RetrogeneDB ID: retro_zmay_23

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 4:195504281..195504977(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AC191097.3_FG007
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GRMZM2G034668
• Aliases: None
• Description: None

Sequence

>retro_zmay_23
ATGACCAAGTCGAAGGGTGGTTCGGTGGACGCGCGCACGCTGGTGGCGCACGTCCTGGCAGCGAGCGCCGTCGTGCTGGT
GCTCCTGTGGTGCATCCACTTCCGCGGCGGCCTCGCCCTCCGCTCCCAGGACAAGCCGCTCATCTTCAACGTCCACCCCG
TGCTCATGGTCCTCGGCCCCATCGTCCTCGGCGGAGAAGCCATCCTCAGCTACCGCTCTCTCCCGCTCGCCCGCGACGCC
AGGAAGAAGGTGCACCTGGCGCTGCACGCCGCGGGCCTCGCTGCGGGCGTCCTCGGCGTCTACGCCGTCTTCAAGTTCCA
CGTCGAGAGCGGCATCCCAAACCTCTACTCGCTGCACTCCTGGGTCGGCATCGCCGCCATCACCCTCTACGGCCTCCAGT
GGACCGCCGGGTTCCTCGCCTACTTCTTCCCGGGCGCCTCCCCCGCCACCAGGCGCAGAACGCTGCCGTGGCACGCCGTC
TTCGGCCTCCTCGTCTTCGTGCTCGCCGTCGGCACCGCGCAGCTGGGCTTCCTCGAGAAGCTCACCTTCATGCAGGGCCC
GCCACTGCGCCTGCCCAAGTACGGCGCAGAGGCGCTGCTCGTCAACTTCACCTCCGTCACCGTGCTCCTCCTCGGCGTCG
CCGTCGTGCTTGCCATCGTCGATATTGACGGGACCCGGTACAACACCATCATCTGA

Alignment

ORF - retro_zmay_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.81 %
• Parental protein coverage: 87.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TYAAHALAAVAAALVLVWCVHFRGGLALEAQNKNLIFNVHPVLMLIGYIILGSEAIMIYKVFPNLNHDTA
          T..AH.LAA.A..LVL.WC.HFRGGLAL..Q.K.LIFNVHPVLM..G.I.LG.EAI..Y...P.L..D..
Retrocopy TLVAHVLAASAVVLVLLWCIHFRGGLALRSQDKPLIFNVHPVLMVLGPIVLGGEAILSYRSLP-LARDAR

Parental  KLTHLILHAVATVLGAFGIYCAFKYHNDSGIANLYSLHSWLGIGTIALYAIQWVFGFVTFFLPGAAPGVR
          K..HL.LHA.....G..G.Y..FK.H..SGI.NLYSLHSW.GI..I.LY..QW..GF...F.PGA.P..R
Retrocopy KKVHLALHAAGLAAGVLGVYAVFKFHVESGIPNLYSLHSWVGIAAITLYGLQWTAGFLAYFFPGASPATR

Parental  RGALPWHALFGLFVYVLALATAELGFLEKLTFLESG--GLDKYGAEAFLVNFTALVVVLLGAFVVVAAV
          R..LPWHA.FGL.V.VLA..TA.LGFLEKLTF.......L.KYGAEA.LVNFT...V.LLG..VV.A.V
Retrocopy RRTLPWHAVFGLLVFVLAVGTAQLGFLEKLTFMQGPPLRLPKYGAEALLVNFTSVTVLLLGVAVVLAIV

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_23 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Zea mays	GRMZM2G034668	1 retrocopy	retro_zmay_23 ,
Leersia perrieri	LPERR04G16060	1 retrocopy	retro_lper_17,
Hordeum vulgare	MLOC_12641	1 retrocopy	retro_hvul_22,
Oryza sativa japonica	OS04G0533500	1 retrocopy	retro_osat_39,
Physcomitrella patens	PP1S194_18V6	1 retrocopy	retro_ppat_14,
Sorghum bicolor	Sb06g023650	1 retrocopy	retro_sbic_21,
Setaria italica	Si010957m.g	1 retrocopy	retro_sita_34,