RetrogeneDB ID: retro_zmay_9

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 1:1663086..1664043(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: GRMZM2G474194
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GRMZM2G013002
• Aliases: None
• Description: None

Sequence

>retro_zmay_9
ATGGCGGTACTGTGGTGGTGGTCATCGTCCTGCTTGTCCTCCCGCGCCGTCGCTGCTGCGCTGCTTTGCCTGCTGGTGGC
TCACGGCAGCGATGGAACCAGGCACAACAGCAACAATGGCGGTGGTAGTGGTAGTTCCAGCAGCAGCAAGAGCCACAAGC
AAGGCGGAGGGGGACGAGCCCATGCCGCGCCGACGACACCGTCTCCGTATCCGTCTCCGTCTCCGGCGGCTGGCAACAAC
AGCAGCAGCGACGACGGGTGGCTGAACGCCCGTGCGACATGGTACGGTGCCCCGAACGGTGCTGGTCCGGACGACAACGG
CGGCGCGTGCGGCTTCAAGGGCGTGAACATGCCACCTTTCTCGGCGATGACGTCGTGCGGCAACGAGCCAATCTTCAAGG
ACGGCAAAGGATGCGGGTCCTGCTACCAGATCCGGTGCAAGGCCCACCCTGCGTGCTCCGGCGTGGCGGAGACGGTGATC
ATCACGGACATGAACTACTACCCGGTGGCCCCCTACCACTTCGACCTGAGCGGCACTGCCTTCGGGGCCATGGCAAAAGA
CGAGCACAACGACGAGCTAAGGCACGCAGGAATCATCGACATCCAGTTCAAGAGGGTTCCCTGCCAGTACCCTGGTCTGA
CGGTGACCTTCCACATCGAGCGTGGCTCCAACCCCAACTACCTGGCGGTGCTGGTGGAGTACGAGAACGGCGACGGCGAC
GTGGTGCAGGTGGACCTGATGGAGTCCAGCCCCGACGACGGCGAGCCCACCGGCGTCTGGGAGCCCATGCGCGAGTCCTG
GGGCTCCATATGGAGGATGGACACCCGCCGGCCGCTGCAGGGGCCCTTCTCGCTGCGCGTCACCAACGAGTCCGGCAAGA
CGCTGGTGGCGGACCAGGTCATTCCGGCAGACTGGCAGCCCGACAACGTCTACAGCTCCATCGTCCAGTTCGAGTAG

Alignment

ORF - retro_zmay_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.0 %
• Parental protein coverage: 80.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WQRARATWYGQPNGAGPDDNGGACGFKHTNQYPFMSMGSCGNQPLFKDGKGCGSCYKIRCRKDPSCSGRT
          W..ARATWYG.PNGAGPDDNGGACGFK..N..PF..M.SCGN.P.FKDGKGCGSCY.IRC...P.CSG..
Retrocopy WLNARATWYGAPNGAGPDDNGGACGFKGVNMPPFSAMTSCGNEPIFKDGKGCGSCYQIRCKAHPACSGVA

Parental  ETVIITDMNYYPVSKYHFDLSGTAFGRLAKPGLNDKLRHSGIIDIEFTRVPCEFPGLKIGFHVEEYSNPV
          ETVIITDMNYYPV..YHFDLSGTAFG..AK...ND.LRH.GIIDI.F.RVPC..PGL...FH.E..SNP.
Retrocopy ETVIITDMNYYPVAPYHFDLSGTAFGAMAKDEHNDELRHAGIIDIQFKRVPCQYPGLTVTFHIERGSNPN

Parental  YFAVLVEYEDGDGDVVQVDLMESKTARGPPTGRWTPMRESWGSVWRMDTNHRMQPPFSIRIRNESGKTLV
          Y.AVLVEYE.GDGDVVQVDLMES....G.PTG.W.PMRESWGS.WRMDT....Q.PFS.R..NESGKTLV
Retrocopy YLAVLVEYENGDGDVVQVDLMESSPDDGEPTGVWEPMRESWGSIWRMDTRRPLQGPFSLRVTNESGKTLV

Parental  ANNVIPANWRPNTFYRSFVQY
          A..VIPA.W.P...Y.S.VQ.
Retrocopy ADQVIPADWQPDNVYSSIVQF

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_9 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 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA033426	1 retrocopy	retro_oind_67,
Zea mays	GRMZM2G013002	1 retrocopy	retro_zmay_9 ,
Oryza longistaminata	KN539761.1_FG003	1 retrocopy	retro_olon_5,
Leersia perrieri	LPERR10G14060	1 retrocopy	retro_lper_25,
Oryza barthii	OBART10G18180	1 retrocopy	retro_obar_7,
Oryza glumaepatula	OGLUM10G18290	1 retrocopy	retro_oglu_25,
Oryza nivara	ONIVA10G20720	1 retrocopy	retro_oniv_16,
Oryza glaberrima	ORGLA10G0133100	1 retrocopy	retro_ogla_8,
Oryza rufipogon	ORUFI10G19380	1 retrocopy	retro_oruf_30,
Oryza sativa japonica	OS10G0556100	1 retrocopy	retro_osat_34,
Physcomitrella patens	PP1S100_99V6	1 retrocopy	retro_ppat_8,