RetrogeneDB ID: retro_drer_8

Retrocopy location

• Organism: Zebrafish (Danio rerio)
• Coordinates: 2:32561124..32562627(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDARG00000007553
• Aliases: opn4.1, opn4, opn4l, opn4m2
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: opn4a
• Ensembl ID: ENSDARG00000022098
• Aliases: opn4a, opn4, opn4d
• Description: opsin 4a (melanopsin) [Source:ZFIN;Acc:ZDB-GENE-070111-2]

Sequence

>retro_drer_8
ATGAGCCATCACTCTTCATGGAGAGGGCATCACTGTGCCCCTGGAGACATCAACTGCACCGCAGGCTTTAAGGAATCTTT
GGGAAGCAGAAACTACAAGTTGCTCCATGTGCCTGTCCATGGGCCAACCCACAGCCACCACCATGATCCTCCACACCCTT
TCCCCACCGTGGATGTTCCGGATCATGCCCACTACATCATCGGCTCTGTTATCTTAATAGTCGGCATCACCGGAGTGATT
GGAAATGCACTGGTGGTCTATGTATTCTGCCGGAGCCGTACTCTTCGCACCGCTGGAAACATGTTTATAGTGAACCTAGC
TGTGGCTGATTTCTTAATGTCCGTCACCCAGTCTCCTGTGTTCTTTGCAGCCAGTTTACACAGGCGCTGGGTATTTGGCG
AGCGCCCTTGCGAGCTCTACGCCTTCTGCGGTGCCCTCTTTGGAATCTGCTCCATGATGACTTTGACCGCTATCGCTGCT
GATCGTTGTCTCGCCATAACTCAGCCTCTCGCCCTAGTAAGCAGAGTTAGCCGACGCAAAGCTGGAGCTGTGTTGGTCGT
TGTGTGGCTCTACTCCCTGGGTTGGAGCCTTCCGCCTTTCTTTGGCTGGAGTGCTTATGTCCCTGAGGGGCTTCAGACGT
CTTGTTCTTGGGATTACATGACCTTCACCCCATCAGTGCGTGCGTACACCATCCTCCTCTTTGTTTTTGTATTCTTCATC
CCACTAGGCATTATAGGCAGCTGCTACTTCGCAATTTTTCAAACAATCCGAGCAGCGGGGAAGGAAATTCGAGAGCTGGA
TTGCGGGGAAACGCACAAGGTGTATGAACGCATGCAGAACGAATGGAAGATGGCGAAAGTCGCTCTTGTAGTCATTGTGC
TTTTTATTATATCCTGGTCGCCCTATTCTGTGGTGGCTCTCACCGCTACGGCTGGTTATTCCCATTTCCTGACTCCCTAT
ATGAATTCAGTACCTGCTGTGATTGCCAAGGCTTCAGCCATCCATAATCCAATCATCTACGCCATTACGCATCCAAAGTA
TCGTGTGGCTATCGCCCGTTACATTCCGGTACTTCGTCCCATCTTGCGTGTGAAAGAGAAGGACCTTCGTTCCTCTTTTA
GCTCTGGCAGTGTTAGTTCTCGTCGTCCAACCCTCACCAGTCAGTGCTCTTTGGGGGTTAGCATGGGCAATGCTGCACGA
GCTAATGGCCGCTGGGGGAAGACGCGATTGTCTTCTGCCTCTGATAGTGATTCTTGCTGGACTGAGAGTGAGGCCGATGG
TTCCAGTGTCAGTTCCCTGACCTTCGGTCGTCGTGTTTCCACAGAAATCTCTACAGATACTGTCATTCTCTCATCTGGAT
CAAGTGTTAGCAATGCTAGTGGGCAGAAATCTGAGAGGGCACACAAAGTTATAAGTGTACCAGTGCCGTCTATTACTTTT
GAAACGGATGCAGCAGACGGGGAATCTCTGTCTGATGGGAAGGCTTTGCTTGGAGGGAACTAA

Alignment

ORF - retro_drer_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60. %
• Parental protein coverage: 69.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YPFPTVDVPDHAHYTIGAVILTVGITGMLGNFLVIYAFSRSRTLRTPANLFIINLAITDFLMCATQAPIF
          .PFPTVDVPDHAHY.IG.VIL.VGITG..GN.LV.Y.F.RSRTLRT..N.FI.NLA..DFLM..TQ.P.F
Retrocopy HPFPTVDVPDHAHYIIGSVILIVGITGVIGNALVVYVFCRSRTLRTAGNMFIVNLAVADFLMSVTQSPVF

Parental  FTTSMHKRWIFGEKGCELYAFCGALFGICSMITLMVIAVDRYFVITRPLASIGVLSQKRALLILLVAWVY
          F..S.H.RW.FGE..CELYAFCGALFGICSM.TL..IA.DR...IT.PLA.....S...A...L.V.W.Y
Retrocopy FAASLHRRWVFGERPCELYAFCGALFGICSMMTLTAIAADRCLAITQPLALVSRVSRRKAGAVLVVVWLY

Parental  SLGWSLPPFFGWSAYVPEGLLTSCTWDYMTFTPSVRAYTMLLFIFVFFIPLIVIIYCYFFIFRSIRTTNE
          SLGWSLPPFFGWSAYVPEGL.TSC.WDYMTFTPSVRAYT.LLF.FVFFIPL..I..CYF.IF..IR....
Retrocopy SLGWSLPPFFGWSAYVPEGLQTSCSWDYMTFTPSVRAYTILLFVFVFFIPLGIIGSCYFAIFQTIRAAGK

Parental  AVGKINGDNKRDSMKRFQRLKNEWKMAKIALIVILMYVISWSPYSTVALTAFAGYSDFLTPYMNSVPAVI
          ...............R.Q...NEWKMAK.AL.VI....ISWSPYS.VALTA.AGYS.FLTPYMNSVPAVI
Retrocopy EIRELDCGETHKVYERMQ---NEWKMAKVALVVIVLFIISWSPYSVVALTATAGYSHFLTPYMNSVPAVI

Parental  AKASAIHNPIIYAITHPKYRLAIAKYIPCLRLLLCVPKRDLH-SFHSSLMSTRRSTVTSQSS--DMSGRF
          AKASAIHNPIIYAITHPKYR.AIA.YIP.LR..L.V...DL..SF.S...S.RR.T.TSQ.S.....G..
Retrocopy AKASAIHNPIIYAITHPKYRVAIARYIPVLRPILRVKEKDLRSSFSSGSVSSRRPTLTSQCSLGVSMGNA

Parental  RRTSTGKSRLSSASDSESGWTDTEA--DLSSMSSRPASRQVSCDISKDTAEMPDFKPCNSSSFKSKLKSH
          .R...........S.S.S....TE...D.SS.SS....R.VS..IS.DT............S.......H
Retrocopy ARANGRWGKTRLSSASDSDSCWTESEADGSSVSSLTFGRRVSTEISTDTVILSSGSSVSNASGQKSERAH

Legend:

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

Expression

RNA-Seq

Danio rerio was not studied using RNA-Seq expression data.

ChIP-Seq

Danio rerio was not studied using ChIP-Seq data.

EST

2 EST(s) were mapped to retro_drer_8 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
CK016800	32561009	32561726	99.8	713	2	711
EH441154	32560995	32561785	99.7	790	0	789

TSS

Danio rerio was not studied using FANTOM5 data.

Lab

retro_drer_8 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_drer_8 has 0 orthologous retrocopies within teleost group .

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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,
Takifugu rubripes	ENSTRUG00000011365	1 retrocopy	retro_trub_44,
Xiphophorus maculatus	ENSXMAG00000015929	1 retrocopy	retro_xmac_7,