RetrogeneDB ID: retro_obra_2

Retrocopy location

• Organism: Oryza brachyantha
• Coordinates: 7:12748496..12750359(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OB07G24140
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OB01G37960
• Aliases: None
• Description: None

Sequence

>retro_obra_2
ATGACGAGACAGAGCAGCACATCGGCGACGATATTGCCGGTAACGGTGAGCTCTGCCATGGCGGCGGCTGCTGCTGCTGC
TGCCAGAAACGAACCTCTCCGATCGGCACACGCTGAGGCCTCTTCCTCGCTAGGACGACTGTTCATCGTCGACCCTCGGG
GTCGCATCTACAGGTGGTGGCAGAAGTTCCTCATCGTGCTGGTGCTGTACTCGGCGTGGGCGTCGCTGTTCGAGCTGGCC
ATGGAGAGAGCGGCGGCGTCTCTCCCGCTTGTTGCCACGGACCTGGTGGTAGACGCCTTCTTCGCCATCGACATTGTCAT
CTCCTTCTTCCTCCTCCCGTACCGTGACACCTCCGCCGGCCTCCTCGTAACCGACCGCGTGAAGATCGCCATTGGGTGCC
TGAGACGGCCCCGTTTCGCGCTCGATGTGGTCTCGACGATTCCTTTTCAAATAATCCACCGGCTTGTGACCGACGAAAGA
CGAGGGCTGTGGGGGTTCCTCAATCTTCTCCGTCTGTGGCGACTATGGCGCGTCGGCGAGCTCTGCTCGGAGCTGGAGAA
GAACGTCAGGCTCAGCTACCTGTGGACCAGGCTCACCAAGATCCTCTGCGTGACGCTGTTCGCGCTGCACTTCGCCGCCT
GCATCTACCTGTGGATGGCGTTCAACTACGGCGTCAAGGAGCTCACCTGGATCGGCAGCGTCGTCGGTGGGTTCGAGCAC
CGCGGCGTGTGGTTCTGCTACACCTACGCGGTGTACTGGTCCGTCGCCACGCTCGCCACGGTCGGCTACGGCGACCTGCA
CGCCGCCAACACCGGCGAGATGCTGTTCAGCATCGCCTTCATGCTCTTCAACATGGGCCTCGCGTCCTACATCATCGGCA
ACATCACCAACCTCGTCGTCCACGAGACGTCCAGCACCTTCAGGATGAGGGACATGGTGCGGCGGGCGTCGGAGTTCGGG
AGCGCGAAACGGCTGCCGGAGCCGATGAGGGAGCAGATGATGGACAGCGTGCAGCTCAGGTTCGGGGCAGAGGAACAGCT
GCAGCAGGAGGTGCTGTCCGAGCTGCCCAAGGCCACGCGGCTGGGCATCATGCAGCATCTGTTCAGGGGAGCGATCGAGA
GCTGCTACCTGTTCCATGGAGTCTCCGACAGCCTCATCGTGCAGCTGGTCGCAGAGATGAAAGCAGAATCCTTTCCCGCC
AAGGCGAACATTATCCTGGAGAACGAGTCCTCGACGGACTGCTACGTCGTCGTCTCCGGCGAAGTGGAGGCATGGACGGC
AACCCTTGCAGACGGGAAGGAGAGGCACGTGATGAGAATCGGACCTCGGGGCATGGCAGGGGAGATCGGGGTGATGCTCG
GCGTCCCGCAGCCATTCGCCGTCCGGAGCAGGACGCTCACCCAGGTTGCTCGCATAAGCCGCGCCCATCTCCTCCAGACT
GTCCGGCCTAACACCGCAGATGGGTGCGTCGTCTTCTCCAACTTCATCCGGTACCTTGAATCTATGAAGTTGCAAACAAA
GGAGGCGGCTTTTGTCAGTGATCTTCTTTGGAATGGAAAGCCAACAACGATTTTGGGAAGGGCAGCCACCATGCTCGATG
TAGATGAATCGAAGGAGACTGCTCGCAAAATGCTGCCTTGCAAGGAGCCCAAACGGGTGGTTATTCATGAGCAACTTCTC
AGTGAGACCGGCGCAGCTTCAAGGGGGAAGCTGGTCTTGCTCCCAGACTCGCTGCAAGAACTGATGAAGCTCTTCGAAAA
GAAGTTTGGAAAGGCTGCAGGAGGGATCCTTACTTTGGAAGGCGCTGAGGTAGAGGACATCGAAGTGATAAGAGATGGCG
ATCACTTGTTCTTTAGTTTGTAA

Alignment

ORF - retro_obra_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.28 %
• Parental protein coverage: 97.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AGMAAGSEILRLPSGEASPSLGR-FVVNPHSCGYWWWQTLLIVLVLYTAWASPFELAMEKSDCGA-LAIT
          A..AA..E.LR....EAS.SLGR.F.V.P....Y.WWQ..LIVLVLY.AWAS.FELAME.......L..T
Retrocopy AAAAARNEPLRSAHAEASSSLGRLFIVDPRGRIYRWWQKFLIVLVLYSAWASLFELAMERAAASLPLVAT

Parental  ELVVDAFFAVDIAASFFVA-YRDTSTGTLVTDRRKIATRHLKRPGFAMDVASTIPLQMIYWIASGKRQTQ
          .LVVDAFFA.DI..SFF...YRDTS.G.LVTDR.KIA...L.RP.FA.DV.STIP.Q.I.......R...
Retrocopy DLVVDAFFAIDIVISFFLLPYRDTSAGLLVTDRVKIAIGCLRRPRFALDVVSTIPFQIIHRLVTDERRGL

Parental  YGFLNLLRLWRLRRVSKLFARLEKDIRFNYLWTRLVKLLGVTVFSLHFAACIYLSMAFHYRDKELTWIGS
          .GFLNLLRLWRL.RV..L...LEK..R..YLWTRL.K.L.VT.F.LHFAACIYL.MAF.Y..KELTWIGS
Retrocopy WGFLNLLRLWRLWRVGELCSELEKNVRLSYLWTRLTKILCVTLFALHFAACIYLWMAFNYGVKELTWIGS

Parental  QIHGFEDRSVWFNYTCAVYWAMTTLATVGYGDLHAANPGEMLFSIAFMLFNIGLTSYIIGNITILVVHGT
          ...GFE.R.VWF.YT.AVYW...TLATVGYGDLHAAN.GEMLFSIAFMLFN.GL.SYIIGNIT.LVVH.T
Retrocopy VVGGFEHRGVWFCYTYAVYWSVATLATVGYGDLHAANTGEMLFSIAFMLFNMGLASYIIGNITNLVVHET

Parental  TNTFKMRDMVQRASVFGRMNGLPRATREQMMESVQLRFRMEERLEQEMLSELPKAVRSGIALHMFRGAVE
          ..TF.MRDMV.RAS.FG....LP...REQMM.SVQLRF..EE.L.QE.LSELPKA.R.GI..H.FRGA.E
Retrocopy SSTFRMRDMVRRASEFGSAKRLPEPMREQMMDSVQLRFGAEEQLQQEVLSELPKATRLGIMQHLFRGAIE

Parental  SCYLFQGASSKLVVQLVADMKAEFFPPKADIILENEAPTDCYIILSGEVEALT-TLEDGREKHVMTIGSR
          SCYLF.G.S..L.VQLVA.MKAE.FP.KA.IILENE..TDCY...SGEVEA.T.TL.DG.E.HVM.IG.R
Retrocopy SCYLFHGVSDSLIVQLVAEMKAESFPAKANIILENESSTDCYVVVSGEVEAWTATLADGKERHVMRIGPR

Parental  GMAGEIGVMFNTPQPFTIRSRTLAQVVRISHSHMVQTVRPNTADGVIVFTNFVQYLESLKVKANEAAFVR
          GMAGEIGVM...PQPF..RSRTL.QV.RIS..H..QTVRPNTADG..VF.NF..YLES.K....EAAFV.
Retrocopy GMAGEIGVMLGVPQPFAVRSRTLTQVARISRAHLLQTVRPNTADGCVVFSNFIRYLESMKLQTKEAAFVS

Parental  DHLRNG-CTTVLG-GATMLNADESKGNAYRMLQCKEPKRVIIHEHLPDGSGTAPNGSPGKLVLLPDSFQE
          D.L.NG..TT.LG..ATML..DESK..A..ML.CKEPKRV.IHE.L....G.A...S.GKLVLLPDS.QE
Retrocopy DLLWNGKPTTILGRAATMLDVDESKETARKMLPCKEPKRVVIHEQLLSETGAA---SRGKLVLLPDSLQE

Parental  LMKLSERKFGKAARGILTVDGAEVDDIEVLRDGDHLFYS
          LMKL.E.KFGKAA.GILT..GAEV.DIEV.RDGDHLF.S
Retrocopy LMKLFEKKFGKAAGGILTLEGAEVEDIEVIRDGDHLFFS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Oryza brachyantha was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza brachyantha was not studied using ChIP-Seq data.

EST

Oryza brachyantha was not studied using EST data.

TSS

Oryza brachyantha was not studied using FANTOM5 data.

Lab

retro_obra_2 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza brachyantha 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA004342	1 retrocopy	retro_oind_32,
Oryza brachyantha	OB01G37960	1 retrocopy	retro_obra_2 ,
Oryza barthii	OBART01G29050	1 retrocopy	retro_obar_20,
Oryza glumaepatula	OGLUM01G33050	1 retrocopy	retro_oglu_27,
Oryza nivara	ONIVA01G33130	1 retrocopy	retro_oniv_11,
Oryza rufipogon	ORUFI01G32100	1 retrocopy	retro_oruf_17,
Oryza sativa japonica	OS01G0718700	1 retrocopy	retro_osat_1,
Setaria italica	Si003861m.g	1 retrocopy	retro_sita_40,