RetrogeneDB ID: retro_zmay_2

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 3:87791575..87793810(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AC197150.3_FG003
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GRMZM2G023037
• Aliases: None
• Description: None

Sequence

>retro_zmay_2
ATGTTCGGGTGCGGCTACCGGACCCAGTTCATCAACGGGCGCAGGGAGAAGTTCGTGAGGCTCGTCGAGGCAGACGCGCC
GGCGGATTCGGCGTCCAGCCCCACTTCCGGCAGCGGCGGCGGTGCCAGCATGGAGCACGGGCACGGGCACGGGCACGGCG
GCGGGTTCCACATGGACAGCTACTTCTCGGGCAACCCGGCGGCGGCCGCCGCCAAGTTCCGTGCGCGGTCGGTTCGGGTG
GCGGCGGGCGTGATGAACCGGTCGGAGCGGCTGAGGAGCATCGGCCTCGTGTTCCAGGAGGACTTCCGGAAGATGTCGCA
GCAGGTGTTCGACCCGCAGGACGCGTTCCTGGCGCGCATGAACCGCGCCTTCGTCTTCGCGTGCATCGTGTCCGTGGCCA
TCGACCCGCTCTTCCTCTACCTCCTGGCCGTCAAGTACACGGACAAGAACACCTGCATCGGCTTCGACCGCAACCTGGCC
ACCGTCGCCACCGTGGTGCGCACCGCCGTGGACGCCTTCTACCTGGCGCGGATCGCGCTGCAGTTCCGGACGGCGTACAT
CGCGCCGTCGTCGCGCGTGTTCGGGCGCGGCGAGCTGGTCATCGACTCGTCCGCCATCGCGCGCCGCTACCTGCGCCGAT
TCTTCGCCGTCGACCTGCTGTCCGTGCTGCCGCTGCCGCAGGTCTCCATCTGGAACTTCCTCAACCGGCCCAAGGGCGCG
GACCTGCTGCCCACCAAGAACGCGCTGCTCTTCACGGTGCTGTCGCAGTACGTGCCCCGCCTGGTGCGCTTCTACCCCAT
CACCTCGGAGCTGAAGCGCACCACGGGGGTGTTCGCCGAGACGGCCTTCGGCGGCGCCGCCTTCTACCTGCTGCTCTACA
TGCTGGCCAGCCACATGGTGGGGGCCTTCTGGTACCTGCTGGCCATCGAGCGGCTGGACGACTGCTGGCGGGACAAGTGC
ACCAACCTCAACTTCCACCAGTGCCGCACCTACATGTACTGCGGCGGCGGCAGCCAGGGCCAGTCGGGCTTCCTCGAGTG
GCGCACCATGATCCGGCAGGTGCTGGCGCAGGAGTGCGCCCCCGTCGACGGCAGCGGCACGGGGTTCCCCTACGGCATCT
ACACCACGGCCATCCAGTCGGGCGTCTACTCCACGGAGAACCTGACGGCCAAGATCCTCTTCTGCCTCTGGTGGGGCCTG
CAGAACCTGAGCACCATCGGCCAGGGCCTGGAGACGACCCACTACAAGGGGGAGCAGCTCTTCTCCATCACGCTCGCGCT
GCTGGGCCTCATCCTCATGGCGCTCCTCATCGGCAACATGCAGACGTACCTGCAGTCCATGACGCTGCGCCTGGAGGAGA
TGCGCCTCAAGCGCAGGGACTCGGAGCAGTGGATGCACCACCGCGTCCTCCCCGACGAGCTCCGGGAGCGGGTGTGGCGG
CACAACCAGTACAAGTGGCTCGAGACGCGCGGCGTCGACGAGGACAGCCTCGTGCGCAGCCTGCCCAAGGACCTGCGCCG
CGACGTCAAGCGGCACCTCTGCCTCCGCCTCGTCCGCCGCGTCCCGCTCTTCGCCAACATGGACGAGCGCCTCCTCGACG
CTATCTGCGAGCGCCTCAAGCCCAGCCTCTGCACCGAGTCCACCTACATCGTGCGCGAGGGGGACCCCGTCGACGAGATG
CTCTTCATCATTCGCGGCCGCCTCGAGAGCTCCACCACCGACGGCGGCCGGATGGGGTTCTACAACCGGGGGCTGCTCAA
GGAGGGCGACTTCTGCGGGGAGGAGCTACTCACGTGGGCGCTCGACCCAAAGGCCGGCGCCAACTTCCCGCTGTCCACGC
GCACCGTTAGGGCCATCTCCGAGGTGGAGGCGTTCGCGCTGCGCGCTGACGAGCTCAAGTTCGTGGCGGGGCAGTTCCGG
CGCCTGCACAGCAAGCAGCTGCAGCAGACCTTCCGCTTCTACTCGCAGCAGTGGCGCACCTGGGCCTCCTGCTTCATACA
GGCCGCATGGAGGAGGTACCTCAAGCGGAAGGCGGCCGAGCAGCGGCGCCGGGAGGAGGAGATGGAGGCCGACTCGTCCG
GGGTTTCCACGAGCAGGTTCAAGACCACGCTCCTCGTGTCGCGCTTCGCCAAGAACGCCATGCGCGGCGTGCAGCGCCAG
CGATCCGTCCGGGCCGACAGCCTCATCATGCTTCCCAGGCCGCCGGAGCCGGATTTCGGCTCCATGGACTACTGA

Alignment

ORF - retro_zmay_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.11 %
• Parental protein coverage: 52.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GQDNPFNFGIYEQALVSKILSPGNFISKLCYCFWWGLQNLSTLGQGLLTSTYPGEVLFSIAICVLGLILF
          G....F..GIY..A..S...S..N...K...C.WWGLQNLST.GQGL.T..Y.GE.LFSI....LGLIL.
Retrocopy GSGTGFPYGIYTTAIQSGVYSTENLTAKILFCLWWGLQNLSTIGQGLETTHYKGEQLFSITLALLGLILM

Parental  ALLIGNMQSYLQSVAIRLEEMRVKKRDAEQWMHHRSLPLDIRHRVRKYERYRWLETRGVDEETLVQTLPK
          ALLIGNMQ.YLQS...RLEEMR.K.RD.EQWMHHR.LP...R.RV.....Y.WLETRGVDE..LV..LPK
Retrocopy ALLIGNMQTYLQSMTLRLEEMRLKRRDSEQWMHHRVLPDELRERVWRHNQYKWLETRGVDEDSLVRSLPK

Parental  DLRRDIKRHLCLGLVKRVPLFENMDERLLDAICERLRPALYTENEFILREGDPVDEMHFILHGCLESVTT
          DLRRD.KRHLCL.LV.RVPLF.NMDERLLDAICERL.P.L.TE...I.REGDPVDEM.FI..G.LES.TT
Retrocopy DLRRDVKRHLCLRLVRRVPLFANMDERLLDAICERLKPSLCTESTYIVREGDPVDEMLFIIRGRLESSTT

Parental  DGGRSGFFNKVQLKEGSFCGDELLTWALDPKSAANFPVSSRTVQALTEVEAFALCAEELKFVASQFRRLH
          DGGR.GF.N...LKEG.FCG.ELLTWALDPK..ANFP.S.RTV.A..EVEAFAL.A.ELKFVA.QFRRLH
Retrocopy DGGRMGFYNRGLLKEGDFCGEELLTWALDPKAGANFPLSTRTVRAISEVEAFALRADELKFVAGQFRRLH

Parental  SRQVQHTFRFYSQQWRTWAACFIQAAWRRYYKRKMAEQRRKEEEAASRPSS-SHPSLGATIYASRFAANA
          S.Q.Q.TFRFYSQQWRTWA.CFIQAAWRRY.KRK.AEQRR.EEE.....S..S......T...SRFA.NA
Retrocopy SKQLQQTFRFYSQQWRTWASCFIQAAWRRYLKRKAAEQRRREEEMEADSSGVSTSRFKTTLLVSRFAKNA

Parental  MRGVHRLRSKAVPTIVRLPKPPEPDFGVDD
          MRGV.R.RS........LP.PPEPDFG..D
Retrocopy MRGVQRQRSVRADSLIMLPRPPEPDFGSMD

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_2 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	GRMZM2G023037	1 retrocopy	retro_zmay_2 ,