RetrogeneDB - Retrocopy retro_xmac

						
>retro_xmac_11
ATGAACGGCACAGAGGGACCCTATTTTTATGTCCCTATGGTTAATACCACTGGTATTGTCCGGAGTCCTTATGAATATCC

TCAGTACTACCTTGTCAGCCCAGCAGCCTACGCTTGTCTGGGTGCCTACATGTTTTTCCTCATTCTCGTCGGCTTCCCCA

TCAACTTTCTCACCCTCTATGTCACCATGGAACACAAGAAGCTGCGAACCCCTCTAAACTACATCCTGCTCAACCTTGCT

GTGGCTGACCTTTTCATGGTGTTTGGAGGATTCACCACAACGATGTACACCTCTATGCATGGCTACTTTGTCCTCGGGCG

CCTTGGCTGCAATCTGGAAGGATACTTTGCTACCCTGGGTGGTGAAATCGGTCTCTGGTCACTGGTTGTTCTGGCTGTTG

AAAGGTGGCTAGTTGTCTGCAAGCCCATCAGCAACTTCCGCTTCGGTGAGAATCATGCTATTATGGGTCTGGTCTTCACC

TGGATCATGGCCAATGGCTGTGCTGCCCCCCCTCTTGTCGGCTGGTCTCGTTACATCCCAGAGGGCATGCAGTGCTCATG

CGGAGTCGACTACTATACCCGTGCTGAGGGTTTCAACAATGAGTCTTTTGTTATCTACATGTTCATCTGCCACTTCTGCA

TTCCTCTTGCCGTTGTGTTCTTCTGCTATGGCCGTCTGCTCTGTGCCGTCAAGGAGGCTGCTGCCGCCCAGCAGGAGTCT

GAGACCACCCAGAGAGCTGAGAGGGAAGTCACCCGCATGGTCGTTATCATGGTCATCGGCTTCCTGATTTGCTGGCTTCC

TTACGCCAGTGTGGCCTGGTACATCTTCACACATCAGGGTTCTGAGTTTGGACCTCTCTTAATGACCATCCCAGCTTTCT

TTGCCAAGTCAGCCTCCATCTACAACCCAATGATCTACATCTGCATGAACAAGCAGTTCCGCCACTGCATGATCACCACC

TTGTGCTGCGGAAAGAATCCCTTCGAAGAGGAGGAGGGAGCATCCACCACTGCCTCCAAAACCGAGGCCTCCTCTGTGTC

CTCCAGCTCCGTGTCTCCTGCATAA

ORF - retro_xmac_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	72.32 %
Parental protein coverage:	100. %
Number of stop codons detected:	0
Number of frameshifts detected	0

Retrocopy - Parental Gene Alignment:

									ParentalMNGTEGPNFYVPMSNRTGLVLSPFEHPQYYLAEPWKYSLLAAYMLFLIIMAFPINFLTLHVTIKHKKLRT
		MNGTEGP.FYVPM.N.TG.V.SP.E.PQYYL..P..Y..L.AYM.FLI...FPINFLTL.VT..HKKLRT
RetrocopyMNGTEGPYFYVPMVNTTGIVRSPYEYPQYYLVSPAAYACLGAYMFFLILVGFPINFLTLYVTMEHKKLRT
ParentalPLNYVLLNLAVADLFMIVGGFTVTLYTALHGYFSLGVTGCNVEGFFATLGGEIALWSLVVLAVERYIVIC
		PLNY.LLNLAVADLFM..GGFT.T.YT..HGYF.LG..GCN.EG.FATLGGEI.LWSLVVLAVER..V.C
RetrocopyPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVLGRLGCNLEGYFATLGGEIGLWSLVVLAVERWLVVC
ParentalKPMTNFRFEEKHAIAGLAFSWVMALTCAAPPLFGWSRYIPEGMQCSCGIDYYTPKPEINNTSFVIYMFVL
		KP..NFRF.E.HAI.GL.F.W.MA..CAAPPL.GWSRYIPEGMQCSCG.DYYT.....NN.SFVIYMF..
RetrocopyKPISNFRFGENHAIMGLVFTWIMANGCAAPPLVGWSRYIPEGMQCSCGVDYYTRAEGFNNESFVIYMFIC
ParentalHFCIPLFIIFFCYSRLLCTVRAAAAQQQESETTQRAEKEVTRMVIVMVISFLVCWVPYATVAWYIFANQG
		HFCIPL...FFCY.RLLC.V..AAA.QQESETTQRAE.EVTRMV..MVI.FL.CW.PYA.VAWYIF..QG
RetrocopyHFCIPLAVVFFCYGRLLCAVKEAAAAQQESETTQRAEREVTRMVVIMVIGFLICWLPYASVAWYIFTHQG
ParentalVEFGPVFMTAPAFFAKSAALYNPVIYILLNRQFRNCMITTVCCGKNPFGDDE-ATAAVSKTQTSSVSSSQ
		.EFGP..MT.PAFFAKSA..YNP.IYI..N.QFR.CMITT.CCGKNPF...E.A....SKT..SSVSSS.
RetrocopySEFGPLLMTIPAFFAKSASIYNPMIYICMNKQFRHCMITTLCCGKNPFEEEEGASTTASKTEASSVSSSS
ParentalVAPA
		V.PA
RetrocopyVSPA

							

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

						

RNA-Seq - click to see more details

Xiphophorus maculatus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Xiphophorus maculatus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_xmac_11 retrocopy.

TSS - click to see more details

Xiphophorus maculatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_xmac_11 was not experimentally validated.

Retrocopy orthology:

Xiphophorus maculatus 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.

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,
Xiphophorus maculatus	ENSXMAG00000015929	1 retrocopy	retro_xmac_7,
Xiphophorus maculatus	ENSXMAG00000017297	1 retrocopy	retro_xmac_11 ,

	RetrogeneDB ID:	retro_xmac_11
Retrocopy location	Organism:	*Platyfish (Xiphophorus maculatus)*
	Coordinates:	JH556804.1:6301..7366(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ENSXMAG00000019635
	Aliases:	None
	Status:	KNOWN_PROTEIN_CODING
Parental gene information	Parental gene summary:
	Parental gene symbol:	RHO (1 of 2)
	Ensembl ID:	ENSXMAG00000017297
	Aliases:	None
	Description:	rhodopsin [Source:HGNC Symbol;Acc:10012]

Parental	MNGTEGPNFYVPMSNRTGLVLSPFEHPQYYLAEPWKYSLLAAYMLFLIIMAFPINFLTLHVTIKHKKLRT
	MNGTEGP.FYVPM.N.TG.V.SP.E.PQYYL..P..Y..L.AYM.FLI...FPINFLTL.VT..HKKLRT
Retrocopy	MNGTEGPYFYVPMVNTTGIVRSPYEYPQYYLVSPAAYACLGAYMFFLILVGFPINFLTLYVTMEHKKLRT

Parental	PLNYVLLNLAVADLFMIVGGFTVTLYTALHGYFSLGVTGCNVEGFFATLGGEIALWSLVVLAVERYIVIC
	PLNY.LLNLAVADLFM..GGFT.T.YT..HGYF.LG..GCN.EG.FATLGGEI.LWSLVVLAVER..V.C
Retrocopy	PLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVLGRLGCNLEGYFATLGGEIGLWSLVVLAVERWLVVC

Parental	KPMTNFRFEEKHAIAGLAFSWVMALTCAAPPLFGWSRYIPEGMQCSCGIDYYTPKPEINNTSFVIYMFVL
	KP..NFRF.E.HAI.GL.F.W.MA..CAAPPL.GWSRYIPEGMQCSCG.DYYT.....NN.SFVIYMF..
Retrocopy	KPISNFRFGENHAIMGLVFTWIMANGCAAPPLVGWSRYIPEGMQCSCGVDYYTRAEGFNNESFVIYMFIC

Parental	HFCIPLFIIFFCYSRLLCTVRAAAAQQQESETTQRAEKEVTRMVIVMVISFLVCWVPYATVAWYIFANQG
	HFCIPL...FFCY.RLLC.V..AAA.QQESETTQRAE.EVTRMV..MVI.FL.CW.PYA.VAWYIF..QG
Retrocopy	HFCIPLAVVFFCYGRLLCAVKEAAAAQQESETTQRAEREVTRMVVIMVIGFLICWLPYASVAWYIFTHQG

Parental	VEFGPVFMTAPAFFAKSAALYNPVIYILLNRQFRNCMITTVCCGKNPFGDDE-ATAAVSKTQTSSVSSSQ
	.EFGP..MT.PAFFAKSA..YNP.IYI..N.QFR.CMITT.CCGKNPF...E.A....SKT..SSVSSS.
Retrocopy	SEFGPLLMTIPAFFAKSASIYNPMIYICMNKQFRHCMITTLCCGKNPFEEEEGASTTASKTEASSVSSSS

Parental	VAPA
	V.PA
Retrocopy	VSPA

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

RetrogeneDB ID:

retro_xmac_11