RetrogeneDB ID: retro_zmay_45

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 10:141945048..141945663(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GRMZM2G145870
• Aliases: None
• Description: None

Sequence

>retro_zmay_45
TTCTATGGTGCTTTAGAAGCTGTGTACAAGCGTAATGGAGTGCCTGCATTGTTTGCTGAGGTCAAGAAAGCATCCCCTAG
TAGGGGCGTGCTCAGGGAGGACTTTAATCCTGTTGAAATTGTTCAACCTTATGAAAAGAATGGAGCTACATGTTTGAGCA
TTTTGACGGATAAAAAATACTTTCAGGGAAGCTTTGAGAATCTTGAGAAGGTGCGCACCTCAGGGGTGAAGTGCCCCCTT
CTATGCAAAGAGTTTGTCATTGATAAGTGGCAAATCTATAATGCTCGCTCTAAGGGTGCTGATACAATTCTACTAATTGC
GGCAGTGCTACCAGATCTTGTCATAAGGAAATTTGTTCAGATTTGTGAAGAGTTGGAAATGACAGCTCTTATTGAGGTTG
ATGATGGAATAGAGATGGAGCGTGTGCTGAACATAAATGGAGTTAAGTTTACTGGTATAAATAACCGAAGCCTTGAGACA
TTTGTTCTTTACACTTCGAACACCAAGATGTTGCTCGGTAGGCATGGGGATAGAATCAGGGAGAAGGGAATTTTGGTTGT
TGGTGAATCAGGTCTGTTTACTCCAGAAGATGTTGCTTCTGTTCAAAATGCTGGT

Alignment

ORF - retro_zmay_45 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.32 %
• Parental protein coverage: 53.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FYGALEAAYKRNGVPALIAEVKKASPSRGVLRENFNPVEIAQAYEKNGAACLSILTDEKYFQGSFDNLEK
          FYGALEA.YKRNGVPAL.AEVKKASPSRGVLRE.FNPVEI.Q.YEKNGA.CLSILTD.KYFQGSF.NLEK
Retrocopy FYGALEAVYKRNGVPALFAEVKKASPSRGVLREDFNPVEIVQPYEKNGATCLSILTDKKYFQGSFENLEK

Parental  VRSSGVKCPLLCKEFVIDKWQIYNARSKGADAILLIAAVLPDLDIRKFLQICEELGMTALIEVHDEREME
          VR.SGVKCPLLCKEFVIDKWQIYNARSKGAD.ILLIAAVLPDL.IRKF.QICEEL.MTALIEV.D..EME
Retrocopy VRTSGVKCPLLCKEFVIDKWQIYNARSKGADTILLIAAVLPDLVIRKFVQICEELEMTALIEVDDGIEME

Parental  RVLKINGVKLIGINNRSLETFVVDTSNTKMLLEKHGDIIREKGILVVGESGLFTPDDVAYVQNAG
          RVL.INGVK..GINNRSLETFV..TSNTKMLL..HGD.IREKGILVVGESGLFTP.DVA.VQNAG
Retrocopy RVLNINGVKFTGINNRSLETFVLYTSNTKMLLGRHGDRIREKGILVVGESGLFTPEDVASVQNAG

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_45 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Zea mays	GRMZM2G145870	2 retrocopies	retro_zmay_45 , retro_zmay_58,