RetrogeneDB ID: retro_olon_21

Retrocopy location

• Organism: Longstamen rice (Oryza longistaminata)
• Coordinates: KN538949.1:93898..94390(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: KN538949.1_FG009
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: KN538949.1_FG004
• Aliases: None
• Description: None

Sequence

>retro_olon_21
ATGGAAGCACAAGCACAGGTTGCCTTGACGAAATCCATCCAACCAGACACCAGCAACGAGGAAATGACATCAGGCAATGT
TGCCGGTAACAATGTTTTACTGCCATTATCCAACAGAACTGAAGCTCCTACTCCGAGGCATGTGATTGTCACTATTTCGC
TCGATGCTGGCCAGAACACAATGGTTGACGACAATGGTGTTAGACAGGGATTAACAGACGAGGAATCCGATACTAAAACG
AAGCTGTTGGAAAGAGGTGTTCTCACGGCTGCCTCTGCTACTGCAGCAATGCTCTCTCATTTCCTGAAAGGAGTATTCAA
TCATCACCAAGAGGGTTACTACATCATCCTCGTCGTATTTCTTATGACGGGGTTGATTCTGGCAACCACTGCCACATGGC
TCGCCCGTAGGCACTCCGCCAAGGTGGTTGTCCTTCTTGCACTAGTCCCACAGGTTCTTGTGGCTGGTGTGATTACCTCA
ACATTTTCTTGA

Alignment

ORF - retro_olon_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.38 %
• Parental protein coverage: 57.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IEAPGHVVVTNS--SDVGQDTMVNNNVAGNYVLLPLSNRSEAP--RHVIVTISLDAGQNTVVDDNGVRQG
          .EA...V..T.S...D.....M...NVAGN.VLLPLSNR.EAP..RHVIVTISLDAGQNT.VDDNGVRQG
Retrocopy MEAQAQVALTKSIQPDTSNEEMTSGNVAGNNVLLPLSNRTEAPTPRHVIVTISLDAGQNTMVDDNGVRQG

Parental  LADEESDTTTKLLERGVLTAASATAAMLSPFLRGVLNHHQEGVIILPLHGLDEGLGHDSCGTLEASLIDG
          L.DEESDT.TKLLERGVLTAASATAAMLS.FL.GV.NHHQEG..I.....L..GL......T..A.....
Retrocopy LTDEESDTKTKLLERGVLTAASATAAMLSHFLKGVFNHHQEGYYIILVVFLMTGLILATTATWLARRHSA

Parental  GIVIRMASFVLPDVSVCCV
          ..V...A....P.V.V..V
Retrocopy KVVVLLA--LVPQVLVAGV

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_21 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	KN538949.1_FG004	1 retrocopy	retro_olon_21 ,