RetrogeneDB ID: retro_olat_24

Retrocopy location

• Organism: Medaka (Oryzias latipes)
• Coordinates: 13:31190005..31190444(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSORLG00000018244
• Aliases: None
• Description: None

Sequence

>retro_olat_24
ATGGCCTCCACTCCTTCCGCCTTTCCCCCTTTCTCCTGCCCCATGTGCCATATGTTTAGTGAGGATCCTGCCTCCTTTAG
TGAAGACAGCGGTAGGTGTGTTAAGTGTAGTCTTGTGTTAGACTTGAAGGCCAGGCTGGAGCAGTTAGAAGCGCGGCTCC
GCACAGTGGAAGCTAAGCTGGCTAGCTAGGTCGTTACTCGTAGCGTGCCGCACTGCCAGGGCTAACCCAGTTAGCACCCC
AGCACCTTCCCAGCAGCCGGGAAACACACAGGGTTTTGCACCGGTTGGGAGGAAACATAGTGCTAAACGCAAGAACTTAG
AGCATCCGAGACTCCACGTTAGTAATAGGTTCTCCCCCCTCAGCGACACACCCGCTGAACACTCAACTCTGGTTATAGGC
TCTTCTGAAGTTAGAAACGTGGAGCTCCCAGCGGCTACA

Alignment

ORF - retro_olat_24 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.95 %
• Parental protein coverage: 53.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MATTPSAFPPFSCSMCHMFSEDPASFSEDSGRCVKCSLVLDLETRLEQLEARRKFASLPATYVSTGRRGL
          MA.TPSAFPPFSC.MCHMFSEDPASFSEDSGRCVKCSLVLDL..RLEQLEAR..............R...
Retrocopy MASTPSAFPPFSCPMCHMFSEDPASFSEDSGRCVKCSLVLDLKARLEQLEARLRTVEAKLAS*VVTRSVP

Parental  RCRANP-VSTPAPSQQPGNTQGFAPVGRKHSAKRKNLEHPRLHVNNRFSPLSDTPAEPSTLVIGSSEVRN
          .C...P.VSTPAPSQQPGNTQGFAPVGRKHSAKRKNLEHPRLHV.NRFSPLSDTPAE.STLVIGSSEVRN
Retrocopy HCQG*P>VSTPAPSQQPGNTQGFAPVGRKHSAKRKNLEHPRLHVSNRFSPLSDTPAEHSTLVIGSSEVRN

Parental  VELPAAT
          VELPAAT
Retrocopy VELPAAT

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_24 retrocopy.

TSS

Oryzias latipes was not studied using FANTOM5 data.

Lab

retro_olat_24 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_olat_24 has 0 orthologous retrocopies within teleost group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Oryzias latipes	ENSORLG00000018244	1 retrocopy	retro_olat_24 ,