RetrogeneDB ID: retro_olat_53

Retrocopy location

• Organism: Medaka (Oryzias latipes)
• Coordinates: scaffold2868:6979..7743(-)
• 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_53
ACCATTGGGGCCATTATCCGGAAGTGGAAAGAACACGGCATTACCATAAACCTGCCACGGCCAGGTGCTCCTCGCAAGAT
TTCAGACAGAGGCGTCAGAACAATCATCAGAAGGGTTCTCCAACAGCCCAGGACCATTCGTGGAGATTTTCAGAAAGACC
TGGAATCAGCAGGTACCGTTGTTTCAAAGAAAATAATAAGTAATGCACTTATCCGCCATGGCCTCCATGCACGCACACCA
CGCAAAAACTCCATTTTTGAAGAAGAAGCATGTTGAAGCTTGTTTGGAGTTAGCGACAACATTTGGATAAACCCATGACA
TTCTGGGAGAAGATACTCTGGTCAGATGAGACCAAAATTGAACTCTTTGGATGTCATAAGACACAACATGTTTGGAGGAA
AAATGGCACCGCACATCTCCCCCAAAACACCATACCAACAGTCAAGTTTGGAGGTAGGAGTATCATGGTGTGGGGCTGTT
TTTCAGCATGCGGTACTGGTAGACTTCATGTCATTGAAGGAATAATGACTGGAGAAAAGTATCGAGACATTCTTGATCAG
AATCTGCTGTCATCTGCCAGGCTGCTGAAGATGAAAAGAGGGTGGATCTTTCAGCAAAACAACGATCCCAAGAACACAGC
CAAGGTAACACTCAACTGGTTGAAGAAAAAGAAAATAAAGCTGCTAGAATGGCCCAGTCAATCCCCAGACTTGAATCCAA
TTGAAAATCTTTGTAAAGAACTCAAGATCCGGGTTCACAGAAGA

Alignment

ORF - retro_olat_53 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.72 %
• Parental protein coverage: 84.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TFGAIIRKWKEHGITINLPRPGVPHKISDRGVRTKLNESTVGPRDDTGELQKDLESAGTVVSKKTISNAL
          T.GAIIRKWKEHGITINLPRPG.P.KISDRGVRT........PR...G..QKDLESAGTVVSKK.ISNAL
Retrocopy TIGAIIRKWKEHGITINLPRPGAPRKISDRGVRTIIRRVLQQPRTIRGDFQKDLESAGTVVSKKIISNAL

Parental  NRHGLHARTPRK-TPFLKKKHVEARLEFAT-HLDKPMTCWEKILWSDETKIELFGCHKTQHVWRKNGSAH
          .RHGLHARTPRK.TPFLKKKHVEA.LE.AT.HLDKPMT.WEKILWSDETKIELFGCHKTQHVWRKNG.AH
Retrocopy IRHGLHARTPRK>TPFLKKKHVEACLELAT>HLDKPMTFWEKILWSDETKIELFGCHKTQHVWRKNGTAH

Parental  HPQNTIPTVKFGGGSIMAWGCFSACGTGRLHIIEGIMTGEKYPDILDQNLLSSARLLKMKRGWIFQQDYH
          .PQNTIPTVKFGG.SIM.WGCFSACGTGRLH.IEGIMTGEKY.DILDQNLLSSARLLKMKRGWIFQQ...
Retrocopy LPQNTIPTVKFGGRSIMVWGCFSACGTGRLHVIEGIMTGEKYRDILDQNLLSSARLLKMKRGWIFQQNND

Parental  PKHTAKVTLNWLKKKKIKLLEWPSQSPDLNPIENLWKELKIRVHRR
          PK.TAKVTLNWLKKKKIKLLEWPSQSPDLNPIENL.KELKIRVHRR
Retrocopy PKNTAKVTLNWLKKKKIKLLEWPSQSPDLNPIENLCKELKIRVHRR

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_53 retrocopy.

TSS

Oryzias latipes was not studied using FANTOM5 data.

Lab

retro_olat_53 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_olat_53 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,