEY...YK..LA.AI..ETSGNYRTFLLSLVG
Retrocopy KAEYHSMYKRSLADAIHAETSGNYRTFLLSLVG

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_25 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	GRMZM2G009136	1 retrocopy	retro_zmay_25 ,
Sorghum bicolor	Sb02g024090	1 retrocopy	retro_sbic_6,
Setaria italica	Si030120m.g	1 retrocopy	retro_sita_33,