RetrogeneDB ID: retro_zmay_63

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 5:91382246..91383230(+)
• Located in intron of: GRMZM2G133308

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GRMZM2G150319
• Aliases: None
• Description: None

Sequence

>retro_zmay_63
ATGGCGGTCGACTCGCAGCAGGTGGTGGCGGGCTTCCTCACCCTCTCCATGTTCGTCATGCTCGGCAACATGATCAAGCA
CGACCACTTCTCTCCCGTCACCGAGGAGCTGGGCTTGGAGGCAACAGGTGTGGTGTCGAACACAAGGAAGCTTGACAACA
ATGCTGAAATGAGCAGCGTTGATACGACTGGAGTGGAGGACCTGATGGACGCTGTCGAGGAAGTTAAACCTTGCTGGACC
AAACCAAAAAATCAGTCGTCTAATGGTTTTGTTACATTCTCCTTGACTATGGGCCCTGAGTATCACATCTCTCAGATCAC
AGATGTTGTGGTTATTGCAAGGTATCTAGGTGCAACACTTGTACTCCCAGACATCAGAGGAAATGAATTAGGAAATAAGC
GAAAATTCCAAGACATGTACAATGTGGATAAGTTTGTGAGGAGCTTGGATGGTGTTGTCGAAGTAATAGAGGATATACCT
GATGAAGTGAGTGCTAAGAAGCCAGCAGTCATCAGAGTACCGAACCGTGTGACTGAAAGCTTCATCACAGGCACCATCCA
GCCCATCTTCCAAAAAAACAAGTACTTAAGACTAGCGGTCATTTTCTCTTCCATAAGTTTAAGGCCAAAGGAGACGAACA
ACAAGGACATGGACACAATTGCTTGCCTTGCGATGTTCGGTGGCCTCGAGCTGAAGCACGAATATTCTGAGGTGGCCAGA
AAAATGCTGGATAGGCTTCAAGAATTAAGCAAGAAGTCAGATGGGAAGGTCTTGGCAATTGATTTGCGGACCGACTTGCT
GGAGAAGAAGAGTTGCAAGACAACCCGTGGCGCTCGAAGAAAAGGCTGCTATAGCCCTGATGAGGTCCTGGCTTTCCTGA
GGAGTGTTGGCTTCTCTGCTAACACAACCATCTACTTGACAGAGACGTCGTGGCACAAAGGCCTGGATGTTCTGAAGGAA
GAATTCCCAAATACATGGTATCAA

Alignment

ORF - retro_zmay_63 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.55 %
• Parental protein coverage: 78.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVDPRQVVAGFLTLSMFVMLGNMIKHDHFSPVTEELGFEATGVVSNTRKLDNDAEMSSVDTAGVEDLMD
          MAVD..QVVAGFLTLSMFVMLGNMIKHDHFSPVTEELG.EATGVVSNTRKLDN.AEMSSVDT.GVEDLMD
Retrocopy MAVDSQQVVAGFLTLSMFVMLGNMIKHDHFSPVTEELGLEATGVVSNTRKLDNNAEMSSVDTTGVEDLMD

Parental  AVEEVKPCWTKPSPKNQPSNGFVTFSLTMGPEYHISQITDAVVIARYLGATLVLPDIRGNELGNKRKFQD
          AVEEVKPCWTKP..KNQ.SNGFVTFSLTMGPEYHISQITD.VVIARYLGATLVLPDIRGNELGNKRKFQD
Retrocopy AVEEVKPCWTKP--KNQSSNGFVTFSLTMGPEYHISQITDVVVIARYLGATLVLPDIRGNELGNKRKFQD

Parental  IYNVDKFVRSLDGVVEVIEDIPDEVSAKKPAVIRVPNRVTESFITGTIQPIFQKNKYLRLAVIFSSVSLR
          .YNVDKFVRSLDGVVEVIEDIPDEVSAKKPAVIRVPNRVTESFITGTIQPIF...KYLRLAVIFSS.SLR
Retrocopy MYNVDKFVRSLDGVVEVIEDIPDEVSAKKPAVIRVPNRVTESFITGTIQPIFXXXKYLRLAVIFSSISLR

Parental  PKETNNKDMDATACLAMFGGLELKHEYSEVARKMLDRLQELSKKSDGKVLAIDLRTDLLEKKSCKTTRGA
          PKETNNKDMD..ACLAMFGGLELKHEYSEVARKMLDRLQELSKKSDGKVLAIDLRTDLLEKKSCKTTRGA
Retrocopy PKETNNKDMDTIACLAMFGGLELKHEYSEVARKMLDRLQELSKKSDGKVLAIDLRTDLLEKKSCKTTRGA

Parental  RRKGCYSPDEVLAFLRSVGFSANTTIYLTETSWYKGLDVLKEEFPNTWYK
          RRKGCYSPDEVLAFLRSVGFSANTTIYLTETSW.KGLDVLKEEFPNTWY.
Retrocopy RRKGCYSPDEVLAFLRSVGFSANTTIYLTETSWHKGLDVLKEEFPNTWYQ

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_63 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	GRMZM2G150319	1 retrocopy	retro_zmay_63 ,