RetrogeneDB ID: retro_zmay_18

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 2:13886994..13888653(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: GRMZM2G032554
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GRMZM2G109009
• Aliases: None
• Description: None

Sequence

>retro_zmay_18
ATGGCTTCCCAGCCGAAGAAGATATCCAGCGAGCCCATCTCTCTGGTTGGCCCGACGCCCGCCGACATCGAGGCCACGGC
GCAGCTGGAGAAGCTCCTGCGCGAAGCGGGAATGTACGAGAGCGCCGAGGAGTCGGCGGTCCGCGCCGAGGTGCTGCGCG
ACCTCCAGGGCATCGTCGACCTCTGGGTCAAGCAGCTCATGCTCAAGCATGGGTACCCCGACGCCATGGTCGACGAGGCA
ACCGCCTTTGTGCTCCCGTTCGGATCGTACCGCCTCGGCGTCCTCGGCGGCGGCTCCGACATCGACGCGCTCGTCGTGGG
GCCCTCCTTCGTCGACCGCGATCAAGATTTCTTCGGTGTGCTGGCCGGCGTGCTGGCCGAGACGGAGGCGGTGACGGAGC
TGCATCCCGTGCCCGGCGCGCACGTCCCCGTCATGAAGCTGAGGTTCCGCGGCGTGCAGGTGGACCTCGTCTACGCCAGC
GTCAACCTCCCCGTGGTGCCCCGGAACCTGGATCTGAGCGACCGCCACGTGCTCCGCGGCCTCGACCACGTCACCGCCCG
CAGCATGAACGGCGTGCGCGTGGCCGACGAGATCGTGCGGCTGGTTCCCGACGCCGCCGCGTTCCGCACGACGCTGCGGT
GCGTGAAGCTGTGGGCCAAGTCGCGGGGCGTCTACTCCAACGTGTCCGGCTTCCTCGGCGGCGTGGCCTGGGCCATCCTG
GTGGCGCGCGTGTGCCAGCTCTACCCCAACGCCGTGCCCAGCATGCTGGTGTCTCGCTTCTTCAAGGTGTTCAGCCATTG
GAGGTGGCCCATCCCGGTGATGCTCTGCGACATCGAGCACGACGACGAGCTCGGACTCCCGGTCTGGGACGTGCGGAGGA
ACCTGCCCGACCGGAGCCACCTCATGCCCGTCATCACGCCGGCGTACCCGTGTATGAACTGCACGTACAATGTCTCTCGG
GCCACCCATAGGGTCATCAAGGAGCAGATCCAGGCCGGGGACGTCGCGTGCCAGAAGATCGCCGCCGGCGGCGGCCGCGA
CTGGGGCGCGCTGTTCCAGCCGTCCCCGTTCTTCAGCACGCACAAGAGCTATCTGCAGGTGGACGCGGCGGTGGCAGGAG
GCGCAGAAGAGCTCCGGGAGTGGAAGGGGTGGGTGGAGTCGCGGCTGCGGCAGCTCGTGGCCAAGGTTGAGAGGGACACG
TTCGGCGAGCTGCTATGCCACCAGAACCCGCGTGCCTACGACGCCGAGCCACACGGCTTGCGGCGCGCGTCGTCGTTTTT
CGTGGGCTTGTCGAAGCCACAGCAGCAGCACAAGCCGCACCCGCCGGAAGGGTATCCGCCGTTTTTTGACCTCCGTGCGA
CGGTGCTCGAGTTCCAGCAGGACGTCTACTCGTACAAGTTCTGGAGGCCCGGCTTGGAGTTGGTCGTCAAGCACGTCCGG
CGGAACAAGCTGCCGGCGTACGTGATGCAGAAGATTGGTGGTCGGAATATCCATGAGCTCAAGAGGAAGCGCGCCGACGA
CGACTCTTCACCTTCGTCGCCGCCATTGTGCTCGTCGTCCTCCGCCTCTTCTGGCGACGGTGACTCCGTGCAAGGACCGA
GCAGCAGGGCAGAGCTGCATCCAAGAAAGGCAATGTTGTTCGATCCCAGTCCCAGCTGA

Alignment

ORF - retro_zmay_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.94 %
• Parental protein coverage: 59.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TKPLSLLGPVEADLQRTEELEKFLLESGLYESPDESARREEVLGKLDQIVKDWVKQLTSQRGYTDQMVEE
          ..P.SL.GP..AD...T..LEK.L.E.G.YES..ESA.R.EVL..L..IV..WVKQL....GY.D.MV.E
Retrocopy SEPISLVGPTPADIEATAQLEKLLREAGMYESAEESAVRAEVLRDLQGIVDLWVKQLMLKHGYPDAMVDE

Parental  ANAVLFTFGSYRLGVHGPGADIDTLCVGPSYVNREEDFFIVLHGILAQTEDVTELQPVPDAHVPVMKFKF
          A.A....FGSYRLGV.G.G.DID.L.VGPS.V.R..DFF.VL.G.LA.TE.VTEL.PVP.AHVPVMK..F
Retrocopy ATAFVLPFGSYRLGVLGGGSDIDALVVGPSFVDRDQDFFGVLAGVLAETEAVTELHPVPGAHVPVMKLRF

Parental  HGISIDLLYASVSLLVVPADLDISQGSVLYDVDEATVRSLNGCRVADQIIRLVPNFENFRTALRCLKYWA
          .G...DL.YASV.L.VVP..LD.S...VL...D..T.RS.NG.RVAD.I.RLVP....FRT.LRC.K.WA
Retrocopy RGVQVDLVYASVNLPVVPRNLDLSDRHVLRGLDHVTARSMNGVRVADEIVRLVPDAAAFRTTLRCVKLWA

Parental  KRRGVYSNVTGFLGGVNWALLVARVCQLYPNAVPSMLVSRFFRVFTQWQWPNPVMLCSIE-EEELGFPVW
          K.RGVYSNV.GFLGGV.WA.LVARVCQLYPNAVPSMLVSRFF.VF..W.WP.PVMLC.IE...ELG.PVW
Retrocopy KSRGVYSNVSGFLGGVAWAILVARVCQLYPNAVPSMLVSRFFKVFSHWRWPIPVMLCDIEHDDELGLPVW

Parental  DPRKNPRDRCHHMPIITPAYPCMNSSYNVSTSTLRVMLEQFQFGNRICQEIEM-NKTSWPALFEPFQFFE
          D.R.N..DR.H.MP.ITPAYPCMN..YNVS..T.RV..EQ.Q.G...CQ.I.......W.ALF.P..FF.
Retrocopy DVRRNLPDRSHLMPVITPAYPCMNCTYNVSRATHRVIKEQIQAGDVACQKIAAGGGRDWGALFQPSPFFS

Parental  AYKNYLQVD-IIAEDDEDLRLWKGWVESRLRQLTLKIERDTYGMLQCHPYPHEY-ADPSRQCAHCAFFMG
          ..K.YLQVD...A...E.LR.WKGWVESRLRQL..K.ERDT.G.L.CH..P..Y.A.P........FF.G
Retrocopy THKSYLQVDAAVAGGAEELREWKGWVESRLRQLVAKVERDTFGELLCHQNPRAYDAEPHGLRRASSFFVG

Parental  LSRKE
          LS...
Retrocopy LSKPQ

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_18 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	GRMZM2G109009	1 retrocopy	retro_zmay_18 ,
Hordeum vulgare	MLOC_32341	1 retrocopy	retro_hvul_46,
Sorghum bicolor	Sb10g022090	1 retrocopy	retro_sbic_8,