RetrogeneDB ID: retro_zmay_54

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 3:41451213..41452266(-)
• Located in intron of: GRMZM2G019810

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GRMZM2G010315
• Aliases: None
• Description: None

Sequence

>retro_zmay_54
TATCCCTATCACATGACAAGTATTGCATGGGAAAAGGCTGAAGAGCTGAAGAAGGAGCATTGTTATATAGCTCTTGATTA
TATGGCAGAGTTGCAGATATTTAAAAACAATAAGGAAGAAGCTGATGACAAAATGAGGTATTGGCAACTACCATGGGTGC
CCCCACCAAAGGAAGAACCACCATCTGAGGAAGAACTTGCAAGGAAAGCAGCTTTGAAGGAAAAGGCTGGTCAGCGTTTG
CGAGACATGGCTGCTGCAAAGAGATCTCAGAAGATAGTGGAACTAGAAAAACAACTTTCCTATCTGGAGGAACTAATGGA
ACAACTTGATGAAGCTGAGGAAGAAGAAGCAACAACTATTCTAGGTAGCTCTAGATATCTTTCCCAGCAGGAAATAAGAG
CTGCCATTTTAAAAGCATCACAATCTTTAAGGAAAGCAAAAGGGGAGTCCAATGGCAACGATGAGAAAACAGATGCCTCA
GCAGTTGATAAGTATCCACTTGTATCTGTCCCTGATGGGACACTGACGCCAGAACAGTTAAAGGAAAAGAAGAAACAAAT
CTTACTTAAAACCACAACAGAGGGCAAATTGCGCGCTAAGCAGAAACGTGCTGAAGAGGAAGCTTTGCAGGAGAAACAAG
AAGAAAAGGGGCGTGCGGAGAACCCAGAGTTATACCTTGAAAAGCTTCAGGCCCGATATTCAGAACTTTCTGATAAATTT
GAGCAGAGGAAGCGACAGAAAGTTAATGGTAGTCAGACAAATGGGAACCATAGTTCATCTGCAGGTGTAGGCTGTGGAGA
ACGACTAAATGCAGCTCAGAAAGAAAGGATGCGGCTGCTTGCCTCAGCTGTTTTTGATCGGGGCAAAGGTGAGGACACTT
TTGGAATGAGAGAAGAGGATTGGTTAGTGTACAACAAGATGAGCAAAGACAATGATGATGACAGCAATGATGATGACGAA
TCGGAACTTGTTCGAATTTCATCGAAGCTCCAGGAGATTGATCCTACATTTGTGTCCAAATCCGAAGTTGTTCAACTGAC
TCCGGAGCCACCC

Alignment

ORF - retro_zmay_54 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.02 %
• Parental protein coverage: 50.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FTLNRASISWEKAEELKKEHCYIAPDYMAELQIFKNNKEEADEKMRYWQLPWVPPPKEEPPSEEELARKA
          ......SI.WEKAEELKKEHCYIA.DYMAELQIFKNNKEEAD.KMRYWQLPWVPPPKEEPPSEEELARKA
Retrocopy YPYHMTSIAWEKAEELKKEHCYIALDYMAELQIFKNNKEEADDKMRYWQLPWVPPPKEEPPSEEELARKA

Parental  ALKEKAGQRLRDMAAAKRSQKIVELEKQLSYLEELMEQLDEAEEEEATAILGSSGYLSQQEIRSAILKAS
          ALKEKAGQRLRDMAAAKRSQKIVELEKQLSYLEELMEQLDEAEEEEAT.ILGSS.YLSQQEIR.AILKAS
Retrocopy ALKEKAGQRLRDMAAAKRSQKIVELEKQLSYLEELMEQLDEAEEEEATTILGSSRYLSQQEIRAAILKAS

Parental  QSLRKAKGESNGNDEKTDASAVDKYPLVSVPDETLTPEQLKEKKKQILLKTTTEGKLRAKQKRAEEEALR
          QSLRKAKGESNGNDEKTDASAVDKYPLVSVPD.TLTPEQLKEKKKQILLKTTTEGKLRAKQKRAEEEAL.
Retrocopy QSLRKAKGESNGNDEKTDASAVDKYPLVSVPDGTLTPEQLKEKKKQILLKTTTEGKLRAKQKRAEEEALQ

Parental  EKQEEKRRAENPELYLEELRARYSELSDKFEQRKRQKVNGSQTNGNHSSSAGVGRGERLNAAQKERMRLL
          EKQEEK.RAENPELYLE.L.ARYSELSDKFEQRKRQKVNGSQTNGNHSSSAGVG.GERLNAAQKERMRLL
Retrocopy EKQEEKGRAENPELYLEKLQARYSELSDKFEQRKRQKVNGSQTNGNHSSSAGVGCGERLNAAQKERMRLL

Parental  ASAAFDRGKGEDTFGMRDEDWLVYNKMSKDNDDDSNDDDESELVRISSKLQEIDPTFVSKSEAVQLTPEP
          ASA.FDRGKGEDTFGMR.EDWLVYNKMSKDNDDDSNDDDESELVRISSKLQEIDPTFVSKSE.VQLTPEP
Retrocopy ASAVFDRGKGEDTFGMREEDWLVYNKMSKDNDDDSNDDDESELVRISSKLQEIDPTFVSKSEVVQLTPEP

Parental  P
          P
Retrocopy P

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_54 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Zea mays	GRMZM2G010315	1 retrocopy	retro_zmay_54 ,