RetrogeneDB ID: retro_tnig_20

Retrocopy location

• Organism: Tetraodon (Tetraodon nigroviridis)
• Coordinates: 9:6477141..6478203(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTNIG00000017909
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RHO (1 of 2)
• Ensembl ID: ENSTNIG00000017925
• Aliases: None
• Description: rhodopsin [Source:HGNC Symbol;Acc:10012]

Sequence

>retro_tnig_20
ATGAACGGCACAGAGGGACCCTTTTTCTATGTCCCTATGCTAAACACCACCGGCATCGTCCGGAGTCCTTATGACTATCC
TCAGTACTATCTCGTCAACCCGGCAGCCTACGCTGCTCTGGGGGCCTACATGTTCCTGCTCATCCTTCTCGGCTTCCCCA
TCAACTTCCTCACTCTGTATGTCACCATTGAACACAAGAAGCTGCGGACCCCTTTGAACTACATCCTGCTCAACCTGGCA
GTGGCCAACCTCTTCATGGTGTTCGGAGGATTCACCACAACGATGTACACCTCCATGCATGGCTACTTCGTGCTGGGACG
CCTTGGTTGCAACCTGGAAGGCTTCTTTGCCACCCTCGGCGGTGAGATTGGCCTCTGGTCGCTGGTTGTTTTGGCCATTG
AAAGGTGGATGGTCGTCTGCAAGCCCATCAGCAACTTCCGCTTCGGAGAGAATCACGCCATCATGGGCTTGGCCTTTACC
TGGATCATGGCCTGCGCCTGCGCCGTTCCCCCTCTCGTTGGCTGGTCCCGTTACATCCCTGAGGGCATGCAGTGTTCATG
CGGAGTCGACTATTACACCCGCGCAGAGGGATTCAACAACGAGTCCTTTGTTGTCTACATGTTTATCTGCCACTTCCTCA
TTCCTATGGCAGTCGTGTTCTTCTGCTACGGCCGTCTGCTCTGCGCCGTCAAAGAGGCTGCTGCCGCCCAGCAAGAATCC
GAGACCACCCAGAGGGCTGAGAGGGAGGTCACCCGCATGGTGGTTATCATGGTCGTGGCCTTCCTGATATGCTGGTTGCC
CTACGCTGGCGTGGCCTGGTGGATCTTCACACATCAGGGCTCTGAGTTCGGACCAGTTTTCATGACCATCCCGGCCTTCT
TTGCTAAGAGCTCTTCCATCTACAACCCGTTGATCTACATCTGCATGAACAAGCAGTTCCGCCATTGCATGATCACTACC
TTGTGCTGCGGGAAGAACCCCTTCGAGGAGGAAGAGGGCGCATCCACTACCTCGAAGACCGAGGCCTCCTCCGTCTCCTC
CAGTTCTGTGTCTCCTGCATAA

Alignment

ORF - retro_tnig_20 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.67 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNGTEGPNFYVPMSNKTGVVRSPFEYPQYYLAEPWKYSLVAAYMLFLIVTAFPVNFLTLFVTVKHKKLRT
          MNGTEGP.FYVPM.N.TG.VRSP..YPQYYL..P..Y....AYM..LI...FP.NFLTL.VT..HKKLRT
Retrocopy MNGTEGPFFYVPMLNTTGIVRSPYDYPQYYLVNPAAYAALGAYMFLLILLGFPINFLTLYVTIEHKKLRT

Parental  PLNYVLLNLAVADLFMVIGGFTVTLYTALHAYFVLGVTGCNIEGFFATLGGEIALWSLVVLAIERYIVVC
          PLNY.LLNLAVA.LFMV.GGFT.T.YT..H.YFVLG..GCN.EGFFATLGGEI.LWSLVVLAIER..VVC
Retrocopy PLNYILLNLAVANLFMVFGGFTTTMYTSMHGYFVLGRLGCNLEGFFATLGGEIGLWSLVVLAIERWMVVC

Parental  KPVTNFRFGEKHAIAGLAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGIDYYTPKPEIHNTSFVIYMFVL
          KP..NFRFGE.HAI.GLAFTWIMA..CAVPPL.GWSRYIPEGMQCSCG.DYYT......N.SFV.YMF..
Retrocopy KPISNFRFGENHAIMGLAFTWIMACACAVPPLVGWSRYIPEGMQCSCGVDYYTRAEGFNNESFVVYMFIC

Parental  HFCIPLAIIFFCYSRLLCTVRAAAALQQESETTQRAEKEVTRMVIVMVISFLVCWVPYASVAWYIFANQG
          HF.IP.A..FFCY.RLLC.V..AAA.QQESETTQRAE.EVTRMV..MV..FL.CW.PYA.VAW.IF..QG
Retrocopy HFLIPMAVVFFCYGRLLCAVKEAAAAQQESETTQRAEREVTRMVVIMVVAFLICWLPYAGVAWWIFTHQG

Parental  TEFGPVFMTAPAFFAKSAALYNPVIYILLNRQFRNCMITTVCCGKNPFGDDDATTSVSKTQSSSVSTSQV
          .EFGPVFMT.PAFFAKS...YNP.IYI..N.QFR.CMITT.CCGKNPF.........SKT..SSVS.S.V
Retrocopy SEFGPVFMTIPAFFAKSSSIYNPLIYICMNKQFRHCMITTLCCGKNPFEEEEGASTTSKTEASSVSSSSV

Parental  APA
          .PA
Retrocopy SPA

Legend:

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

Expression

RNA-Seq

Tetraodon nigroviridis was not studied using RNA-Seq expression data.

ChIP-Seq

Tetraodon nigroviridis was not studied using ChIP-Seq data.

EST

Tetraodon nigroviridis was not studied using EST data.

TSS

Tetraodon nigroviridis was not studied using FANTOM5 data.

Lab

retro_tnig_20 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_tnig_20 has 0 orthologous retrocopies within teleost group .

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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,