RetrogeneDB ID: retro_olat_32

Retrocopy location

• Organism: Medaka (Oryzias latipes)
• Coordinates: 2:7088531..7089346(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSORLG00000013353
• Aliases: None
• Description: None

Sequence

>retro_olat_32
ACCATTGGGGCCATCATCCGGAAGTGGAAAGAACACGGCATTACCATAAACCTGCCACGACCAGGTGCTCCTCGCAAGAT
TTCAGACAGAGGAGTCAGAACAATCATCAGAAAGGTTCTCCAACAGCCCAGGACCACTCGTGGAGAGCTTCAGAAAGACC
TGGAATCAGCAGGTACCGTTGTTTCAAAGAAAACAATAAGTAATGCACTCAACCGCCATGGCCTCCATGCACGCACACCA
CGAAAGACTCCATTTTTGAAGAAGAAGCATGTTGAAGCTCGTTTGGAGTTTGCGACAACATTTGGATAAACCCATGACAT
TGGAGAAGATACTCTGGTCAGATGAGACCAAAATTGAACTCTTCGGATGTCATAAGACACAACATGTTTGGAGGAAAAAT
GGCACCGCACATCACCCCCAAAACACCATACCAACAGTCAAGTTTGGAGGTGGGAGCATCATGGCGTGGGGCTGTTTTTC
AGCATGTGGCACTGGTAGACTTCATATCATTGAAGGAATAATGACTGGAGAAAAGTATCAAGACATTCTTGATCAGAATC
TGCTGTCATCTGCCAGGCTGCTAAAGATGAAAAGAGGGTGGATCTTTCAGCAAGACAACGATCCCAAGCACACAGCCAAG
GTAACACTCAACTGGTTGAAGAAAAAGAAAATAAAGCTGCTAGAATGGCCCAGTCAATCACCAGACTTGAATCCAATTGA
AAATCTTTGGAAAGAACTGAAGAGCCGGGTTCACAGAAGAGACCCCCGGAACCTTGAAGATTTGAAGGCCAATTCATGTG
GATGAATGGGCCAAA

Alignment

ORF - retro_olat_32 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.88 %
• Parental protein coverage: 90.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TFGAIIRKWKEHGITINLPRPGVPHKISDRGVRTKLNESTVGPRDDTGELQKDLESAGTVVSKKTISNAL
          T.GAIIRKWKEHGITINLPRPG.P.KISDRGVRT........PR...GELQKDLESAGTVVSKKTISNAL
Retrocopy TIGAIIRKWKEHGITINLPRPGAPRKISDRGVRTIIRKVLQQPRTTRGELQKDLESAGTVVSKKTISNAL

Parental  NRHGLHARTPRKTPFLKKKHVEARLEFAT-HLDKPMTCWEKILWSDETKIELFGCHKTQHVWRKNGSAHH
          NRHGLHARTPRKTPFLKKKHVEARLEFAT.HLDKPMT..EKILWSDETKIELFGCHKTQHVWRKNG.AHH
Retrocopy NRHGLHARTPRKTPFLKKKHVEARLEFAT>HLDKPMTL-EKILWSDETKIELFGCHKTQHVWRKNGTAHH

Parental  PQNTIPTVKFGGGSIMAWGCFSACGTGRLHIIEGIMTGEKYPDILDQNLLSSARLLKMKRGWIFQQDYHP
          PQNTIPTVKFGGGSIMAWGCFSACGTGRLHIIEGIMTGEKY.DILDQNLLSSARLLKMKRGWIFQQD..P
Retrocopy PQNTIPTVKFGGGSIMAWGCFSACGTGRLHIIEGIMTGEKYQDILDQNLLSSARLLKMKRGWIFQQDNDP

Parental  KHTAKVTLNWLKKKKIKLLEWPSQSPDLNPIENLWKELKIRVHRRDPRNLEDLKA-VCVDEWAK
          KHTAKVTLNWLKKKKIKLLEWPSQSPDLNPIENLWKELK.RVHRRDPRNLEDLKA...VDEWAK
Retrocopy KHTAKVTLNWLKKKKIKLLEWPSQSPDLNPIENLWKELKSRVHRRDPRNLEDLKA>IHVDEWAK

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_32 retrocopy.

TSS

Oryzias latipes was not studied using FANTOM5 data.

Lab

retro_olat_32 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_olat_32 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,