RetrogeneDB ID: retro_zmay_29

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 3:40063525..40064863(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: GRMZM2G419111
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GRMZM2G105644
• Aliases: None
• Description: None

Sequence

>retro_zmay_29
ATGGCCGCCGCCGCCTGCTATTCGCCAGCGCGCATCATCATCTCCTGCTCAGCCACCACCACCTCCTCATCGTCGTCAGC
GCGCACGCTGCGCGTCGCCGTAGTGGGGGGTGGCCCCGCGGGCGCGTCGGCTGCCGAGGCGCTGGCCTCGGCGGGGGCCC
GGACGTTCCTCCTCGAGCGCAGCCCCGCGGGCGCCAAGCCCTGCGGCGGTGCCATCCCACTCTGTATGCTGGACGAGTTC
GCCATCCCGCGGGACCTCGTTGACCGCCGCGTCACCCGGATGCGCGTGCTCTCCCCCTCCAACCTCGCAGCCGACTTCTC
CCGCGCGCTGCCCCCCGGGGCGCACATCCCCATGCTCCGCCGCGAGGTGCTCGACTCCTTCCTCCGCCGCCGCGCCGTCG
AGGCCGGGGCCGAGCTCGTCCCGGGCCTCGTCACCTCGCTCTCGCTCCCCGCGGGGCCCGCCGACCCCTACCTCGTCCAC
TACATCTCGTCCTCCCCGGAGGGCGTGGGAGCGGGACGGAGCGTGCTGGAGGTGGACGCCATCGTCGGCGCGGACGGCGC
CAACAGCCGCGTGGCGCGCGAGGTCGGGGCCGGGGACTACACGACGGCCATCGCGTTCCAGGAGCGCATCCGCCTCCCCG
ACGCCGGCATGGCGTACTACGACGACCTCGCCGAGATGTACGTGGGCGGGGACGTGTCCCCGGACTTCTACGGCTGGGTG
TTCCCCAAGTGCGACCACGTGGCCGTCGGGACCGGCACCGTCGCCGCCAAGCCGGAGATCAAGCGCCTCCAGTCCGGCAT
CCGGGCGCGCGCGGGCCCCAAGATCGCCGGCGGCCGCGTAGTCAAGGTGGAGGCCCACCCGATCCCAGAGCACCCGCGCC
CGCGCCGCGTCGTGGGGCGCGTGGCCCTAGTCGGCGACGCGGCGGGGTACGTCACGCGGTGCTCCGGCGAGGGCATCTAC
TTCGCGGCAAAGTCGGGGCGGCTGTGCGGGCAGGCCATGGCGGAGGAGTGGGCGCGCACGGGCTCCGTGACGGAGGCCGG
GCTGAGGCGCGGCTACCTGCGGCGTTGGGACGACGAGTTCCTGCTCATGTTCCGGTTCCTGGACCTGCTGCAGCGCGTGT
TCTACGGCGGGAATGCCGGCCGCGAGGCGCTGGTGGAGATGTGCTCCGACGACTACGTGCAGCGGCGGACGTTCGAAAGC
TACCTGTACAAGCGGATGGTGCCTGGCGAGCCGTGGGGCGACCTCCGGCTGCTGTGGCGGACGGTGGCCAGCATGGTGCG
CTGCGGCGTCATCGGCAGGGAGGTGGAGCGCCTGCGACGGCTGGAGCTGCAAGGCTAG

Alignment

ORF - retro_zmay_29 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.77 %
• Parental protein coverage: 94.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ARMVVTRAAASSPKLPNGRRLRVAVVGGGPAGGAAAEALAKGGVETVLIERKMDNCKPCGGAIPLCMVSE
          AR......A.........R.LRVAVVGGGPAG..AAEALA..G..T.L.ER.....KPCGGAIPLCM..E
Retrocopy ARIIISCSATTTSSSSSARTLRVAVVGGGPAGASAAEALASAGARTFLLERSPAGAKPCGGAIPLCMLDE

Parental  FDLPLDLVDRKVRKMKMISPSNVAVDIGRTLAPHEYIGMVRREVLDAYLRSRAQSVGAEVVNGLFLRYEA
          F..P.DLVDR.V..M...SPSN.A.D..R.L.P...I.M.RREVLD..LR.RA...GAE.V.GL......
Retrocopy FAIPRDLVDRRVTRMRVLSPSNLAADFSRALPPGAHIPMLRREVLDSFLRRRAVEAGAELVPGLVTSLSL

Parental  PKEPNGSYVVHYNHYDGSNGKVGGEKRSFEVDAIVGADGANSRVAKDMGAGDYEYAIAFQERVKIPDDKM
          P..P...Y.VHY.....S...VG......EVDAIVGADGANSRVA...GAGDY..AIAFQER...PD..M
Retrocopy PAGPADPYLVHY--ISSSPEGVGAGRSVLEVDAIVGADGANSRVAREVGAGDYTTAIAFQERIRLPDAGM

Parental  VYYEERAEMYVGDDVSPDFYGWVFPKCDHVAVGTGTVTHKADIKKFQAATRLRAKDKIEGGKIIRVEAHP
          .YY...AEMYVG.DVSPDFYGWVFPKCDHVAVGTGTV..K..IK..Q...R.RA..KI.GG....VEAHP
Retrocopy AYYDDLAEMYVGGDVSPDFYGWVFPKCDHVAVGTGTVAAKPEIKRLQSGIRARAGPKIAGGRVVKVEAHP

Parental  IPEHPRPKRVSGRVTLVGDAAGYVTKCSGEGIYFAAKSGRMCAEAIVAGSANGTRMVEESDLRKYLAEFD
          IPEHPRP.RV.GRV.LVGDAAGYVT.CSGEGIYFAAKSGR.C..A.....A......E....R.YL...D
Retrocopy IPEHPRPRRVVGRVALVGDAAGYVTRCSGEGIYFAAKSGRLCGQAMAEEWARTGSVTEAGLRRGYLRRWD

Parental  RLYWPTYKVLDILQKVFYRSNAAREAFVEMCADDYVQKMTFDSYLYKRVVPGNPLDDIKLAVNTIGSLVR
          .........LD.LQ.VFY..NA.REA.VEMC.DDYVQ..TF.SYLYKR.VPG.P..D..L...T..S.VR
Retrocopy DEFLLMFRFLDLLQRVFYGGNAGREALVEMCSDDYVQRRTFESYLYKRMVPGEPWGDLRLLWRTVASMVR

Parental  ATALRREMEKV
          .....RE.E..
Retrocopy CGVIGREVERL

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_29 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI3G59430	1 retrocopy	retro_bdis_46,
Zea mays	GRMZM2G105644	1 retrocopy	retro_zmay_29 ,
Oryza meridionalis	OMERI02G30980	1 retrocopy	retro_omer_17,
Oryza nivara	ONIVA06G04710	1 retrocopy	retro_oniv_24,
Oryza punctata	OPUNC02G29860	1 retrocopy	retro_opun_22,
Oryza rufipogon	ORUFI02G34000	1 retrocopy	retro_oruf_42,
Oryza sativa japonica	OS02G0744900	1 retrocopy	retro_osat_44,
Sorghum bicolor	Sb04g028050	1 retrocopy	retro_sbic_27,
Triticum aestivum	Traes_6DL_0FF72D765	1 retrocopy	retro_taes_28,