RetrogeneDB ID: retro_trub_18

Retrocopy location

• Organism: Fugu rubripes (Takifugu rubripes)
• Coordinates: scaffold_527:78265..79327(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTRUG00000004527
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TRU.1921
• Ensembl ID: ENSTRUG00000010617
• Aliases: None
• Description: rod-like opsin [Source:RefSeq peptide;Acc:NP_001029021]

Sequence

>retro_trub_18
ATGAACGGCACGGAGGGACCATTTTTCTATGTCCCCATGGTAAACACCACCGGCGTCGTCCGGAGTCCTTATGATTACCC
TCAGTACTATCTCGTCAACCCAGCAGCTTACGCCGCTCTGGGGGCCTACATGTTCCTGCTCATCCTTCTCGGCTTCCCCA
TCAACTTCCTCACTCTGTATGTCACCATTGAACACAAGAAGCTGCGGACCCCTCTAAACTACATCTTGCTCAACCTGGCA
GTCGCCGACCTCTTCATGGTGTTCGGAGGATTCACCACAACGATGTACACCTCTATGCACGGCTACTTTGTGCTTGGACG
CCTTGGTTGCAATCTGGAAGGCTTCTTCGCCACCCTGGGAGGTGAGATTGGCCTCTGGTCGCTAGTTGTTTTGGCTATTG
AAAGGTGGGTGGTCGTCTGCAAGCCCATCAGCAACTTCCGCTTCGGGGAGAATCACGCAATCATGGGTTTGGCCTTCACC
TGGATCATGGCCTCTGCCTGTGCCGTTCCCCCTCTCGTCGGCTGGTCCCGTTACATCCCTGAGGGCATGCAGTGTTCATG
CGGAGTCGACTACTACACCCGTGCAGAGGGATTCAATAACGAGTCCTTTGTTATCTACATGTTCGTCTGCCACTTCCTCA
TTCCACTGATAATCATCTTCTTCTGCTACGGCCGTCTGCTCTGCGCCGTCAAGGAGGCCGCTGCTGCCCAGCAAGAGTCC
GAGACCACCCAGAGGGCTGAGAGGGAGGTCACCCGCATGGTCATTCTCATGGTCATTTCCTTCCTGGTATGTTGGTTACC
ATATGCTGGTGTGGCCTGGTACATCTTCACACATCAGGGCTCTGAGTTTGGACCCGTCTTCATGACCATCCCGGCCTTCT
TTGCCAAGAGCTCCTCCATCTACAACCCGATGATCTACATCTGCATGAACAAGCAGTTCCGCCACTGCATGATCACCACC
TTGTGCTGCGGGAAGAACCCCTTCGAGGAGGAAGAGGGCGCGTCCACTACTTCCAAGACCGAGGCCTCTTCCGTCTCCTC
GAGTTCTGTGTCTCCTGCGTAA

Alignment

ORF - retro_trub_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.5 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWKYSLVAAYMLFLIITAFPVNFLTLFVTVKHKKLRT
          MNGTEGP.FY.PM.N.TGVVRSP..YPQYYL..P..Y....AYM..LI...FP.NFLTL.VT..HKKLRT
Retrocopy MNGTEGPFFYVPMVNTTGVVRSPYDYPQYYLVNPAAYAALGAYMFLLILLGFPINFLTLYVTIEHKKLRT

Parental  PLNYVLLNLAVADLFMVIGGFTVTLYTALHAYFVLGVTGCNIEGFFATLGGEIALWSLVVLAVERYIVVC
          PLNY.LLNLAVADLFMV.GGFT.T.YT..H.YFVLG..GCN.EGFFATLGGEI.LWSLVVLA.ER..VVC
Retrocopy PLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVLGRLGCNLEGFFATLGGEIGLWSLVVLAIERWVVVC

Parental  KPMTNFRFGEKHAIAGLVFTWIMALTCATPPLLGWSRYIPEGMQCSCGIDYYTPKPEINNTSFVIYMFIL
          KP..NFRFGE.HAI.GL.FTWIMA..CA.PPL.GWSRYIPEGMQCSCG.DYYT.....NN.SFVIYMF..
Retrocopy KPISNFRFGENHAIMGLAFTWIMASACAVPPLVGWSRYIPEGMQCSCGVDYYTRAEGFNNESFVIYMFVC

Parental  HFSIPLAIIFFCYSRLLCTVRAAAALQQESETTQRAEKEVTRMVIVMVISFLVCWVPYASVAWYIFANQG
          HF.IPL.IIFFCY.RLLC.V..AAA.QQESETTQRAE.EVTRMVI.MVISFLVCW.PYA.VAWYIF..QG
Retrocopy HFLIPLIIIFFCYGRLLCAVKEAAAAQQESETTQRAEREVTRMVILMVISFLVCWLPYAGVAWYIFTHQG

Parental  TEFGPVFMTAPAFFAKSAALYNPVIYILLNRQFRNCMITTVCCGKNPFGDDDAATTVSKTQSSSVSSSQV
          .EFGPVFMT.PAFFAKS...YNP.IYI..N.QFR.CMITT.CCGKNPF.....A.T.SKT..SSVSSS.V
Retrocopy SEFGPVFMTIPAFFAKSSSIYNPMIYICMNKQFRHCMITTLCCGKNPFEEEEGASTTSKTEASSVSSSSV

Parental  APA
          .PA
Retrocopy SPA

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

2 EST(s) were mapped to retro_trub_18 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AL837136	78241	78660	98.9	414	5	409
AL837161	78240	78602	98.7	356	4	350

TSS

Takifugu rubripes was not studied using FANTOM5 data.

Lab

retro_trub_18 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_trub_18 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 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 ,
Takifugu rubripes	ENSTRUG00000011365	1 retrocopy	retro_trub_44,
Xiphophorus maculatus	ENSXMAG00000017297	1 retrocopy	retro_xmac_11,