RetrogeneDB ID: retro_olon_18

Retrocopy location

• Organism: Longstamen rice (Oryza longistaminata)
• Coordinates: KN540774.1:33949..34738(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: KN540774.1_FG001
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: KN539869.1_FG002
• Aliases: None
• Description: None

Sequence

>retro_olon_18
ATGCGGTTCGCCATCAGCAACAACGTGACGGTGCGAGGGCTCAAGGTGCAGAACAGCCCGGAGTTCCACTTCCGGTTTGA
CAACTGCAACGGCGTGCGCGTCGACGGCCTGTCCATCAGCTCGCCGGCGCTGAGCCCCAACACCGACGGCATCCACGTCG
AGAACACCCAGGACGTCCTCATCACCAACACCGTCGTCTCCAACGGCGACGACTGCGTCTCCATCGGCGCCGGCACGCTC
AACGTCCACATCGAGAACGTCACCTGCGGGCCCGGGCACGGCATCAGCATCGGCAGCCTGGGGAAGGCCGGGACCAAGGC
GTGCGTGGCGAACGTGACGGTGCGGAACGCGGTGATCCGGCACTCGGACAACGGCGTGCGCATCAAGACGTGGCAGGGCG
GGTCCGGCTCCGTGTCGGCGGTGGCGTTCGAGAACGTGAGGATGGACGCGGTGCGCAACCCGATCATCATCGACCAGTAC
TACTGCCTCACCAAGAGCTGCGAGAACGAGACCACCGCCGTGTTCGTGAACGGCGTCTCCTACTCCGGCATCCGGGGCAC
CTACGACGTGCGCGGCCCGCCCATCCACTTCGGCTGCAGCGACGCCGTGCCGTGCACCAACATCACGCTCTCCGACGTCG
AGCTGCTGCCGGCGTCCGGCGACACCGTCGACGAGCCCTTCTGCTGGAACGTCTACGGCAACGCCGCCACGCCCACCGTG
CCGCCGGTGTCGTGCCTCAGCGCCGGCTTCCCCAACTACACCGAGAAAAAGGACCTCCAGTGTTACTGA

Alignment

ORF - retro_olon_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.79 %
• Parental protein coverage: 53.8 %
• 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  ISFDTVSMENVRNCIIIDQYYCLDKRCMNQSTAVHVTDVSYANVRGSYDVRAAPIHFACSDTVPCTNITM
          ..F..V.M..VRN.IIIDQYYCL.K.C.N..TAV.V..VSY...RG.YDVR..PIHF.CSD.VPCTNIT.
Retrocopy VAFENVRMDAVRNPIIIDQYYCLTKSCENETTAVFVNGVSYSGIRGTYDVRGPPIHFGCSDAVPCTNITL

Parental  SEVELLPFSGELVDDPFCWSAYGLQQTPTIPPIYCLQDGLSDSLLDNPDLRC
          S.VELLP.SG..VD.PFCW..YG...TPT.PP..CL..G.........DL.C
Retrocopy SDVELLPASGDTVDEPFCWNVYGNAATPTVPPVSCLSAGF-PNYTEKKDLQC

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza longistaminata was not studied using ChIP-Seq data.

EST

Oryza longistaminata was not studied using EST data.

TSS

Oryza longistaminata was not studied using FANTOM5 data.

Lab

retro_olon_18 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza longistaminata 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,