RetrogeneDB ID: retro_zmay_6

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 8:78155852..78157349(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AC203862.4_FG001
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GRMZM2G093032
• Aliases: None
• Description: None

Sequence

>retro_zmay_6
ATGGCGAGTCGTCGCCTCCTCTTTGCCGTGCAGCTCCTCGTACTGATCGCCGCAGTGGCCGGCACACGGTGGCAGGACTT
CCTCCGCCTGCCGTCGGAGTCGGAGTCGGTGGGGACCAGGTGGGCCGTCCTCATCGCCGGCTCCAATGGCTACTACAACT
ACCGTCATCAGGTAGTAATTTCATCCATTACGTTATCATTATGCTTTGCGACCACTCTTGTTGAGCAGATCCTGCTACAT
GCCTACATCCATATCCATGGACAGGCGGACGTGTGCCACGCGTACCAGGTCTTGAAGAAGGGCGGGCTCAAGGACGAGAA
CATCGTCGTCTTCATGTACGACGACATCGCCGACAGCCCCGACAACCCCAGGCCGGGCGTCATCATCAACCACCCATCCG
GCGGAGACGTGTACGCGGGGGTCCCCAAGGACTACACGGGCAAGGACGTGAACGCCAACAACTTCCTCGCCGCCTTGCTG
GGCAACAGGTCCGCCGTCACCGGCGGCGGCAGCGGCAAGGTGGTCGCCAGCGGGCCGGCCGACCACGTCTTCGTCTACTA
CAGCGACCACGGCGGGCCTGGGGTGCTCGGGATGCCGTCGTCGGACGACTACCTGTACGCCAAGGACCTGGTGGACGCTC
TCAGGAAGAAGCACGCCGCGGGGGGCTACCGGAGCCTGGTGTTCTACCTGGAGGCGTGCGAGTCCGGGAGCATCTTCGAG
GGGCTCCTGCCGCCCGACATCGCCGTGTACGCCACCACGGCGGCGAACGCGGAGGAGAGCAGCTGGGGCACCTACTGCCC
CGGCGACGACCCGGGCCCGCCGCCCGAGTTCGACACCTGCCTCGGGGACCTCTACAGCGTCGCGTGGATGGAGGACAGCG
ACGCGCGCCGCGACCGCCGCGCCGAGACGCTGAGGCAGCAGTACCTGGCGGTGAAGGACCGGACGTCGGCGCACGGCACC
TACAGCCTCGGCTCCCACGCCATGGAGTACGGCGACGTGCAGGGCCTCGGCGCGCAGAGCCTGTACACGTTCATGGGCAG
CGACGACGCCACCGCCGCGAGCTTATCCGGCCGTGGCCGTGGGCAGCCAGCCGTGAGCCAGCGCGACGCTGACCTCGTCT
ACTTCTGGCGGAGGTACCGCAGGGCGGCGGAGAGGACGCCCGAGAAGGCCGAGGCCCGGACGCGGCTGCTGCGGGCGGTG
TCCCGCCGGTCCCGCGTCGACAGCATCATGGAGCTCATCGGAGGCCTCCTGTTCGGCTCGGAGGGAGGTCCCAGGGTGCT
CGGTGCCGTGCGGCCGGCGGGACAGCCCCTGGCCGACGACTGGGACTGCCTCAAGTCCTTGGTGCGTGCGTACGAGCGCA
GCTGCGGGCCGCTCGGGCAGTACGGGATGAAGCACATGCGTGGCTTCGCCAACATCTGCAATGCCGGCGTCGGGGAGGAC
GGCATGGCCAAGGTGGCGTCCGAGGCCTGCGCCGCCGTCGCCCGTTCTGACGACTGA

Alignment

ORF - retro_zmay_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.75 %
• Parental protein coverage: 86.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NGYYNYRHQADICHAYQIMKKGGLKDENIVVFMYDDIAHSPENPRPGVIINHPQGGDVYAGVPKDYTGRE
          ..Y.....QAD.CHAYQ..KKGGLKDENIVVFMYDDIA.SP.NPRPGVIINHP.GGDVYAGVPKDYTG..
Retrocopy HAYIHIHGQADVCHAYQVLKKGGLKDENIVVFMYDDIADSPDNPRPGVIINHPSGGDVYAGVPKDYTGKD

Parental  VNVDNFFAVLLGNKTALRGG-SGKVVDSGPNDHIFVFYSDHGGPGVLGMPTYP-YLYGDDLVDVLKKKHA
          VN..NF.A.LLGN..A..GG.SGKVV.SGP.DH.FV.YSDHGGPGVLGMP....YLY..DLVD.L.KKHA
Retrocopy VNANNFLAALLGNRSAVTGGGSGKVVASGPADHVFVYYSDHGGPGVLGMPSSDDYLYAKDLVDALRKKHA

Parental  AGTYKSLVFYLEACESGSIFEGLLPNDINVYATTASNAEESSWGTYCPGEFPSPPPEYDTCLGDLYSVAW
          AG.Y.SLVFYLEACESGSIFEGLLP.DI.VYATTA.NAEESSWGTYCPG..P.PPPE.DTCLGDLYSVAW
Retrocopy AGGYRSLVFYLEACESGSIFEGLLPPDIAVYATTAANAEESSWGTYCPGDDPGPPPEFDTCLGDLYSVAW

Parental  MEDSDFH-NLRTESLKQQYNLVKDRTAVQDTFSYGSHVMQYGSLE-LNVKHLFSYIGTNPANDDNTFIED
          MEDSD.....R.E.L.QQY..VKDRT....T.S.GSH.M.YG....L....L....G.....DD.T....
Retrocopy MEDSDARRDRRAETLRQQYLAVKDRTSAHGTYSLGSHAMEYGDVQGLGAQSLYTFMGS----DDATAASL

Parental  NSLPSFSKAVNQRDADLVYFWQKYRKLADSSPEKNEARKELLEVMAHRSHVDSSVELIGSLLFGSEDGPR
          ........AV.QRDADLVYFW..YR..A...PEK.EAR..LL.....RS.VDS..ELIG.LLFGSE.GPR
Retrocopy SGRGRGQPAVSQRDADLVYFWRRYRRAAERTPEKAEARTRLLRAVSRRSRVDSIMELIGGLLFGSEGGPR

Parental  VLKAVRAAGEPLVDDWSCLKSTVRTFEAQCGSLAQYGMKHMRSFANICNAGILPEAVSKVAAQACTSI
          VL.AVR.AG.PL.DDW.CLKS.VR..E..CG.L.QYGMKHMR.FANICNAG.......KVA..AC...
Retrocopy VLGAVRPAGQPLADDWDCLKSLVRAYERSCGPLGQYGMKHMRGFANICNAGVGEDGMAKVASEACAAV

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_6 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.

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Zea mays	GRMZM2G093032	1 retrocopy	retro_zmay_6 ,
Oryza longistaminata	KN538817.1_FG009	1 retrocopy	retro_olon_1,
Oryza brachyantha	OB01G29280	1 retrocopy	retro_obra_23,
Oryza barthii	OBART01G19640	1 retrocopy	retro_obar_1,
Oryza glumaepatula	OGLUM01G23260	1 retrocopy	retro_oglu_32,
Oryza meridionalis	OMERI01G18100	1 retrocopy	retro_omer_24,
Oryza punctata	OPUNC01G20010	1 retrocopy	retro_opun_12,
Oryza glaberrima	ORGLA01G0161200	1 retrocopy	retro_ogla_9,
Oryza sativa japonica	OS01G0559600	1 retrocopy	retro_osat_9,