RetrogeneDB ID: retro_olat_2

Retrocopy location

• Organism: Medaka (Oryzias latipes)
• Coordinates: scaffold625:10394..11363(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSORLG00000018822
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSORLG00000003393
• Aliases: None
• Description: None

Sequence

>retro_olat_2
ATGTCTTTTCTCCGGACGGCTTTGAACAGCTCCGTCATCATTCATCCTCCAGGCTTCTACATCATCGGATTTGAGTCTTT
ACCATCTGTCAACATCTACTTCATCTTTCTAGCATTTGTTTATGTGGTTACAGTGCTGTTTAACGGTTTGCTGATTATTG
TTGTGGTTATTAATCCATCCTTACACACTCCAAAATTTCTGGCTGTCATCAACCTTGCAGTGATTGATTTATGTCTAAAC
ACTTGCACTATTCCTGGTATGATAAAGATATTTTTGGTTAAAGATAATTTTATCCCATTCAACTTGTGTTTGGTGCAAAT
GTTTATTTATTATGCATTTGCATCATTAGAGTCTTACGCCCTCACTATACTTGCTTATGACAGGTTGGTGGCTATTTGTT
TCCCTTTGCGCCAAAACTCCATCAACACAATGCGCAGCATGTGCTGCATCATCACCTTTACCTGGTCAATTTCTTTGGGG
GTCATGAGCTACATCACAAATTTGGTAACAAAACTGTCATTTTGTAACTCTGTCAGGGTGTTTAGTTATTTTTGTGACTA
TGCACCCGTGTTCAGGCTTGCCTGTAATGATTATTCAATGCAGTGGTTTGCAGGTTCCTTTTTGAGCATGCTGACCCTTG
CAGGGCCTTTTGCTTTCATAGTGCTGTCATACGTCAGCATCCTGGTGACTGTGTTCAGAATGAAGACTTTAGATCGGCGC
CTAAAAGCACTGGCTACTTGTGTGGAACACATCATCATTGTTGCAATCTTTTTTATTCCTCTTCTTGTCATTTTCACAAT
TGGCTACCATTTGGGAGCAGTTAACCCAGATCATAGAGTTCTAAGTCTGTCGATGGCCTCTTGCCTTCCACCTTGCATTA
ATCCTATTGTATATTCTTTGAAAACTAAAGAGATCAAAACCCGAGCACTGACGCTTATTAAAAAAAATACTATTATTCCG
ACTAAATCT

Alignment

ORF - retro_olat_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.26 %
• Parental protein coverage: 98.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSFLRTALNSSVIIHPPGFYIIGFESLPSVNIYFIFLAIVYVVTVLFNGLLIIVVVINPSLHTPKFLAVI
          MSFLRTALNSSVIIHPPGFYIIGFESLPSVNIYFIFLA.VYVVTVLFNGLLIIVVVINPSLHTPKFLAVI
Retrocopy MSFLRTALNSSVIIHPPGFYIIGFESLPSVNIYFIFLAFVYVVTVLFNGLLIIVVVINPSLHTPKFLAVI

Parental  NLAVIDLCLNTCTIPGMIKIFLVKDNFIPFNLCLVQMYFYYFFANSESYALTILAYDRLVAICFPLRQNS
          NLAVIDLCLNTCTIPGMIKIFLVKDNFIPFNLCLVQM..YY.FA..ESYALTILAYDRLVAICFPLRQNS
Retrocopy NLAVIDLCLNTCTIPGMIKIFLVKDNFIPFNLCLVQMFIYYAFASLESYALTILAYDRLVAICFPLRQNS

Parental  INTMRSMCCIITFTWCLVLGITTFSTSLMTKLSFCNSVRVFSYFCDYAPVFRLACNDYSMQWFAASFLSM
          INTMRSMCCIITFTW...LG.....T.L.TKLSFCNSVRVFSYFCDYAPVFRLACNDYSMQWFA.SFLSM
Retrocopy INTMRSMCCIITFTWSISLGVMSYITNLVTKLSFCNSVRVFSYFCDYAPVFRLACNDYSMQWFAGSFLSM

Parental  MTLVGPFAFIVLLLPSPCINPIVYSLKTKEIKTRALVLIRIKNTEVIQIFWIKFLFIMLL
          .TL.GPFAFIVL...S......V...KT......AL............IF.I..L.I...
Retrocopy LTLAGPFAFIVLSYVSILVT--VFRMKTLDRRLKALATC-VEHIIIVAIFFIPLLVIFTI

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_2 retrocopy.

TSS

Oryzias latipes was not studied using FANTOM5 data.

Lab

retro_olat_2 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_olat_2 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryzias latipes	ENSORLG00000003393	1 retrocopy	retro_olat_2 ,