RetrogeneDB ID: retro_onil_10

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL831416.1:128610..130011(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSONIG00000020410
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: OPN4 (1 of 3)
• Ensembl ID: ENSONIG00000015868
• Aliases: None
• Description: opsin 4 [Source:HGNC Symbol;Acc:14449]

Sequence

>retro_onil_10
ATGAGTCACATCCACTCGAGCAGGAAGTCAGCTCTGTGCCCTCTGGGAGGAAACTGCACTGAGCACCATCACCAGGTTAG
GATGTCTAAACTGCTCCACCTGCCTGACCACGCCCCCACACAGAGTGCTCATGCTCAGTCTCACCTGTTTCCTACCGTGG
ATGTCCCTGACCACGCCCACTACATCATTGGCTCAGTCATCCTGTTGGTAGGGGTAACAGGCATGCTGGGAAATGCTCTG
GTCATCTACGTGTTCTGTCGCAGTCAGACACTGAGGTCGCCCAGCAACCTGCTAGTGGTTAACTTGGCGGCCGCCGACTT
CCTGATGTCCTTGACACAGTCTCCGGTCTTCTTTGTGGCCAGCCTGCACCGCCGCTGGGTGTTTGGGGAGCTGGCCTGCG
AGCTGTACGCCTTCTCTGGTGCTCTCTTTGGCATCACCTCCATGATAACGCTGACGGCAATTGCGGTGGACCGTTGCCTG
GCTATCACGCGTCCGCTGGCGATGCTGGGCGGGGTGAGTCATCAGAGAGTGTTGGTGGTGGTGGCAGTTGTGTGGCTGTA
CTCTCTTGGCTGGAGTCTGCCGCCGTTCTTCGGGTGGAGCGCCTATGTCCCTGAGGGCCTGCAGACATCCTGCAGCTGGG
ACTACATGAGCTTTACAGCTGCTGTACGCACCTACACCCTCCTGCTGTTCTCCTTCGTCTTCTTCATCCCGCTCGCTGTC
ATCGCTGCGTGCTACTTTGCCATTTTCCGGGCAGTGCAGCAGGCGGGGCGGGAGATGGAGCAGCTGAACTGTGGCGAGGT
CAACAAGGCATATGAGCGTCTGTGCAGTGAGTGGCGGATGGCTAAGGTGGCTCTGGGAGTAATCATGCTCTTCATTGTTT
CCTGGTCACCATACTCTGTGGTTGCTCTCACTGCCACCGCCGGCTACGCCCACATGCTGACTCCATACATGAACTCGGTG
CCAGCCGTCATTGCCAAGGCCTCCGCAATCCACAACCCCATTATCTATGCCATCACACACCCAAAGTACCGCGCTGCCAT
CAGTCACTATGTCCCTTTTCTTCGCAGCGTGCTACGGCTCCAGGAGAAGGACTTGCGCTCCTCTTTCAGCTCGAGCGCCA
CTTCGTCTCGCTGTACCACTTTTACCAGCTCGCCAAAAGTTCGACTTAATGCCAGCGTCAGGACCAATGGCCACCAGGCT
AAGAACCGCCTATCCTCAGTGTCTGACAGCGAGTCGTGCTGGACGGAGAGCGATGCCAATGGCTCGAGCGGAAGATCAAA
GAGGCAGGCATCCTCAGAGGTCACCGCTAACCCCTTGGACTCCGCCCCGCCAAGCCAGCACATGGGCCAGACCGACGCTA
GTTCATCTGACGGCGCCGTACTGCAGGCCAAACTTCTGCTG

Alignment

ORF - retro_onil_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.8 %
• Parental protein coverage: 66.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TTGSMVRDYPFPTVDVPDHAHYTIGVVIFAVGITGLLGNFLVIYAFCRSRSLRTPSNIFIINLAVTDFLM
          T.........FPTVDVPDHAHY.IG.VI..VG.TG.LGN.LVIY.FCRS..LR.PSN....NLA..DFLM
Retrocopy TQSAHAQSHLFPTVDVPDHAHYIIGSVILLVGVTGMLGNALVIYVFCRSQTLRSPSNLLVVNLAAADFLM

Parental  CLTQTPIFFITSMHKHWIFGKKGCELYAFCGALFGICSMMTLMVIAVDRYVVITRPLASLGVMSRKKAFT
          .LTQ.P.FF..S.H..W.FG...CELYAF.GALFGI.SM.TL..IAVDR...ITRPLA.LG..S......
Retrocopy SLTQSPVFFVASLHRRWVFGELACELYAFSGALFGITSMITLTAIAVDRCLAITRPLAMLGGVSHQRVLV

Parental  TVAVAWLYSMGWSLPPFFGWSAYVPEGLMTSCSWDYMTFTPSVRSYTMLLFTFVFFIPLFVIIFCYCCIF
          .VAV.WLYS.GWSLPPFFGWSAYVPEGL.TSCSWDYM.FT..VR.YT.LLF.FVFFIPL.VI..CY..IF
Retrocopy VVAVVWLYSLGWSLPPFFGWSAYVPEGLQTSCSWDYMSFTAAVRTYTLLLFSFVFFIPLAVIAACYFAIF

Parental  RAIRHTTRAITKINCEGTRDSAKRFHKMRSEWRMAKIALIVILLFVISWAPYSCTALTAFAGYADLLTPY
          RA.....R.....NC........R.....SEWRMAK.AL.VI.LF..SW.PYS..ALTA.AGYA..LTPY
Retrocopy RAVQQAGREMEQLNCGEVNKAYER---LCSEWRMAKVALGVIMLFIVSWSPYSVVALTATAGYAHMLTPY

Parental  MNSVPAVIAKASAIHNPIIYAITHPKYRSAISRYVPYLGVLLCMKGRDRFS--SSSFQSTRRSTLTSQSE
          MNSVPAVIAKASAIHNPIIYAITHPKYR.AIS.YVP.L...L.....D..S..SSS..S.R..T.TS...
Retrocopy MNSVPAVIAKASAIHNPIIYAITHPKYRAAISHYVPFLRSVLRLQEKDLRSSFSSSATSSRCTTFTSSPK

Parental  FK-GPSRTHNSSQSESESAQFSDTE
          .....S...N..Q........SD.E
Retrocopy VRLNASVRTNGHQAKNRLSSVSDSE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Oreochromis niloticus was not studied using RNA-Seq expression data.

ChIP-Seq

Oreochromis niloticus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_onil_10 retrocopy.

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_10 was not experimentally validated.

Homology

Retrocopy orthology:

Oreochromis niloticus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Danio rerio	ENSDARG00000022098	1 retrocopy	retro_drer_8,
Oreochromis niloticus	ENSONIG00000015868	1 retrocopy	retro_onil_10 ,
Oreochromis niloticus	ENSONIG00000017219	1 retrocopy	retro_onil_16,
Xiphophorus maculatus	ENSXMAG00000015929	1 retrocopy	retro_xmac_7,