RetrogeneDB ID: retro_zmay_40

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 1:224837919..224838842(-)
• Located in intron of: GRMZM2G414848

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GRMZM2G142502
• Aliases: None
• Description: None

Sequence

>retro_zmay_40
ATGAACGCGTCCAGGAAATCCAGCCATCTCTCCAGCAAGGACAGTGCAGAGACTGCGAGGGATATCATCACCACGTCCGG
CCAATTCCAACCCTTCAAAATCCCGGACGTTGTTGCTGCGCTCGCACAGGCTGCTGCAAAGGCAAATGGTGAGACCGAGA
AATATCTTCCAGGGTGGCCGTTGTTCTCGCCTCCTAAGGTGCAGCTGGACAAGTGTACCAAGTGCTCCAGAGAATTCTGT
TCTGCAATCAACTTCCGGAGGCATACACGTGTTCATCGTAGATCCCTCAAGATAGATAGGGATTTTCCAAAGAATAGAGA
CCTTCTCGCTGCATTCTGGAATAAACTCACTATGGATGATGCCAGCAAAATTTTGTCCTTGACAGGTGTTGTTATTGAGG
GTGTAACTGGTTCATCAATTTTGACAGCACTGTCATCATGGATGTGTAAACCAGGGTATGCTTCGTTGCCAGTTGCATAT
GCCAGAGCTGGCAGTGAGCTTCTGGATCTAATTCAAGCAAAGCCTTCAATGCATCTGCATGTGTCATCGGATGAACTATT
TAGTTTGCTCGATGAAGCAAGTGAAAAAACATTTCTTTGCACAAATACAGCTGCTTGTATACAGAAGTTTTTATTTGATG
GAGAGGTATAAAAAAATGCAACTGAGTTGAAAAATGTTGTTTCGTGCGCTAGTTACATGCTTGAACAAAAGCTGCTTGAA
GCATGGTGTGCTGATAAGACTGCTGAAGCATTAAGATGCCAGAAGTTGCTGGAGGATGAAGAGGAAGCTGCTCAGAAAAG
GCAAGCTGAACTGATGGAAAGGAAGCGGATGAAGAAACTTAGGCAGAAAGAACAGAGGTTAAAAAACCTCAAGGATGAGA
TACAGCCATTCAAAGTGTGAATTTCATTTATGATCCTGACTGT

Alignment

ORF - retro_zmay_40 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.85 %
• Parental protein coverage: 53.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNASRKSSHLSSKDSAETARDIITTSGQIQPLKIPDAVAALAQAAAKANGETEKYLPGWPLFSPPKVQLD
          MNASRKSSHLSSKDSAETARDIITTSGQ.QP.KIPD.VAALAQAAAKANGETEKYLPGWPLFSPPKVQLD
Retrocopy MNASRKSSHLSSKDSAETARDIITTSGQFQPFKIPDVVAALAQAAAKANGETEKYLPGWPLFSPPKVQLD

Parental  KCTKCSREFCSAINFRRHTRVHRRSLKIDRDFPKNRDLLAAFWNKLTVDDASKILSLTGVVIEGVTGSSI
          KCTKCSREFCSAINFRRHTRVHRRSLKIDRDFPKNRDLLAAFWNKLT.DDASKILSLTGVVIEGVTGSSI
Retrocopy KCTKCSREFCSAINFRRHTRVHRRSLKIDRDFPKNRDLLAAFWNKLTMDDASKILSLTGVVIEGVTGSSI

Parental  LTALSSWMCKPGYASLPVAYARAGSELLDLIQAKPSMHLPVSSDELFSLLDEASEKTFLCTNTAACIQKF
          LTALSSWMCKPGYASLPVAYARAGSELLDLIQAKPSMHL.VSSDELFSLLDEASEKTFLCTNTAACIQKF
Retrocopy LTALSSWMCKPGYASLPVAYARAGSELLDLIQAKPSMHLHVSSDELFSLLDEASEKTFLCTNTAACIQKF

Parental  LFDGEVEKIATELKNVVSCASYMLEQKLLEAWCADKTAEALRCQKLLEDEEEAAQKRQAELMERKRMKKL
          LFDGEV...ATELKNVVSCASYMLEQKLLEAWCADKTAEALRCQKLLEDEEEAAQKRQAELMERKRMKKL
Retrocopy LFDGEVXXXATELKNVVSCASYMLEQKLLEAWCADKTAEALRCQKLLEDEEEAAQKRQAELMERKRMKKL

Parental  RQKEQRLKNLKDE-DATVQSPEIMDDATC
          RQKEQRLKNLKDE.D...QS.....D..C
Retrocopy RQKEQRLKNLKDE<DTAIQSVNFIYDPDC

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_40 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	GRMZM2G142502	1 retrocopy	retro_zmay_40 ,