RetrogeneDB ID: retro_olon_16

Retrocopy location

• Organism: Longstamen rice (Oryza longistaminata)
• Coordinates: KN540608.1:40648..42028(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: KN540608.1_FG002
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: KN538781.1_FG018
• Aliases: None
• Description: None

Sequence

>retro_olon_16
ATGGCCTTCCTGGGTCCTGCTGGATCCAAACGTGTCGGACTACAGATTTTGCATCAGTCCAACAGCAAAAGGGTGGAAGG
TCGTCGATTTTATGAACAAGTACTACGGAGCCGGGAAGTATGGCCAATTGATGGCGGAGTGTCTGAAGCTATATGTGCGC
CTCGCCGACGGGGCCTGGATCAATCAGAGTTGGCCATCACTGCAAACGACGGGGTCATCCGCTCCATCATAGAGGAAGAG
CTCACGGAAGAATCTGGCTGCCTGAAGATGGATCTTCACGGGATCGTACACGCCTCGTGTGTCACCGGCTACGTCGAGAT
CGCGGACAAGAACCTCATCATCCTCACCGTGTCTTTCTCCTTCGCTCGTGACAATTACTACCTCATCTACAATGCCACTC
TCCGGTCGCTCTCCATGATGCCCCACGTAGATGCTCATCCCTATTGCCAGGCCTACTACCCGTGCGACCCTCTCCCTGTG
CGCTACGGCGACGAGTGCACCCTTGTACTCCTCGCGCGGAACTTGGAGTACCAGAAAGAAGAACAAGGATGCAACTACTA
CCACCGTGATGTGCTCTGCCTGTGGCCGCCGCCGCCATCGTCGGAGATACCGCCTCTGCTGCTGCGGGACACCCCGGGTC
CCTCCATTGAGCCGTGGCACTTGAAGGAGCCCGTCTTCCCGGAGGGGAAGACGCCATCGGAGTTCCGCCACCACGTCAAG
TTCACGTCCAGAAGCCATGCTTTCTGGGCTGACCTCAAGAAGGGCGTCCTGTGCTGCCGCTGCAGCGACCTCTTCGACAG
CTACCACGTCAACTTCAGCTTCATCGAGCTGCCCCATGGGTGCGAGTGTGACGCCTTGGACATGCCGGATACTGCGCCGG
CGGAGATATACCGGACCATGGGTTGCACCTCTGGGAGCTCGATCAAGTTCGTCTCCATCTCCTTCGAAGATTCTATGCCG
GTGGATGAAAAGACCATGACAGTGTGGACTCTGGACACGGCCTCTTGGGGATGGACAAAGGATGTGGAGCTTAGCCTGGG
AAGTCTGTGGGAGCTGGAGGACTTCAAGAAGAATGGATTGCCGGAGACTCAGCCAGTCTACCCTCTCCTGAGGAAGGAGG
AAGATGAAGACAATGTCCTCTACTTCACGCTGTCCAGTTTACTGTTGGGGCCAATCAGCGAATGTGGGGAACCTGCGGTG
CACCACATGTGCCGCTTCGACATGAGAAGCATGAGGCTCGAGTCCAGCCCTCTTTCCTTTCCCCCAGATATGATTGTTCC
GCAGCGTTTGTTTGGCTCTGAGTTCTTCAGATACCTTGACCGTCATGTTCAGGTTCCTGGTTGTGGCAAAGGCAAGAGGA
AGTTGAATGAGGACTACTGA

Alignment

ORF - retro_olon_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.12 %
• Parental protein coverage: 59.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SYVTGYVRMADENLIILTVSFPFTDDQYYLVYDAILQSMSMIPHISSGPFCQGYSPANPLPVRCGDMYTL
          S.VTGYV..AD.NLIILTVSF.F..D.YYL.Y.A.L.S.SM.PH....P.CQ.Y.P..PLPVR.GD..TL
Retrocopy SCVTGYVEIADKNLIILTVSFSFARDNYYLIYNATLRSLSMMPHVDAHPYCQAYYPCDPLPVRYGDECTL

Parental  VHFARNMEYDEEEG--EYIYRDMLCLWPPPPSSKLPPPPLPNAYTCPSIEPWYFMEPCFPMEMTLVQFRH
          V..ARN.EY..EE....Y..RD.LCLWPPPPSS..PP..L......PSIEPW...EP.FP...T...FRH
Retrocopy VLLARNLEYQKEEQGCNYYHRDVLCLWPPPPSSEIPPLLLRDT-PGPSIEPWHLKEPVFPEGKTPSEFRH

Parental  HVKFTSSSYAFWADLTQGVLCCCSSDIFGDSYSVNFSFIELPPGCECESCDTLDVSDIGPAEMFRTIGCT
          HVKFTS.S.AFWADL..GVLCC..SD.F.DSY.VNFSFIELP.GCEC...D.LD..D..PAE..RT.GCT
Retrocopy HVKFTSRSHAFWADLKKGVLCCRCSDLF-DSYHVNFSFIELPHGCEC---DALDMPDTAPAEIYRTMGCT

Parental  TGDSIKFISISFDDSVPETEKTVEELSLGTL-WELEDFKKYGLPKTKPLYPLLRKGEEDDGALYFILSNE
          .G.SIKF.SISF.DS.P..EKT.....L.T..W.........L.....L......G.......Y..L..E
Retrocopy SGSSIKFVSISFEDSMPVDEKTMTVWTLDTASWGWTKDVELSLGSLWELEDFKKNGLPETQPVYPLLRKE

Parental  WDD
          .D.
Retrocopy EDE

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_16 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza longistaminata	KN538781.1_FG018	1 retrocopy	retro_olon_16 ,