RetrogeneDB ID: retro_olat_56

Retrocopy location

• Organism: Medaka (Oryzias latipes)
• Coordinates: scaffold645:73186..73909(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSORLG00000014268
• Aliases: None
• Description: None

Sequence

>retro_olat_56
TGGGAAATTTTACCTCTATCCCTACTGGGTAGAGTAGAAGCGGTGAGGATGAATGTGCTTCCTCGTCTTTTGTTTTTGTT
TCAATCTCTTCCGGTAAACATTCCGGTGTCAACTTTCAACGTGTTAAACAAAATGATTACTCAATTTATATGGCAGCGAA
AAAGACCCAGAATTAGATTAAAAACATTATTTTTGCCAAAAAATAAGGGAGGTTTGGCTCTACCAAACCTAAAATTTTAC
TATTGGGCAGCTCAGTTGACGGCAATCGTGGCCTGGATTAGAGAGGATGAGGAAGTAAAATGGTTTAAAGTGGAACAAGG
TGAAACTAAAGGGCTGTGGCTGTCTACTCTTCCATTTACTGATTTAAAATCTGTCAACAAAATCAAAATTGGAAACAATT
GGATCAAGCATACTTTAAAGATATGGACGGTAGTAAAAAAAATGCTACTTGACACAGGGTCAATTTCCAGAGCAATGCCT
ATTGTCGGTAATATAGACTTTCTGCCTTCAATGTGGGATCCCACCTTTAAGACATGGGCCACTAAAGGCCTTATAACTCT
TAACCAGTTGTTCAATGGAACAGAACTTAAGTCCTTTTCACAGCTTCAAGGACAATTTGGACTTCTGCCGAATGATTTTT
ATAAATATCTACAAATCAGGCATTACATCATGAAGCACAAAGAGCGAGACAGAATCAATAAAACCCCAAACTGCATAGAA
CAA

Alignment

ORF - retro_olat_56 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.53 %
• Parental protein coverage: 51.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WNISNLNQVLLKXEAARMNVLPRLL-LFQSLPVNIPVSTFNVLNKMITQFIWQRKRPRIRLKTLFLPKNK
          W.I..L...L...EA.RMNVLPRLL.LFQSLPVNIPVSTFNVLNKMITQFIWQRKRPRIRLKTLFLPKNK
Retrocopy WEILPLS-LLGRVEAVRMNVLPRLLFLFQSLPVNIPVSTFNVLNKMITQFIWQRKRPRIRLKTLFLPKNK

Parental  GGLALPNLKFYYWAAQLTAIVAWIREDEEVKWFKVEQGETKGVRLSTLPFTDLKSVNKIKIGNNWIKHTL
          GGLALPNLKFYYWAAQLTAIVAWIREDEEVKWFKVEQGETKG..LSTLPFTDLKSVNKIKIGNNWIKHTL
Retrocopy GGLALPNLKFYYWAAQLTAIVAWIREDEEVKWFKVEQGETKGLWLSTLPFTDLKSVNKIKIGNNWIKHTL

Parental  EIWTVVKKMLLDTGSISRAMPIVGNIDFPPSMWDPTFKTWATKGLITLNQLFDGTELKSNFSQLQRQFGL
          .IWTV....LLDTGSISRAMPIVGNIDF.PSMWDPTFKTWATKGLITLNQLF.GTELKS.FSQLQ.QFGL
Retrocopy KIWTVXXXXLLDTGSISRAMPIVGNIDFLPSMWDPTFKTWATKGLITLNQLFNGTELKS-FSQLQGQFGL

Parental  LPNDFYTYLQIRHYIMKHKERDRINKTPNCIEQ
          LPNDFY.YLQIRHYIMKHKERDRINKTPNCIEQ
Retrocopy LPNDFYKYLQIRHYIMKHKERDRINKTPNCIEQ

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_56 retrocopy.

TSS

Oryzias latipes was not studied using FANTOM5 data.

Lab

retro_olat_56 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_olat_56 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryzias latipes	ENSORLG00000003375	1 retrocopy	retro_olat_21,
Oryzias latipes	ENSORLG00000014268	1 retrocopy	retro_olat_56 ,