RetrogeneDB ID: retro_obar_17

Retrocopy location

• Organism: Oryza barthii
• Coordinates: 1:9679316..9680105(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OBART01G12400
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OBART05G09920
• Aliases: None
• Description: None

Sequence

>retro_obar_17
ATGCGGTTCGCCATCAGCAACAACGTGACGGTGCGAGGGCTCAAGGTGCAGAACAGCCCGGAGTTCCACTTCCGGTTCGA
CAACTGCAACGGCGTGCGCGTCGACGGCCTGTCCATCAGCTCGCCGGCGCTGAGCCCCAACACCGACGGCATCCACGTCG
AGAACACCCAGGACGTCCTCATCACCAACACCGTCGTCTCCAACGGCGACGACTGCGTCTCCATCGGCGCCGGCACGCTC
AACGTCCACATCGAGAACGTCACCTGCGGGCCCGGGCACGGCATCAGCATCGGCAGCTTGGGGAAGGCCGGGACCAAGGC
GTGCGTGGCGAACGTGACGGTGCGGAACGCGGTGATCCGGCACTCGGACAACGGCGTGCGCATCAAGACGTGGCAGGGCG
GGTCCGGCTCCGTGTCGGCGGTGGCGTTCGAGAACGTGAGGATGGACGCGGTGCGCAACCCCATCATCATCGACCAGTAC
TACTGCCTCTCCAAGAGCTGCGAGAACGAGACCACCGCCGTGTTCGTCAACGGCGTCTCCTACTCCGGCATCCGGGGCAC
CTACGACGTGCGCGGCCCGCCCATCCACTTCGGCTGCAGCGACGCCGTGCCGTGCACCAACATCACGCTCTCCGACGTCG
AGCTGCTGCCGGCGTCCGGCGACACCGTCGACGAGCCCTTCTGCTGGAACGTCTACGGCAACGCCGCCACGCCCACCGTG
CCGCCGGTGTCGTGCCTCAGCTCCGGCTTCCCCAACTACACCGAGAAAAAGGACCTCCAGTGTTACTGA

Alignment

ORF - retro_obar_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.18 %
• Parental protein coverage: 54.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VRFFMSRNLVVEGLRVENSPEFHFRFDGCSDVRVDGLSIRSPANSPNTDGIHVENTQRVAIYNSMISNGD
          .RF..S.N..V.GL.V.NSPEFHFRFD.C..VRVDGLSI.SPA.SPNTDGIHVENTQ.V.I.N...SNGD
Retrocopy MRFAISNNVTVRGLKVQNSPEFHFRFDNCNGVRVDGLSISSPALSPNTDGIHVENTQDVLITNTVVSNGD

Parental  DCISIGTGSYDVDIQNVSCGPGHGISIGSLGVHNSQACVANVTVRNAVIRNSDNGLRIKTWQGGMGSVSG
          DC.SIG.G...V.I.NV.CGPGHGISIGSLG.....ACVANVTVRNAVIR.SDNG.RIKTWQGG.GSVS.
Retrocopy DCVSIGAGTLNVHIENVTCGPGHGISIGSLGKAGTKACVANVTVRNAVIRHSDNGVRIKTWQGGSGSVSA

Parental  INFDTVSMENVRNCIIIDQYYCLDKRCMNQSTAVHVTDVSYANVRGSYDVRAAPIHFACSDTVPCTNITM
          ..F..V.M..VRN.IIIDQYYCL.K.C.N..TAV.V..VSY...RG.YDVR..PIHF.CSD.VPCTNIT.
Retrocopy VAFENVRMDAVRNPIIIDQYYCLSKSCENETTAVFVNGVSYSGIRGTYDVRGPPIHFGCSDAVPCTNITL

Parental  SEVELLPFSGELVDDPFCWSAYGLQQTPTIPPIYCLQDGLPDSLLDNPDLRC
          S.VELLP.SG..VD.PFCW..YG...TPT.PP..CL..G.P.......DL.C
Retrocopy SDVELLPASGDTVDEPFCWNVYGNAATPTVPPVSCLSSGFP-NYTEKKDLQC

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza barthii was not studied using ChIP-Seq data.

EST

Oryza barthii was not studied using EST data.

TSS

Oryza barthii was not studied using FANTOM5 data.

Lab

retro_obar_17 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza barthii 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza longistaminata	KN539869.1_FG002	1 retrocopy	retro_olon_18,
Oryza barthii	OBART05G09920	1 retrocopy	retro_obar_17 ,
Oryza sativa japonica	OS05G0279900	1 retrocopy	retro_osat_7,