RetrogeneDB ID: retro_zmay_16

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 5:48087636..48088722(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: GRMZM2G020657
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GRMZM2G099765
• Aliases: None
• Description: None

Sequence

>retro_zmay_16
ATGGTGAGAGCTGCTGAGGTCGCAACGACCATGGCGGCGGCACTAGTCGTGGTCATCGCATTGTCCACTACGCCGGCGGC
AAGCGCCATTGACTACACCGAGCATGACCTGGCGTCGGAGGAGTCCCTGTGGGCACTGTACGAGCGTTGGTGTGCACACT
ACAACATGGCGCGCGACCTCGGCGAGAAGACCCGGCGGTTCAACTTGTTCAAGGAGAACGCGCACCGCATCTACGAGCAC
AACCAAGGCAATGCGACGTACACGCTGGGCCTCAACCGCTTCAGCGACATGACCGACGAGGAGTTCAGCCGCTCCCCGTA
CGGACGTTGCTTGTTTGCCCCGGTCCAGCGCATTTCTGACGGCGAGAACGAAGAGCTCCAGCAGCATGAGGACGTGTCGT
TCAACCTCACGCACGGCGGCGCCACCGCAGCGCTGGGCCTCCCGCCGTCAGTGGACTGGCGCGGGAGGTCGGTGACGCGC
GTGAAGGACCAGGGGCTCACCTGCGGGAGTTGCTGGGCCTTCGCAGCGATCGCGGCGGTGGAGGGCATCAACGCCATCCG
GACATGGAGCCTGGTGACGCTGTCGGAGCAGCAGCTGGTGGACTGCGACAATGTGGACCATGGCTGCGCTGGTGGTTGGA
TACCCTCGGCGTTGGACTTCATCGTGAGGAACCGCGGCATCGTGCCGGAGGGCACGTACCCGTACATAGGCACGCAGGGC
CGTTGCCGGCACGTCATGGCCCCGCCGGTGACCATCGACGGGTACCGGCGAGTTCTGCCGTTCGACGTGAATGCACTGAT
GTCTGCGGTGGCTGCCCAGCCTGTGGCAGTGGCGATGGAGTCTAGCGCCTGGGCCTTCAGGCACTACCAAGGGGGCGTCT
TTAATGGGAACTGCGGGGGGAGGCTGGGTCACGCGGCGGCGGTGGTGGGGTACGGCGACGGGGCCGGCGGCCCTTTCTGG
ATCGTCAAGAATTCATGGGGTCCCAAGTGGGGCGAGGGCGGGTACGTCCGCATCAGCCGCAACGCGCCCAACAGGCTGGG
GATCTGCGGCATTCTCACACAACCGTTGTACCCTGTGAAGCGCTAG

Alignment

ORF - retro_zmay_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.48 %
• Parental protein coverage: 59.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HGRGGSGTTNLPPAVDWRLRGAVTGVKDQG-QCGSCWAFSAIAAVEGVNKIMTGKLVSLSEQELVDCDDV
          HG.G......LPP.VDWR.R..VT.VKDQG..CGSCWAF.AIAAVEG.N.I.T..LV.LSEQ.LVDCD.V
Retrocopy HG-GATAALGLPPSVDWRGR-SVTRVKDQGLTCGSCWAFAAIAAVEGINAIRTWSLVTLSEQQLVDCDNV

Parental  DNQGCDGGLMDYAFQYIQRNGGVTTESNYPYLAEQRSCNKAKERSHDVTIDGYEDVPANNEDALQKAVAS
          D..GC.GG....A...I.RN.G...E..YPY...Q..C.........VTIDGY..V......AL..AVA.
Retrocopy DH-GCAGGWIPSALDFIVRNRGIVPEGTYPYIGTQGRCRHV--MAPPVTIDGYRRVLPFDVNALMSAVAA

Parental  QPVAVAIEASGQDFQFYSEGVFTGSCGTDLDHGVAAVGYGTTGDGTKYWTVKNSWGEDWGERGYIRMQRG
          QPVAVA.E.S...F..Y..GVF.G.CG..L.H..A.VGYG..G.G...W.VKNSWG..WGE.GY.R..R.
Retrocopy QPVAVAMESSAWAFRHYQGGVFNGNCGGRLGHAAAVVGYG-DGAGGPFWIVKNSWGPKWGEGGYVRISRN

Parental  VPDSRGLCGIAMEPSYPTKK
          .P...G.CGI...P.YP.K.
Retrocopy APNRLGICGILTQPLYPVKR

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_16 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI4G19707	2 retrocopies	retro_bdis_26, retro_bdis_41,
Zea mays	GRMZM2G099765	1 retrocopy	retro_zmay_16 ,
Hordeum vulgare	MLOC_73076	2 retrocopies	retro_hvul_23, retro_hvul_68,
Oryza barthii	OBART11G08490	1 retrocopy	retro_obar_27,
Oryza glumaepatula	OGLUM05G09560	1 retrocopy	retro_oglu_31,
Oryza meridionalis	OMERI11G07520	1 retrocopy	retro_omer_2,
Setaria italica	Si026545m.g	1 retrocopy	retro_sita_27,