RetrogeneDB ID:

retro_xmac_14

Retrocopy
location
Organism:Platyfish (Xiphophorus maculatus)
Coordinates:AGAJ01046704.1:7049..8876(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSXMAG00000019590
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:LINGO3 (2 of 2)
Ensembl ID:ENSXMAG00000019316
Aliases:None
Description:leucine rich repeat and Ig domain containing 3 [Source:HGNC Symbol;Acc:21206]


Retrocopy-Parental alignment summary:






>retro_xmac_14
ATGGGGGTTGGCCTGGGCGTATGTTGGCTGCTGCCTTTCCTCTTCTTGCTGCTTATGATCACAGTGTCCTCCACCCAAAG
TCAAGGATGTCCCCTGCGTTGTGACTGCATTGCGAAGCTGAAGACTGTGTCCTGTTTTGGTAAACGTCTGTCCTCCTTGC
CGGAGGGAATCCCGCCTGACACCAAAGTTTTGGACCTAAGTGGGAATAAACTTCGCTGGATAGAACAGGATGATCTGCTT
CCATATACACGCCTGGAGAAGCTGGAACTCAGTGATAACATGATCAGTGTCCTGGAGCCAAATGCGTTTTCAAGTCTTCA
GAACTTGCAGTCACTTTCACTGAGGGGTAACCAGCTAAAACTGGTTCCCATGGGAGCTTTCTCGCGTCTCTCCAACCTCA
CCTCCTTAGATTTGAGTGGAAATAAGATTGTAATTCTTTTGGACTTCACTTTCCAAGACCTAAAAAGTCTTAAGAACCTG
GAGGTTGGTGACAATGATCTGGTTTACATTTCTAACAAGGCTTTTCTGGGATTAGTAGGACTCAAGGAGCTGACAATTGA
GAGATGCAACCTGACGTCGGTGTCCAGCCAATCGTTATCCTATCTGCACAACCTGGTGACTCTGCGACTCAGGTATCTTA
GCATCTCCTCCTTAGACGACCAGAACTTTCGAAAACTTGGAAATCTTAGAGGTCTGGAGATTGATCATTGGCCCTTTTTG
GAATATATCTCCCCTCATAGCCTTCAAGGCCTTAATTTGTCTTGGCTGTCCATTACTCACACCAACATCACCTCTGTGCC
CACCTCTGCCCTTCGTAGTTTGGCTCACCTCACTAGCCTCAACCTCTCCTATAATCCAATCACTGTGTTAGAGTCCTGGG
GTCTGCGGGATCTCATCAGACTGAAGGAGCTGCATCTGGTGAACACTAACCTGGCAGTAGTTCAACCTTATGCACTAGGT
GGTCTGAGGCAAATCCGCCTTCTTAATCTTTCAACCAACAGCTTAGTGACCTTGGAAGAGGGAGCCTTTCAGTCAGTCAA
CACTCTTGAGACGCTGCGCTTGGATAGAAACCCTCTTGCCTGTGACTGCCGCCTCCTCTGGATCCTTCAGCGTAGGAAGA
CCCTTAATTTTGATGGTGCCTCCCCTGTGTGTATGACCCCTGTTGAAGTCCAAGGCCGGGCTCTTAGTGCTTTCACCGAC
TCAGCTCTTTTTGACCACTTTACTTGCCAGAAACCTAAAATTCGCAACAGGAAACTGCAGCAAATTTCAGCCCGCGAAGG
GCAAGTAGTGTCGTTTATCTGCAGAGCAGAAGGTGAGCCAACGCCGGTGATATTCTGGATTTCTCCTCAGCGTCGACGCA
TAACCACAAAGAGCAGTGGGCGACTGACTGTGTTACCAGAGGGCACTCTAGAAATACGCTACGCCCAGGTAACTGATAGT
GGAACCTACATCTGCATCGCTAGCAATGCTGGTGGAAATGACACCTACTTTGCTACGCTCACAGTCAGTGGGCTACCACT
GGATGCAGCACTCATGGCCAACCGCACCTATTATGCTGGGGACCTTAACGACACAAATCTGAATGACACCAGGGTGTTCT
TGAAGTTCACCCTTGACCTCAAGACCATTCTAATATCTACAGCTATGGGCTGTATCATGTTTCTGGGAGTGGTCTTGTTC
TGCTTCATCCTGCTATTTGTGTGGAGTCGGGGTAGAGGACAGCACAAAAACAACTTCTCAGTTGAATATTCTTTCAGAAA
AGTGGACGGACCAGCAGCCAGCGGAGGACAGGGGGGAGCACGAAAGTTCAACATGAAAATGATTTGA

ORF - retro_xmac_14 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.31 %
Parental protein coverage: 96.78 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalWVLASSLVSVIALTLPESSKACPPRCECSAQLRSVSCQRRRLTNVPEGIPTETRVLDLSKNRLRWVQSGD
W.L...............S..CP.RC.C.A.L..VSC...RL...PEGIP..T.VLDLS.N.LRW....D
RetrocopyWLLPFLFLLLMITVSSTQSQGCPLRCDCIAKLKTVSCFGKRLSSLPEGIPPDTKVLDLSGNKLRWIEQDD
ParentalLAPYPRLEEVDLSENLIATLEPNAFAALQNLKVLKLRGNQLKLVPMGAFAKLGNLTSLDLSENKMVILLD
L.PY.RLE...LS.N.I..LEPNAF..LQNL..L.LRGNQLKLVPMGAF..L.NLTSLDLS.NK.VILLD
RetrocopyLLPYTRLEKLELSDNMISVLEPNAFSSLQNLQSLSLRGNQLKLVPMGAFSRLSNLTSLDLSGNKIVILLD
ParentalYTFQDMRNLKQLEVGDNDLVYISHKAFSGLLGLEDLTIERCNLTSISGQTLSYLHSLVTLRLRHLSITAL
.TFQD...LK.LEVGDNDLVYIS.KAF.GL.GL..LTIERCNLTS.S.Q.LSYLH.LVTLRLR.LSI..L
RetrocopyFTFQDLKSLKNLEVGDNDLVYISNKAFLGLVGLKELTIERCNLTSVSSQSLSYLHNLVTLRLRYLSISSL
ParentalEDQNFRKLSNLRGLDIDHWPYLEYISPLSFQGLDLHWLFITNTNITTVPSNSFKNLVHLTHLNLSYNPIT
.DQNFRKL.NLRGL.IDHWP.LEYISP.S.QGL.L.WL.IT.TNIT.VP......L.HLT.LNLSYNPIT
RetrocopyDDQNFRKLGNLRGLEIDHWPFLEYISPHSLQGLNLSWLSITHTNITSVPTSALRSLAHLTSLNLSYNPIT
ParentalTLEPWAFKDLLRLKELIMVSTGLLTVESHALGGLRQIRVLNFSSNDLQTLEEGSFHSVNSLETLRVDGNP
.LE.W...DL.RLKEL..V.T.L..V...ALGGLRQIR.LN.S.N.L.TLEEG.F.SVN.LETLR.D.NP
RetrocopyVLESWGLRDLIRLKELHLVNTNLAVVQPYALGGLRQIRLLNLSTNSLVTLEEGAFQSVNTLETLRLDRNP
ParentalLLCDCRLLWILQRRKTLNFDGRVPVCAGPVEVQGVSLSAFSDSALFDHFTCQKPKIRNRKMQQVVAREGQ
L.CDCRLLWILQRRKTLNFDG..PVC..PVEVQG..LSAF.DSALFDHFTCQKPKIRNRK.QQ..AREGQ
RetrocopyLACDCRLLWILQRRKTLNFDGASPVCMTPVEVQGRALSAFTDSALFDHFTCQKPKIRNRKLQQISAREGQ
ParentalPVSFVCRADGDPTPAIIWISPQRRRITAKSSGRITVLPSGTLEIRYAQLTDSGTYICIATNAGGNDTYFA
.VSF.CRA.G.PTP.I.WISPQRRRIT.KSSGR.TVLP.GTLEIRYAQ.TDSGTYICIA.NAGGNDTYFA
RetrocopyVVSFICRAEGEPTPVIFWISPQRRRITTKSSGRLTVLPEGTLEIRYAQVTDSGTYICIASNAGGNDTYFA
ParentalTLTVRGQPLDSASAFFLNRSLYSGEYFNDTNLNSTRVFLKFTLDLTTILVSTAMGCITFLGVVLFCFLLL
TLTV.G.PLD...A...NR..Y.G...NDTNLN.TRVFLKFTLDL.TIL.STAMGCI.FLGVVLFCF.LL
RetrocopyTLTVSGLPLD--AALMANRTYYAGD-LNDTNLNDTRVFLKFTLDLKTILISTAMGCIMFLGVVLFCFILL
ParentalFVWSRGRGQRRNNFTVEYSFRKSE-PTTGSSTGGTRKFNMKMI
FVWSRGRGQ..NNF.VEYSFRK...P......GG.RKFNMKMI
RetrocopyFVWSRGRGQHKNNFSVEYSFRKVDGPAASGGQGGARKFNMKMI

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_14 retrocopy.

TSS - click to see more details

Xiphophorus maculatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_xmac_14 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 5 parental genes, and 5 retrocopies.

Species Parental gene accession Retrocopies number
Danio rerio ENSDARG000000678151 retrocopy
retro_drer_4,
Gasterosteus aculeatus ENSGACG000000152711 retrocopy
retro_gacu_3,
Oreochromis niloticus ENSONIG000000101991 retrocopy
retro_onil_14,
Tetraodon nigroviridis ENSTNIG000000153191 retrocopy
retro_tnig_4,
Xiphophorus maculatus ENSXMAG00000019316 1 retrocopy
retro_xmac_14 ,




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