RetrogeneDB ID: retro_olat_31

Retrocopy location

• Organism: Medaka (Oryzias latipes)
• Coordinates: 18:1911911..1912554(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSORLG00000018922
• Aliases: None
• Description: None

Sequence

>retro_olat_31
GCAAGACTCCATTTTTGAAGAAGAAGCATGTTGAAGCTCGTTTGGAGTTTGCCACACAACATTTGGTTAACCCATGACAT
TCTGGGAGAAGATACTCTGGTCAGATGAGACCAAAATTGAACTCTTTTGGAGAAAAAATGGCACCGCACATCACCCCCAA
AACACCATACCAACAGTCAAGTTTGGAGGTGGGAGCATCATGGCGTGGGGCTGTTTTTCAGCATGTGGCACTGGTAGACT
TCATATCATTGAAGGAATAATGACTGGAGAAAAGTATGGAGACATTCTTGATCAGAATCTGCTGTCATCTGCCAGGCTGC
TGAAGATGAAAAGAGGGTGGATCTTTCATCAAGATAACGATCCAAAGCACACAGCCAAGGTAACACTCAACTGGTTGAAG
AAAAAGAAAATCAAGCTGCTAGAATGGCCCAGTCAATCGCCAGACTTGAATCCAATTGAAAATCTTTGGAAAGAACTGAA
GATCCGGGTTCACTGAAGAGACCCCCGGAACCTTGAAGATTTGAAGGCAGTTTGTGTGGATGAATGGGCCAAAATCACAC
CTGAGCAATGTATTCCACTGGTTTCTCCATACAGGAGGCGTCTTGAGGCTGGAATCACCAACAAAGGTTTTTGCACTAAG
TAT

Alignment

ORF - retro_olat_31 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.93 %
• Parental protein coverage: 62.43 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ARLEFATQHLIFTV-GVAKNNWETVKYFEEIPLIYFDX--TCLEEKWH-PHQPQNTIPTVKFGGGSIMAW
          ARL.F........V.....N.W.T.....E..L...D...T.LE.KWH..H.PQNTIPTVKFGGGSIMAW
Retrocopy ARLHF*RRSMLKLVWSLPHNIWLTHDILGEDTLVR*DQN*TLLEKKWH>AHHPQNTIPTVKFGGGSIMAW

Parental  GCFSACGTGRLHIIEGIMTGKKYRDILDQNLLSSARLLKMKRGWIFQQDNDPKHTAKVTLNWLKKKKIKL
          GCFSACGTGRLHIIEGIMTG.KY.DILDQNLLSSARLLKMKRGWIF.QDNDPKHTAKVTLNWLKKKKIKL
Retrocopy GCFSACGTGRLHIIEGIMTGEKYGDILDQNLLSSARLLKMKRGWIFHQDNDPKHTAKVTLNWLKKKKIKL

Parental  LQWPSQSPDLNPIENLWKELKIRVNRRDPRNLEDLKAVCVDEWAKITPEQCIPLVSPYRRRLEAVITNKG
          L.WPSQSPDLNPIENLWKELKIRV..RDPRNLEDLKAVCVDEWAKITPEQCIPLVSPYRRRLEA.ITNKG
Retrocopy LEWPSQSPDLNPIENLWKELKIRVH*RDPRNLEDLKAVCVDEWAKITPEQCIPLVSPYRRRLEAGITNKG

Parental  FCTKY
          FCTKY
Retrocopy FCTKY

Legend:

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

Expression

RNA-Seq

Oryzias latipes was not studied using RNA-Seq expression data.

ChIP-Seq

Oryzias latipes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_olat_31 retrocopy.

TSS

Oryzias latipes was not studied using FANTOM5 data.

Lab

retro_olat_31 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_olat_31 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryzias latipes	ENSORLG00000010891	1 retrocopy	retro_olat_22,
Oryzias latipes	ENSORLG00000013353	2 retrocopies	retro_olat_32, retro_olat_53,
Oryzias latipes	ENSORLG00000014457	2 retrocopies	retro_olat_35, retro_olat_43,
Oryzias latipes	ENSORLG00000018922	1 retrocopy	retro_olat_31 ,
Oryzias latipes	ENSORLG00000019689	1 retrocopy	retro_olat_40,
Oryzias latipes	ENSORLG00000019879	1 retrocopy	retro_olat_28,
Oryzias latipes	ENSORLG00000020726	1 retrocopy	retro_olat_26,