RetrogeneDB ID: retro_onil_16

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL831137.1:7610691..7611756(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSONIG00000021142
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RHO (1 of 2)
• Ensembl ID: ENSONIG00000017219
• Aliases: None
• Description: rhodopsin [Source:HGNC Symbol;Acc:10012]

Sequence

>retro_onil_16
ATGAATGGCACAGAGGGACCCTTTTTCTATGTCCCTATGGTAAACACCACCGGTATTGTCCGGAGTCCTTATGAATACCC
TCAGCACTACCTTGTCAGCCCAGCAGCTTATGCTGCTCTGGGTGCCTACATGTTCTTTCTCATCCTTGCTGGATTCCCCA
TCAACTTCCTTACTCTCTATGTCACCATTGAACACAAGAAGCTGCGAACCCCACTAAACTACATCCTTCTGAACCTTGCG
GTGGCTGACCTCTTCATGGTATTTGGAGGATTCACCACAACGATGTACACCTCTATGCATGGCTACTTCGTCCTAGGACG
CCTTGGCTGCAATCTGGAAGGATTCTTTGCTACCCTCGGTGGTGAGATTGGTCTCTGGTCACTGGTTGTCCTTGCTGTTG
AAAGGTGGTTAGTCGTCTGCAAGCCCATTAGCAACTTCCGCTTTGGGGAGAACCACGCTATTATGGGCTTGGCCTTCACC
TGGCTAGCGGCCCTTTCTTGCGCTGGACCCCCTCTTGTCGGCTGGTCTCGTTACATCCCTGAGGGCATGCAGTGCTCATG
TGGAGTCGACTACTACACACGTGCAGAAGGCTTCAACAACGAGTCGTTTGTTATCTACATGTTCATCTGCCACTTCCTGA
TTCCACTGACTGTTGTGTTTTTCTGCTACGGCCGCCTGCTCTGTGCTGTCAAGGAGGCTGCTGCTGCCCAGCAGGAGTCT
GAGACCACCCAGAGGGCTGAGAGGGAAGTCACCCGCATGGTTGTTATCATGGTTATTTCCTTCCTGATATGTTGGCTGCC
CTATGCCGGAGTGGCCTGGTATATCTTCACGCATCAGGGATCTGAATTTGGACCAGTCTTCATGACCCTCCCAGCCTTCT
TTGCCAAGAGCTCTTCCATCTACAACCCTTTGATTTACATCTGCATGAACAAGCAGTTCCGCCACTGCATGATCACCACC
TTGTGCTGCGGGAAAAATCCCTTTGAAGAAGAGGAGGGAGCATCTACTACTGCCTCCAAGACCGAGGCTTCCTCTGTGTC
CTCCAGCTCTGTGTCTCCTGCATAA

Alignment

ORF - retro_onil_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.88 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNGTEGPNFYVPMSNKTGVVRSPFEYPQYYLAEPWKYSLLAAYMLFLIISSFPINFLTLYVTVKHKKLRT
          MNGTEGP.FYVPM.N.TG.VRSP.EYPQ.YL..P..Y..L.AYM.FLI...FPINFLTLYVT..HKKLRT
Retrocopy MNGTEGPFFYVPMVNTTGIVRSPYEYPQHYLVSPAAYAALGAYMFFLILAGFPINFLTLYVTIEHKKLRT

Parental  PLNYVLLNLAVADLFMVVGGFTVTLYTALHGYFVLGVSGCNIEGFFATLGGEIALWSLVVLAIERYIVVC
          PLNY.LLNLAVADLFMV.GGFT.T.YT..HGYFVLG..GCN.EGFFATLGGEI.LWSLVVLA.ER..VVC
Retrocopy PLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVLGRLGCNLEGFFATLGGEIGLWSLVVLAVERWLVVC

Parental  KPMTNFRFGEKHAMAGLGFTWVMALTCAAPPLFGWSRYRYIPEGMQCSCGIDYYTPKPEINNTSFVIYMF
          KP..NFRFGE.HA..GL.FTW..AL.CA.PPL.GWS..RYIPEGMQCSCG.DYYT.....NN.SFVIYMF
Retrocopy KPISNFRFGENHAIMGLAFTWLAALSCAGPPLVGWS--RYIPEGMQCSCGVDYYTRAEGFNNESFVIYMF

Parental  VLHFCIPLFIIFFCYTSLLCTVRAAAAQQQESETTQRAEKEVTRMVIVMVISFLVCWVPYASVAWYIFAN
          ..HF.IPL...FFCY..LLC.V..AAA.QQESETTQRAE.EVTRMV..MVISFL.CW.PYA.VAWYIF..
Retrocopy ICHFLIPLTVVFFCYGRLLCAVKEAAAAQQESETTQRAEREVTRMVVIMVISFLICWLPYAGVAWYIFTH

Parental  QGTEFGPVFMTAPAFFAKSAALYNPVIYILLNRQFRNCMITTVCCGKNPFGEDEGA---VSKTQTSSVSS
          QG.EFGPVFMT.PAFFAKS...YNP.IYI..N.QFR.CMITT.CCGKNPF.E.EGA....SKT..SSVSS
Retrocopy QGSEFGPVFMTLPAFFAKSSSIYNPLIYICMNKQFRHCMITTLCCGKNPFEEEEGASTTASKTEASSVSS

Parental  SQVAPA
          S.V.PA
Retrocopy SSVSPA

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

34 EST(s) were mapped to retro_onil_16 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
GR592789	7610658	7610932	99.7	271	1	269
GR592811	7610644	7610983	98.3	333	4	325
GR592851	7610714	7610854	97.9	140	0	139
GR593062	7610697	7610804	100	106	0	105
GR593153	7610644	7610951	98.7	300	2	291
GR593174	7610676	7610984	98.1	300	4	291
GR593243	7611020	7611204	95.7	183	0	179
GR593287	7610644	7611138	98.6	486	5	476
GR593368	7610979	7611211	95.7	228	3	221
GR593698	7611089	7611342	100	252	0	251
GR593776	7610641	7611183	99.3	536	2	528
GR593835	7610655	7610930	99.7	273	0	271
GR593836	7610709	7610862	100	152	0	151
GR593847	7610633	7611161	98.3	522	1	514
GR593900	7610669	7611148	99.6	475	1	470
GR593970	7610652	7610964	99.7	309	0	305
GR594018	7610655	7611181	99.5	520	1	513
GR594215	7610912	7611160	100	244	0	242
GR594249	7610701	7610864	99.4	160	1	158
GR594393	7610702	7611160	98.3	457	1	453
GR594400	7610639	7611158	97	515	3	504
GR594480	7610808	7610936	100	126	0	125
GR594546	7610886	7611002	99.2	114	1	112
GR594558	7610644	7611177	99.9	530	1	527
GR594611	7610659	7611081	99.6	420	0	416
GR594655	7610641	7611222	99.7	577	2	573
GR594837	7610640	7611015	100	373	0	371
GR594939	7610689	7611080	99.5	386	2	382
GR595076	7610764	7611050	99.7	278	0	272
GR595191	7610706	7610866	98.8	155	0	149
GR595208	7610811	7610932	96.7	120	0	117
GR595287	7610711	7610877	95.8	157	6	148
GR595308	7610751	7610934	97.9	179	3	174
GR634098	7610603	7611190	99.5	584	3	581

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_16 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Gadus morhua	ENSGMOG00000013755	1 retrocopy	retro_gmor_7,
Oreochromis niloticus	ENSONIG00000015868	1 retrocopy	retro_onil_10,
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,