RetrogeneDB ID: retro_olat_61

Retrocopy location

• Organism: Medaka (Oryzias latipes)
• Coordinates: scaffold764:43413..43902(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSORLG00000020283
• Aliases: None
• Description: None

Sequence

>retro_olat_61
GTGTTCCTGATCTGCCTGTGCTGGGGCTGCTCCGCCCTCTACAACGGCTGCATTCTGATGGGACAGCGGCCGCACAGGGT
CCACAGCTGCCACGGCGAGTGCGTGGTGGTCATCAGCCACACATCAGGAAGTGTCCACCTGTTCCTCTGGTTAGTCGGCC
CCTGCTCTGTCATGCTGGTGCTGTACGCCCGGGTGTTGGTGGCGGCCGTGTCTCAGGTCTGGCGCCTGCAGACGGTCCCT
TCTGTTCCCACGGTGAAGAGGTCGGAGTGGAAAGCAGCCCGGACCCTGGGCATGGTGATGGCAGTGTTTCTCATGTGCTT
CTGCCCGTACTACTACCCTTCCCTGGCAGGCCAAGACCCCCCCACAAAGCCGTGGTATTATGCCATCTTATCTTGGGTCA
TGCTGCTGAACTCCTGCATGAATCCCCTCATCTATGCCTTGTTCTATCCCTGCTTCAGGAAGACCACCAGACTGATCTTC
ACCCTTAAA

Alignment

ORF - retro_olat_61 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.12 %
• Parental protein coverage: 55. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VFLICLCWGCSTLYNDCILMGHLQRPHRVHSCHGECVVVISHTSGTVHLFFWLVGPRSVMLVLYARVLVA
          VFLICLCWGCS.LYN.CILMG..QRPHRVHSCHGECVVVISHTSG.VHLF.WLVGP.SVMLVLYARVLVA
Retrocopy VFLICLCWGCSALYNGCILMG--QRPHRVHSCHGECVVVISHTSGSVHLFLWLVGPCSVMLVLYARVLVA

Parental  AVSQVWRLQTVPSVPTVKRWEWKAARTLGMVMAVFLMCFCPYYYPSLAGQDPPTKLWMFCLLSWVMLLNS
          AVSQVWRLQTVPSVPTVKR.EWKAARTLGMVMAVFLMCFCPYYYPSLAGQDPPTK.W....LSWVMLLNS
Retrocopy AVSQVWRLQTVPSVPTVKRSEWKAARTLGMVMAVFLMCFCPYYYPSLAGQDPPTKPWYYAILSWVMLLNS

Parental  CMNPLIYALFYPCFRKTTRLIFTLK
          CMNPLIYALFYPCFRKTTRLIFTLK
Retrocopy CMNPLIYALFYPCFRKTTRLIFTLK

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_61 retrocopy.

TSS

Oryzias latipes was not studied using FANTOM5 data.

Lab

retro_olat_61 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_olat_61 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	ENSORLG00000002214	1 retrocopy	retro_olat_9,
Oryzias latipes	ENSORLG00000020283	1 retrocopy	retro_olat_61 ,