RetrogeneDB ID: retro_trub_44

Retrocopy location

• Organism: Fugu rubripes (Takifugu rubripes)
• Coordinates: scaffold_623:50530..51508(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OPN4
• Ensembl ID: ENSTRUG00000011365
• Aliases: None
• Description: None

Sequence

>retro_trub_44
TTCCCCACCGTGGACGTCCCTGACCATGCTCACTACATCATTGGCTCGGTCATCTTGCTCGTGGGCCTGACGGGCATGTC
GGGAAACGCTCTCGTCATCTACGTCTTCTGCCGCAGCCGCACCCTGCGGTCGCCTAGCAACCTGCTGGTGGTGAACCTGG
CAGCCGCCGACTTCCTGATGTCGCTGACGCAGTCCCCGGTGTTCTTCGTGGCCAGCCTGCACCGCCGCTGGTTGTTTGGA
GAGCTGGCCTGTGAACTGTACGCCTTCTGCGGCGCGCTCTTTGGCATCGCCTCTATGATGACCCTCACCGCCATCGCCGT
GGACCGCTGCCTGGCCATCACGCGGCCGCTGGCCCGGCTGGGCGGCATGAGTCCCGGGGGGGTGCTGGCGGTGCTGGCGG
GCGTGTGGCTGTACTCGCTGTGCTGGAGTCTGCCGCCGTTCTTTGGGTGGAGTGCTTATGTCCCTGAGGGCCTCCAGACG
TCCTGCAGCTGGGACTACATGAGCTTCACCGCTGCCGTGCGCTCCTACACCATCCTGCTCTTTGCTTTTGTCTTCTTTGT
CCCGCTCGGTCTCATCGCCGGCTGCTACTTCGCCATCTTCCGGGCGGTGCGGCGTGCGGGTCAGGAGGTGGAGCGGCTGA
ACTGTGGACAGATGAACAAGGCGTATGAGCGTCTGCGCAGCGAGTGGCACTTAGCTAAGGTGGCTCTGGGAGTCATCCTG
CTCTTCGTCGTGTCCTGGGCGCCATACTCCGCCGTGGCCCTGACCGCCACTGCGGGCTACGCCCACCTGCTGACCCCCTA
CATGAACTCCGTTCCTGCCGTCATTGCCAAGGCTTCAGCCATCCACAACCCCATCATCTACGCCATCACACACCCCAAGT
ATCGGGCTGCCATTGGCCGATGTGTCCCACTGCTGCGTCCTCTGCTGCGTCTCCAGGACAAGGACCTTCGCTCGTCCATC
AGCTCTAGCAGCGCTTTG

Alignment

ORF - retro_trub_44 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.42 %
• Parental protein coverage: 75.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FPTVDVPDHAHYTIGSVILVIGITGMIGNFLVIYAFCRSRSLRTPANMFIINLAVTDLLMCVTQTPIFFT
          FPTVDVPDHAHY.IGSVIL..G.TGM.GN.LVIY.FCRSR.LR.P.N....NLA..D.LM..TQ.P.FF.
Retrocopy FPTVDVPDHAHYIIGSVILLVGLTGMSGNALVIYVFCRSRTLRSPSNLLVVNLAAADFLMSLTQSPVFFV

Parental  TSMYKRWIFGEKGCELYAFCGALFGICSMITLTVIAIDRYFVITRPLTSIGVLSRKRAFVILMTVWIYSL
          .S...RW.FGE..CELYAFCGALFGI.SM.TLT.IA.DR...ITRPL...G..S..........VW.YSL
Retrocopy ASLHRRWLFGELACELYAFCGALFGIASMMTLTAIAVDRCLAITRPLARLGGMSPGXXXXXXXXVWLYSL

Parental  GWSLPPFFGWSAYVPEGLLTSCTWDYMTFSPSVRAYTMLLFIFVFFLPLFIIIYCYFFIFRAIRATNKSV
          .WSLPPFFGWSAYVPEGL.TSC.WDYM.F...VR.YT.LLF.FVFF.PL..I..CYF.IFRA.R.....V
Retrocopy CWSLPPFFGWSAYVPEGLQTSCSWDYMSFTAAVRSYTILLFAFVFFVPLGLIAGCYFAIFRAVRRAGQEV

Parental  GMCMCPHIRRESVKNFQRLQNEWKMAKIALMVILLYVISWSPYSCVALTAFAGYADMLTPYMNSVPAVIA
          ....C............RL..EW..AK.AL.VILL.V.SW.PYS.VALTA.AGYA..LTPYMNSVPAVIA
Retrocopy ERLNCGQMNKA----YERLRSEWHLAKVALGVILLFVVSWAPYSAVALTATAGYAHLLTPYMNSVPAVIA

Parental  KASAIHNPIIYAITHPKYRLALAKYIPCLGFLLCISPHELQSTSSSFMSL
          KASAIHNPIIYAITHPKYR.A.....P.L..LL......L.S..SS...L
Retrocopy KASAIHNPIIYAITHPKYRAAIGRCVPLLRPLLRLQDKDLRSSISSSSAL

Legend:

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

Expression

RNA-Seq

Takifugu rubripes was not studied using RNA-Seq expression data.

ChIP-Seq

Takifugu rubripes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_trub_44 retrocopy.

TSS

Takifugu rubripes was not studied using FANTOM5 data.

Lab

retro_trub_44 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_trub_44 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Danio rerio	ENSDARG00000022098	1 retrocopy	retro_drer_8,
Takifugu rubripes	ENSTRUG00000010617	1 retrocopy	retro_trub_18,
Takifugu rubripes	ENSTRUG00000011365	1 retrocopy	retro_trub_44 ,