RetrogeneDB ID: retro_zmay_14

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 3:202254644..202255475(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: GRMZM2G015908
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GRMZM2G035134
• Aliases: None
• Description: None

Sequence

>retro_zmay_14
ATGGCCGGGGTCGTTGTGGTGTTCGACTTCGACAAGACGATCATCGACGTCGACAGCGACAACTGGGTCGTGGACAGCCT
CGGCTTCACCGAGCCGTTCGAGCGCCTCCTGCCCACCATGCCCTGGAACACGCTCATGGACACCATGATGGGGGAGCTGC
ACGCGCACGGCAGGACCCTGGACGACGTCGCCGAGGCGCTCCGTGCGGCGCCCGTCGTCGCGGGCGTCCCCGCCGCCATC
AAGGCCGCCTACGCGCTCGGCTGCGACCTGCGCGTCCTCAGCGACGCCAACGCCTTCTTCATCGACACCGTCCTGGCGCA
CCACGGCCTGCTGGGCTGCTTCTCCCAGATCAACACCAACCCCAGCCACCCCGACGCCGACGCCGACGGCCGCCTCCGCA
TCGGGCCCTACCACGACCTGCACGGGTGCGGCGTCGGCACCTGCCCGCCCAACATGTGCAAGGGCCAGGTGCTGGACCGC
ATCCTCCGCGAGGCGTCGTCGTCGGCCGCCGGCAGGAAGCGCGTCGTGTACCTGGGCGACGGCCGCGGCGACTACTGCCC
GGCGCTGCGGCTGGCAAGGGAGGACTTCGTCATGCCGCGCAGGGGCTTCCCCGTGTGGGACCTCATCTGCGAGGACCCCG
CGCGGCTGCAGGCGGAGGTGCACCCCTGGGCCGACGGCGCCGAGCTGGAGGAGACGCTGCTGCGCCTCGTCGGGAGGGCG
CGCGTGGAGGAGGCCGCACTGCTGCCGCCGCTCGACTGCAAGCTCGAGTCCATGCCCGTTGCCGCGCAGGAGGGCATGGG
ACCCATCATGCCGCTCGGCGTCAAGCACTGA

Alignment

ORF - retro_zmay_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.23 %
• Parental protein coverage: 82.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VVVVFDFDRTIIDWDSDDWVITKLGAADAFQRLRPTMRWNPLMDRMMAELHARGKTPEDIRDCLRSAPLD
          VVVVFDFD.TIID.DSD.WV...LG....F.RL.PTM.WN.LMD.MM.ELHA.G.T..D....LR.AP..
Retrocopy VVVVFDFDKTIIDVDSDNWVVDSLGFTEPFERLLPTMPWNTLMDTMMGELHAHGRTLDDVAEALRAAPVV

Parental  THVVSAVKTAAALGCDLKVVSDANTFFIETVLAHHGVLGCFSEIVTNPA--SVDADGRLRISPFHDPASA
          ..V..A.K.A.ALGCDL.V.SDAN.FFI.TVLAHHG.LGCFS.I.TNP.....DADGRLRI.P.HD....
Retrocopy AGVPAAIKAAYALGCDLRVLSDANAFFIDTVLAHHGLLGCFSQINTNPSHPDADADGRLRIGPYHDLHGC

Parental  PHGCSLCPDNMCKGKILGRI-QATGSDKKRRRRFIYIGDGKGDYCPSLKLGEGDHVMARENYPLWHLICD
          ..G...CP.NMCKG..L.RI.....S....R.R..Y.GDG.GDYCP.L.L...D.VM.R...P.W.LIC.
Retrocopy --GVGTCPPNMCKGQVLDRILREASSSAAGRKRVVYLGDGRGDYCPALRLAREDFVMPRRGFPVWDLICE

Parental  NKQLLKAEVHPWNSGEELEKTLLKLAG
          ....L.AEVHPW..G.ELE.TLL.L.G
Retrocopy DPARLQAEVHPWADGAELEETLLRLVG

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_14 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.

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA001283	1 retrocopy	retro_oind_8,
Brachypodium distachyon	BRADI2G42720	1 retrocopy	retro_bdis_19,
Zea mays	GRMZM2G035134	1 retrocopy	retro_zmay_14 ,
Hordeum vulgare	MLOC_52823	1 retrocopy	retro_hvul_27,
Oryza brachyantha	OB01G31280	1 retrocopy	retro_obra_4,
Oryza glumaepatula	OGLUM01G25430	1 retrocopy	retro_oglu_22,
Oryza meridionalis	OMERI01G19970	1 retrocopy	retro_omer_22,
Oryza nivara	ONIVA01G24910	1 retrocopy	retro_oniv_37,
Oryza punctata	OPUNC01G21870	1 retrocopy	retro_opun_7,
Oryza rufipogon	ORUFI01G24440	1 retrocopy	retro_oruf_27,