RetrogeneDB ID: retro_zmay_12

Retrocopy location

• Organism: Maize (Zea mays)
• Coordinates: 7:174791943..174793773(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: GRMZM2G434792
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GRMZM2G087186
• Aliases: None
• Description: None

Sequence

>retro_zmay_12
ATGGACACCAGCGGCATCGTCGGGTCCGTGGACGGGCACAGGCCCGCGGCGAGCGGCGCGGTGGCCTGCCCTGCATCCGG
CGTTTCAGGCTTCATCACGTCCACCGGCGGCGGCGGGGAGCCTCCTCCTAGGGACGCGACCCTGGGCCGGCACCTGGCGC
GGCGGCTGGTGCAGGTGGGCGTGAGCGACGTGTTCGCCGTGCCGGGGGACTTCAACCTGACGCTGCTGGACCACCTGATC
GCGGAGCCCGGCCTCCGCGTGGTCGGCTGCTGCAACGAGCTCAACGCCGGGTACGCCGCCGACGGGTACGCGCGCGCGCG
GGGCGTGGGCGCCTGCGTTGTCACCTTCACCGTGGGCGGGCTCAGCGTGCTCAACGCCATCGCCGGCGCCTACAGCGAGA
ACCTGCCCGTGGTGTGCGTGGTGGGCGGGCCCAACTCCAACGACTACGGCACCAACCGCGTCCTCCACCACACCATCGGC
CTCCCGGACTTCTCGCAGGAGCTGCGGTGCTTCCAGCCCGTCACCTGCCACCAGGCCGTCGTCAACAACCTGGAGGACGC
GCACGAGCAGATCGACGGGGCCATCTCCACGGCGCTCAGGGAGAGCAAGCCCGTCTACATGAGCGTCAGCTGCAACCTGC
CGGGGCTGCCGCATCCGACGTTCGCCACGGACCCTGTGCCATACTTGCTGGCGCCAAGGCCTAGCAACCTGACGGGTCTC
GCCGCCGCCGTCGAGGCCACCGTGTCGTTCCTCGACAAGGCCGTGAAGCCGGTGGTGGTGGCCGGCCCCAAGATCCGCGT
GGCCAAGGCCGCCGCCGCCTTCGTGGAGCTGGCGGAGGCGAGCGGGTACGCGGTGGCGGCCATGCCGTCGGCCAAGGGCC
TGGTGCCGGAGACGCTGCCGCGGTTCCTGGGCACCTACTGGGGCGCCGTGAGCACGGCGTTCTGCGCCGAGATCGTGGAG
TCCGCCGACGCCTACCTCTTGGCGGGCCCCATCTTCAACGACTACAGCTCCGTGGGCTACTCCATCCTGCTCAGGAAGGA
CAAGGCGGTGGTGGTGCAGCCGGACCGCGTCACCGTCGGCAACGGCCCCACCTTCGGCTGCGTCATGATGAGGGACTTCC
TGTCGGCGCTGGCCAAGCGCGTGCGCCCCAACACCACCGCCTACGACAACTACCGGAGGATCTTCGTCCCCGGCGGGCAG
CCGCCCGAGTGCGAGGCCGGCGAGCCCCTCCGCGTCAACGTCCTCTTCAAGCACATCCAGAGGATGCTCAGCGGCGGCAG
CGCCGTCATCGCGGAGACGGGAGACTCGTGGTTCAACTGCCAGAAGCTGCGGCTACCCGACGGCTGCGGGTACGAGTTCC
AGATGCAGTACGGGTCCATCGGCTGGTCGGTTGGCGCGCTGCTCGGCTACGCCCAGGGCGCCCCCGACAAGCGCGTCATC
GCCTGCATCGGCGACGGCAGCTTCCAGGTGACGGCGCAGGACGTGTCGACGATGCTCCGGTGCGAGCAGAGGAGCATCAT
CTTCCTCATCAACAACGGCGGCTACACCATCGAGGTGGAGATCCACGACGGGCCCTACAACGTCATCAAGAACTGGGACT
ACACGGGCCTCGTCGACGCCATCCACAACGGCCAGGGGAGGTGCTGGACCGCTAGGGTGGCCACGGAGGAGGAGCTCACG
GCGGCCATCGCCACGGCCACCGGCGACGACAGAAAGGACTGCCTCTGCTTCATCGAGGTGGTGGTGCACAAGGATGACAC
CAGCAAGGAGCTCCTGGAATGGGGCTCCAGGGTCTCCGCCGCAAACTCCAGGCCACCCAACCCGCAGTAG

Alignment

ORF - retro_zmay_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.76 %
• Parental protein coverage: 99.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IGSVNGAASNQTVGCPASAPGCPMASTPAQPAATLSAGEASLGRHLARRLVQVGVNDVFAVPGDFNLTLL
          .GSV.G............A.G.....T............A.LGRHLARRLVQVGV.DVFAVPGDFNLTLL
Retrocopy VGSVDGHRPAASGAVACPASGVSGFITSTGGGGEPPPRDATLGRHLARRLVQVGVSDVFAVPGDFNLTLL

Parental  DHLIAEPGLRLVGCCNELNAGYAADGYARARGVGACAVTFTVGGLSVLNAIAGAYSENLPVICIAGGPNS
          DHLIAEPGLR.VGCCNELNAGYAADGYARARGVGAC.VTFTVGGLSVLNAIAGAYSENLPV.C..GGPNS
Retrocopy DHLIAEPGLRVVGCCNELNAGYAADGYARARGVGACVVTFTVGGLSVLNAIAGAYSENLPVVCVVGGPNS

Parental  NDYGTNRILHHTIGLPDFSQELRCFQTVTCHQAVVNNLDDAHEQIDTAIATALRESKPVYLSISCNLPGL
          NDYGTNR.LHHTIGLPDFSQELRCFQ.VTCHQAVVNNL.DAHEQID.AI.TALRESKPVY.S.SCNLPGL
Retrocopy NDYGTNRVLHHTIGLPDFSQELRCFQPVTCHQAVVNNLEDAHEQIDGAISTALRESKPVYMSVSCNLPGL

Parental  PHPTFSRDPVPFFLTPRTSNKMGLEAAVEATVEFLNKAVKPVLVAGPKLRVAKAGKAFVDMVDASGYAYA
          PHPTF..DPVP..L.PR.SN..GL.AAVEATV.FL.KAVKPV.VAGPK.RVAKA..AFV....ASGYA.A
Retrocopy PHPTFATDPVPYLLAPRPSNLTGLAAAVEATVSFLDKAVKPVVVAGPKIRVAKAAAAFVELAEASGYAVA

Parental  VMPSAKGLVPETHPHFIGTYWGAVSTAFCAEIVESADAYLFAGPIFNDYSSVGYSFLLKKEKAIIVQPER
          .MPSAKGLVPET.P.F.GTYWGAVSTAFCAEIVESADAYL.AGPIFNDYSSVGYS.LL.K.KA..VQP.R
Retrocopy AMPSAKGLVPETLPRFLGTYWGAVSTAFCAEIVESADAYLLAGPIFNDYSSVGYSILLRKDKAVVVQPDR

Parental  VIVGNGPAFGCVMMKEFLSELAKRVNKNTTAYENYKRIFVPEGQPLESEPNEPLRVNVLFKHVQKMLTGD
          V.VGNGP.FGCVMM..FLS.LAKRV..NTTAY.NY.RIFVP.GQP.E.E..EPLRVNVLFKH.Q.ML.G.
Retrocopy VTVGNGPTFGCVMMRDFLSALAKRVRPNTTAYDNYRRIFVPGGQPPECEAGEPLRVNVLFKHIQRMLSGG

Parental  SAVIAETGDSWFNCQKLKLPEGCGYEFQMQYGSIGWSVGALLGYAQGANHKRVIAFIGDGSFQVTAQDVS
          SAVIAETGDSWFNCQKL.LP.GCGYEFQMQYGSIGWSVGALLGYAQGA..KRVIA.IGDGSFQVTAQDVS
Retrocopy SAVIAETGDSWFNCQKLRLPDGCGYEFQMQYGSIGWSVGALLGYAQGAPDKRVIACIGDGSFQVTAQDVS

Parental  TMLRCEQNSIIFLINNGGYTIEVEIHDGPYNVIKNWNYTGFVDAIHNGLGKCWTSKVKSEEELTAAIETA
          TMLRCEQ.SIIFLINNGGYTIEVEIHDGPYNVIKNW.YTG.VDAIHNG.G.CWT..V..EEELTAAI.TA
Retrocopy TMLRCEQRSIIFLINNGGYTIEVEIHDGPYNVIKNWDYTGLVDAIHNGQGRCWTARVATEEELTAAIATA

Parental  LG-EKKDCLCFIEVIAHKDDTSKELLEWGSRVSAANSRPPNPQ
          .G...KDCLCFIEV..HKDDTSKELLEWGSRVSAANSRPPNPQ
Retrocopy TGDDRKDCLCFIEVVVHKDDTSKELLEWGSRVSAANSRPPNPQ

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_12 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Zea mays	GRMZM2G087186	1 retrocopy	retro_zmay_12 ,
Oryza barthii	OBART03G13620	1 retrocopy	retro_obar_6,
Oryza glumaepatula	OGLUM03G13720	1 retrocopy	retro_oglu_28,
Oryza meridionalis	OMERI02G33690	1 retrocopy	retro_omer_19,
Oryza punctata	OPUNC03G13130	1 retrocopy	retro_opun_18,
Oryza rufipogon	ORUFI03G14280	1 retrocopy	retro_oruf_25,