RetrogeneDB ID: retro_zmay_4

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 3:9332393..9332930(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: GRMZM2G062186
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GRMZM2G043275
• Aliases: None
• Description: None

Sequence

>retro_zmay_4
ATGTGTGATCTGGTGGCCCGCACGGGCCGGCACCTGCAGCGCTACGAGAACGGCCGTCGCCTTGTGGCCGGGTGCATACC
ATTCAGATACATGGATATTGATGATGGAGCTTCTGATGATGAACAAAAGAAACTTGTTGAAGTTCTCATGATCAGCTCAC
AAAGTGGACCGGGTCTTCTATTTCCAAAGGGAGGCTGGGAGAATGATGAAGCTGTTGAAGAGACAGCTGCAAGGGAAGCT
ATCGAAGAAGCTAGAGTGCGAGGAGATTTAGTGCAACTGCTGGGGTTCTACGATTTCAAGAGCAAGCAGCCCGAAGCAAC
GTGTAGAGCCGCAATCTTTGCTCTGCACGTGAAGGAAGAGCGAGCATCCTGGCCAGAACAGAGCACCCGACAGAGGAGCT
GGCTCACAGTTCCCGAGGCGGCGGAGCGGAGCTGCTACCTGTGGATGCAGGAGGCCCTCGTGACAGGCTTCTCCTCCTGG
CTCGAGAACTGGAGAAACGGTGGTGGCGGCGGCTGCGTGGACCGAACTGAGAGATGA

Alignment

ORF - retro_zmay_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.89 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MCDLVARTGRHLQRYENGRRLVAGCIPFRYRDINDGASDDEQKKLVEVLMISSQSGPGLLFPKGGWENDE
          MCDLVARTGRHLQRYENGRRLVAGCIPFRY.DI.DGASDDEQKKLVEVLMISSQSGPGLLFPKGGWENDE
Retrocopy MCDLVARTGRHLQRYENGRRLVAGCIPFRYMDIDDGASDDEQKKLVEVLMISSQSGPGLLFPKGGWENDE

Parental  TVEEAAAREAIEEAGVRGDLVQLLGFYDFKSKQPEATCRAAIFALHVKEELASWPEQSTRQRSWLTVPEA
          .VEE.AAREAIEEA.VRGDLVQLLGFYDFKSKQPEATCRAAIFALHVKEE.ASWPEQSTRQRSWLTVPEA
Retrocopy AVEETAAREAIEEARVRGDLVQLLGFYDFKSKQPEATCRAAIFALHVKEERASWPEQSTRQRSWLTVPEA

Parental  AERSRYPWMQEALVTGFSAWLENWRNGGGGGGGCVDRTER
          AERS.Y.WMQEALVTGFS.WLENWRN..GGGGGCVDRTER
Retrocopy AERSCYLWMQEALVTGFSSWLENWRN--GGGGGCVDRTER

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_4 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	GRMZM2G043275	1 retrocopy	retro_zmay_4 ,