RetrogeneDB ID: retro_olat_6

Retrocopy location

• Organism: Medaka (Oryzias latipes)
• Coordinates: 7:17099101..17100166(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSORLG00000010599
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RHO (2 of 2)
• Ensembl ID: ENSORLG00000010979
• Aliases: None
• Description: rhodopsin [Source:HGNC Symbol;Acc:10012]

Sequence

>retro_olat_6
ATGAATGGCACAGAGGGACCATATTTTTATGTCCCTATGGTGAACACCACCGGCATTGTCCGGAGTCCTTATGAATATCC
TCAGTATTACCTTGTCAGCCCAGCAGCCTATGCTGCTCTGGGTGCCTACATGTTTTTTCTCATCCTGGTTGGCTTCCCCA
TCAACTTCCTCACTCTCTACGTCACCCTCGAACACAAGAAGCTGCGAACCCCTCTAAACTACATCCTGCTAAACCTCGCG
GTGGCCGACCTCTTCATGGTGTTCGGAGGATTCACTACAACGATGTACACCTCCATGCACGGCTACTTTGTCCTTGGACG
TCTCGGCTGCAATCTGGAAGGATTCTTTGCTACCCTTGGTGGTGAAATTGGTCTCTGGTCACTGGTTGTTCTGGCTATTG
AGAGATGGGTGGTTGTCTGCAAGCCCATCAGCAACTTCCGCTTTGGTGAGAATCATGCTATTATGGGTTTGGTCTTCACC
TGGATCATGGCTGCCTCCTGTGCCGTGCCCCCTCTCGTCGGCTGGTCTCGTTACATCCCAGAGGGCATGCAGTGCTCATG
TGGAGTCGACTACTACACCCGTGCAGAGGGCTTCAACAACGAGTCCTTTGTTGTCTACATGTTCGTCTGCCACTTCCTAA
TTCCACTGATCGTTGTGTTCTTCTGCTACGGCCGTCTGCTCTGCGCTGTCAAGGAGGCTGCTGCTGCCCAGCAGGAGTCT
GAGACCACCCAGAGAGCTGAGAGGGAAGTCACCCGCATGGTTGTCATCATGGTCATCGGCTTCCTGGTATGTTGGCTTCC
CTATGCCAGTGTGGCCTGGTACATCTTCACAAATCAGGGCTCTGAATTCGGGCCACTCTTCATGACCATCCCAGCCTTCT
TTGCCAAGAGTTCTTCCATCTACAACCCAGCAATCTACATCTGCATGAACAAGCAGTTCCGCAACTGCATGATCACCACC
CTGTGCTGTGGGAAGAATCCCTTTGAAGAGGAGGAGGGAGCCTCCACTACTGCTTCCAAGACCGAGGCCTCATCTGTCTC
CTCAAGCTCTGTGTCCCCTGCATAA

Alignment

ORF - retro_olat_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.73 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNGTEGPDFYVPMSNRTGLVRSPFEYPQYYLAEPWKYSLLAAYMLFLIITAFPINFLTLHVTVKHKKLRN
          MNGTEGP.FYVPM.N.TG.VRSP.EYPQYYL..P..Y..L.AYM.FLI...FPINFLTL.VT..HKKLR.
Retrocopy MNGTEGPYFYVPMVNTTGIVRSPYEYPQYYLVSPAAYAALGAYMFFLILVGFPINFLTLYVTLEHKKLRT

Parental  PLNYVLLNLAVADLFMIVGGFTVTLYTALHGYFILGVTGCNVEGFFATLGGEIALWSLVVLAIERYVVVC
          PLNY.LLNLAVADLFM..GGFT.T.YT..HGYF.LG..GCN.EGFFATLGGEI.LWSLVVLAIER.VVVC
Retrocopy PLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVLGRLGCNLEGFFATLGGEIGLWSLVVLAIERWVVVC

Parental  KPMTNFRFEEKHAIAGLAFSWVMALTCAAPPLFGWSRYIPEGMQCSCGIDYYTPKPEINNTSFVIYMFVL
          KP..NFRF.E.HAI.GL.F.W.MA..CA.PPL.GWSRYIPEGMQCSCG.DYYT.....NN.SFV.YMFV.
Retrocopy KPISNFRFGENHAIMGLVFTWIMAASCAVPPLVGWSRYIPEGMQCSCGVDYYTRAEGFNNESFVVYMFVC

Parental  HFSIPLFIIFFCYSRLLCTVRAAAALQQESETTQRAEREVTRMVIVMVISFLVCWVPYATVAWYIFANQG
          HF.IPL...FFCY.RLLC.V..AAA.QQESETTQRAEREVTRMV..MVI.FLVCW.PYA.VAWYIF.NQG
Retrocopy HFLIPLIVVFFCYGRLLCAVKEAAAAQQESETTQRAEREVTRMVVIMVIGFLVCWLPYASVAWYIFTNQG

Parental  TEFGPVFMTVPAFFAKSAALYNPVIYILLNRQFRNCMITTVCCGKNPFGEDDAGA--VSKTQTSSVSSSQ
          .EFGP.FMT.PAFFAKS...YNP.IYI..N.QFRNCMITT.CCGKNPF.E........SKT..SSVSSS.
Retrocopy SEFGPLFMTIPAFFAKSSSIYNPAIYICMNKQFRNCMITTLCCGKNPFEEEEGASTTASKTEASSVSSSS

Parental  VAPA
          V.PA
Retrocopy VSPA

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_6 retrocopy.

TSS

Oryzias latipes was not studied using FANTOM5 data.

Lab

retro_olat_6 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_olat_6 has 1 orthologous retrocopies within teleost group .

Species	RetrogeneDB ID
Gasterosteus aculeatus	retro_gacu_20

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Gadus morhua	ENSGMOG00000013755	1 retrocopy	retro_gmor_7,
Oreochromis niloticus	ENSONIG00000017219	1 retrocopy	retro_onil_16,
Oryzias latipes	ENSORLG00000010979	1 retrocopy	retro_olat_6 ,
Tetraodon nigroviridis	ENSTNIG00000017925	1 retrocopy	retro_tnig_20,
Takifugu rubripes	ENSTRUG00000010617	1 retrocopy	retro_trub_18,
Xiphophorus maculatus	ENSXMAG00000017297	1 retrocopy	retro_xmac_11,