RetrogeneDB - Retrocopy retro_xmac

                        
>retro_xmac_24
ATGTTGTCCAGGAAGGGACTCATTCCTGAGGATTACTTGCTGACACGATTAGCTGAGGATGTTCTGCAGCCGAAGTTCAA

GGCCAAACAAGGGAAGGCTCGGTTTGTGGGGAAGAACGGCACCTGCAACGTTGCGCACACCAACATCCGAGAACAGGGTC

GGTTCTTACAGGACGTGTTCACCACACTAGTGGATTTGAAATGGCTCCACACTCTCATCATTTTCACCATGTCCTTCCTG

TGCAGCTGGCTCCTGTTCGGGATGATCTGGTGGCTTGTGGCTTTTGCGCACGGGGACCTGGGTGAAAAGGGGGATGATTT

TGTCCCGTGCGTAACCGACATCCACTCCTTCTCCTCCGCCTTCCTCTTCTCCATAGAAGTCCAGGTGACCATCGGCTTCG

GGGGTCGGATGATCACGGAGGAGTGCATCTCGGCCATCATCATCCTCATAGTGCAGAACATCGTGGGACTGGTCATCAAC

GCCATCATGCTGGGCTGCATCTTCATGAAAACTGCGCAGGCTCATCGGCGCGCGGAGACGCTCATCTTCAGCAAGCACGC

AGTCATCTCCCTCCGAAACAGCAAGCTGTGTTTTATGATCCGCATAGGAGACCTGAGGAAAAGCATGATCATCAGCGCCA

CCGTGCGGATGCAGGTGGTGAGGAGGAGCACCACGGAGGAGGGAGAGGTGGTGCCCCTTGACCAGATCGACATCCACATG

GATAATCCGGTGGGGACCAACGGGGTCTTCCTGGTGTCCCCCCTCATCATCTGCCATGTCATCGACAAGTCCAGCCCCTT

GTACGAGCTTTCACCGAACGACCTGCAGCACCAGGACCTGGAGGTGATCGTGGTGCTGGAGGGGGTGGTGGAGACCACCG

GCATCACCACGCAGGCCAGGACTTCCTACGTGTCGGAGGAGATCCTGTGGGGCCAGCGCTTCGTGCCGACGGTGTCCGAA

GACGACGGCATGTACGCAGTGGACTACTCCAAGTTTGGCAACACCGTCAAGGTACCGACGCCGTGCTGCAGCGCCAAGAA

GCTGGATGAGGCCGGTGGCATCGCACGGTTTAAGCTGAACGAGGGCGTCACCATGCGGCCGTCCGTGAGAAGGCGGAGGG

GGACCGCGATAGTGCGCAGGTCCAGAATGGAGAACAAGTGAGGC

ORF - retro_xmac_24 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	65.81 %
Parental protein coverage:	91.92 %
Number of stop codons detected:	1
Number of frameshifts detected:	0

Retrocopy - Parental Gene Alignment:

                                ParentalMLARKSIIPEEFGLPGLASRLPRKPVFRDRVNKARFIAKNGSCNLAHKNIREQGRFLQDVFTTLVDLKWR
ML.RK..IPE...L..LA......P.F.....KARF..KNG.CN.AH.NIREQGRFLQDVFTTLVDLKW.
RetrocopyMLSRKGLIPEDYLLTRLAEDV-LQPKFKAKQGKARFVGKNGTCNVAHTNIREQGRFLQDVFTTLVDLKWL
ParentalFTLVIFTTTFVSSWLLFAMSWWLVAFAHGDMDPARKNETHCVTDVESFISAFLFSIEVQVTIGFGGRMIT
.TL.IFT..F..SWLLF.M.WWLVAFAHGD..........CVTD..SF.SAFLFSIEVQVTIGFGGRMIT
RetrocopyHTLIIFTMSFLCSWLLFGMIWWLVAFAHGDLGEKGDDFVPCVTDIHSFSSAFLFSIEVQVTIGFGGRMIT
ParentalEHCLAAITVLILQNIVGLIINAVMLGCIFMKTAQSNRRAETLIFSRHAVIAVRNNRLCFMIRIGDLRKSM
E.C..AI..LI.QNIVGL.INA.MLGCIFMKTAQ..RRAETLIFS.HAVI..RN..LCFMIRIGDLRKSM
RetrocopyEECISAIIILIVQNIVGLVINAIMLGCIFMKTAQAHRRAETLIFSKHAVISLRNSKLCFMIRIGDLRKSM
ParentalIIGATVRLQVVRKTTTPEGEIIPIHQIDVQTESAVASNSLFLLAPLIICHVIDKNSPLYDLSAMELQCSD
II.ATVR.QVVR..TT.EGE..P..QID......V..N..FL..PLIICHVIDK.SPLY.LS...LQ..D
RetrocopyIISATVRMQVVRRSTTEEGEVVPLDQIDIHMDNPVGTNGVFLVSPLIICHVIDKSSPLYELSPNDLQHQD
ParentalLEVIVILEGVVETTGITTQARTSYVSEEIQWGHRFVPIVTEEEGVYSVDYSKFGNTVKVSTPSCSARELD
LEVIV.LEGVVETTGITTQARTSYVSEEI.WG.RFVP.V.E..G.Y.VDYSKFGNTVKV.TP.CSA..LD
RetrocopyLEVIVVLEGVVETTGITTQARTSYVSEEILWGQRFVPTVSEDDGMYAVDYSKFGNTVKVPTPCCSAKKLD
ParentalEKPYILIQTLQKSELSHQNSLRKRNS--MRRNNSMRKGG
E...I....L...........R.R.....RR.....K.G
RetrocopyEAGGIARFKLNEGVTMRPSVRRRRGTAIVRRSRMENK*G

                            

                            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_24 retrocopy.

TSS - click to see more details

Xiphophorus maculatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_xmac_24 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Gasterosteus aculeatus	ENSGACG00000001115	1 retrocopy	retro_gacu_7,
Tetraodon nigroviridis	ENSTNIG00000006480	1 retrocopy	retro_tnig_7,
Takifugu rubripes	ENSTRUG00000009953	1 retrocopy	retro_trub_1,
Xiphophorus maculatus	ENSXMAG00000017494	1 retrocopy	retro_xmac_24 ,

	RetrogeneDB ID:	retro_xmac_24
Retrocopy location	Organism:	*Platyfish (Xiphophorus maculatus)*
	Coordinates:	JH556751.1:1481796..1482960(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	kcnj8
	Ensembl ID:	ENSXMAG00000017494
	Aliases:	None
	Description:	potassium inwardly-rectifying channel, subfamily J, member 8 [Source:ZFIN;Acc:ZDB-GENE-060308-1]

Parental	MLARKSIIPEEFGLPGLASRLPRKPVFRDRVNKARFIAKNGSCNLAHKNIREQGRFLQDVFTTLVDLKWR
	ML.RK..IPE...L..LA......P.F.....KARF..KNG.CN.AH.NIREQGRFLQDVFTTLVDLKW.
Retrocopy	MLSRKGLIPEDYLLTRLAEDV-LQPKFKAKQGKARFVGKNGTCNVAHTNIREQGRFLQDVFTTLVDLKWL

Parental	FTLVIFTTTFVSSWLLFAMSWWLVAFAHGDMDPARKNETHCVTDVESFISAFLFSIEVQVTIGFGGRMIT
	.TL.IFT..F..SWLLF.M.WWLVAFAHGD..........CVTD..SF.SAFLFSIEVQVTIGFGGRMIT
Retrocopy	HTLIIFTMSFLCSWLLFGMIWWLVAFAHGDLGEKGDDFVPCVTDIHSFSSAFLFSIEVQVTIGFGGRMIT

Parental	EHCLAAITVLILQNIVGLIINAVMLGCIFMKTAQSNRRAETLIFSRHAVIAVRNNRLCFMIRIGDLRKSM
	E.C..AI..LI.QNIVGL.INA.MLGCIFMKTAQ..RRAETLIFS.HAVI..RN..LCFMIRIGDLRKSM
Retrocopy	EECISAIIILIVQNIVGLVINAIMLGCIFMKTAQAHRRAETLIFSKHAVISLRNSKLCFMIRIGDLRKSM

Parental	IIGATVRLQVVRKTTTPEGEIIPIHQIDVQTESAVASNSLFLLAPLIICHVIDKNSPLYDLSAMELQCSD
	II.ATVR.QVVR..TT.EGE..P..QID......V..N..FL..PLIICHVIDK.SPLY.LS...LQ..D
Retrocopy	IISATVRMQVVRRSTTEEGEVVPLDQIDIHMDNPVGTNGVFLVSPLIICHVIDKSSPLYELSPNDLQHQD

Parental	LEVIVILEGVVETTGITTQARTSYVSEEIQWGHRFVPIVTEEEGVYSVDYSKFGNTVKVSTPSCSARELD
	LEVIV.LEGVVETTGITTQARTSYVSEEI.WG.RFVP.V.E..G.Y.VDYSKFGNTVKV.TP.CSA..LD
Retrocopy	LEVIVVLEGVVETTGITTQARTSYVSEEILWGQRFVPTVSEDDGMYAVDYSKFGNTVKVPTPCCSAKKLD

Parental	EKPYILIQTLQKSELSHQNSLRKRNS--MRRNNSMRKGG
	E...I....L...........R.R.....RR.....K.G
Retrocopy	EAGGIARFKLNEGVTMRPSVRRRRGTAIVRRSRMENK*G

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

RetrogeneDB ID:

retro_xmac_24