RetrogeneDB ID:

retro_gacu_3

Retrocopy
location
Organism:Stickleback (Gasterosteus aculeatus)
Coordinates:groupVIII:16041765..16043610(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSGACG00000012652
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:LINGO3 (1 of 2)
Ensembl ID:ENSGACG00000015271
Aliases:None
Description:leucine rich repeat and Ig domain containing 3 [Source:HGNC Symbol;Acc:21206]


Retrocopy-Parental alignment summary:






>retro_gacu_3
AGGAGTGGCATGGGGACGAGGCCGGGCCGGGACGAGCTGGGCTGGCTCCCGCCTTTCCTGGTCTTGCTACTGATGAGCAC
GGTGTCGCCCGCCCAGAGTCAAGGATGTCCCCAGCGTTGCGATTGTTTCGCCAAACTCAAGACTGTGTCCTGTTTTGGTA
AACGGCTGTCCTCGCTGCCCGACGGCATCCCGCTGGACACCAAGGTCCTGGACCTGAGTGGGAATAAACTCCGCTGGGTG
GAGCAGAGTGACCTGCTTTCATATCCACGTCTGGAAAAACTGGACCTGAGTGACAACATGGTCAGCAGCCTGGAACCGAA
TGCCTTTTCCAGTCTGCAGAACCTGCGGTCGCTTTCACTGAGGGGCAACCAATTGAAACTGGTCCCCATGGGGGCTTTCT
CCCGTCTGTCCAACCTAACATCACTGGACCTCAGTGGGAATAAGATTGTCATTCTTTTGGACTTTACTTTCCAAGACCTG
AAAAGTTTGAAAAACCTTGAAGTTGGAGACAATGACTTGGTTTATATTTCCAACAAAGCCTTCCTGGGTCTGGTGGGGCT
GAGGGAGCTGACCATCGAGAGGTGCAACCTGACTTCTGTGTCCAGCCAGTCTTTGTCCTACCTGCAAAACCTGGTGGATC
TGCGCCTCCGCTACCTCAGCATCTCCACCTTGGAGGACCAGAACTTCCGTAAGCTGGCAAACCTGAGGGGCCTCGAGATC
GACCACTGGCCCTTCCTGGAGCACGTTCCCCCTCACAGCCTGCAGGGGCTCAACTTATCTTGGCTGTCTATTACTCACAC
TAACATCACCTCTGTGCCCACCTCCGCCCTCCGCAGTCTGGCTCACCTCACCAGCCTCAACCTCTCGTACAACCCCATCT
CCGTGCTGGAGTCCTGGGCCCTGCGGGACCTCATTCGGCTGAAGGAGCTGCATCTGGTCAACACAAATCTGGCGGTGGTG
CAGCCGTACGCGCTGGGCGGTCTGAGGCAGATCAGCCTCCTGAACCTCTCCACCAACGGCCTGGTGTCCCTGGAGGAGGG
AGCCTTTCAGTCCGTCAACACTCTGGAGACGCTGCGTTTGGACGGAAACCCTCTGGCCTGCGACTGCCGCTTGCTGTGGA
TCCTCCAGCGCCGGAAGACCCTGAATTTCGACGGCGCCTCCCCTGTGTGCATGTCGCCCGTGGAGGTGCAGGGACGGGCC
CTGAACGCCTTCTCCGACTCGGCCCTCTTCGATCACTTCACTTGCCAGAAGCCCAAAATCCGCAACAGGAAACTGCAGCA
GGTCTCGGCCCGCGAGGGGCAGGTCGTGTCGTTCGTTTGCAGAGCGGAAGGCGAGCCGGCGCCGGTGATATTCTGGATCT
CGCCCCAGCGCCGCCGCATCACCACAAAGAGCAGCGGCCGCCTGACGGTGTTACCAGAGGGCACACTGGAGATACGGTAC
GCCCAGGTGACAGACAGCGGCACCTACATCTGCATAGCCAGCAACGCGGGCGGAAACGACACCTATTTCGCCACGCTCAC
GGTCAGCGGGCTGCCGCTCGACGCGGCCCTGCTGGCCAACCGCACGTACTACGCGGGCGACCTCAACGACACGAATCTGA
ATGACACCAGGGTCTTCTTGAAGTTCACTCTGGACCTCAAGACCATCCTGATATCCACGGCCATGGGCTGCATCATGTTC
CTGGGGGTGGTGCTCTTCTGTTTCATCCTGCTGTTCGTGTGGAGTCGAGGGAGAGGCCAGCACAAGAACAATTTCTCCGT
GGAGTATTCCTTCAGGAAGGTGGACGGACCCGCCGCCAGCGGAGGGCAGGGCGGCGCTCGCAAGTTCAACATGAAAATGA
TTTGA

ORF - retro_gacu_3 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.31 %
Parental protein coverage: 96.47 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalWLLAASLVAVITFTLPGNSEACPPRCDCSAQLRSVSCQRRRLTNIPEGIPTETRLLDLSKNRLRWVQAGD
WL.............P..S..CP.RCDC.A.L..VSC...RL...P.GIP..T..LDLS.N.LRWV...D
RetrocopyWLPPFLVLLLMSTVSPAQSQGCPQRCDCFAKLKTVSCFGKRLSSLPDGIPLDTKVLDLSGNKLRWVEQSD
ParentalLAPYPRLEEVDLSENLIATLEPNAFASLLSLKVLKLRGNQLKLVPMGAFAKLGNLTSLDLSENKMVILLD
L..YPRLE..DLS.N....LEPNAF.SL..L..L.LRGNQLKLVPMGAF..L.NLTSLDLS.NK.VILLD
RetrocopyLLSYPRLEKLDLSDNMVSSLEPNAFSSLQNLRSLSLRGNQLKLVPMGAFSRLSNLTSLDLSGNKIVILLD
ParentalYTFQDLRGLKHLEVGDNDLVYISHKAFSGLLGLEDLTIERCNLTSISGQTLSYLRSLVTLRLRHLSIIAL
.TFQDL..LK.LEVGDNDLVYIS.KAF.GL.GL..LTIERCNLTS.S.Q.LSYL..LV.LRLR.LSI..L
RetrocopyFTFQDLKSLKNLEVGDNDLVYISNKAFLGLVGLRELTIERCNLTSVSSQSLSYLQNLVDLRLRYLSISTL
ParentalDDQNFRKLSNLRALDIDHWPYLEYISPLSFQGLDLHRLSITNTNITSVPSSSFKNLVHLTHLNLSYNPIT
.DQNFRKL.NLR.L.IDHWP.LE...P.S.QGL.L..LSIT.TNITSVP.S....L.HLT.LNLSYNPI.
RetrocopyEDQNFRKLANLRGLEIDHWPFLEHVPPHSLQGLNLSWLSITHTNITSVPTSALRSLAHLTSLNLSYNPIS
ParentalTLEPWAFKDLLRLKDLIMVSTGLMTVELHALGGLRQIRVLNFSSNDLQTLEEGSFHSVNSLETLRVDGNP
.LE.WA..DL.RLK.L..V.T.L..V...ALGGLRQI..LN.S.N.L..LEEG.F.SVN.LETLR.DGNP
RetrocopyVLESWALRDLIRLKELHLVNTNLAVVQPYALGGLRQISLLNLSTNGLVSLEEGAFQSVNTLETLRLDGNP
ParentalLMCDCRLLWILQRRKTLNFDGRVPVCAGPVEVQGFSLSAFTDSALFDHFTCQKPKIRNRKLQQVIAREGQ
L.CDCRLLWILQRRKTLNFDG..PVC..PVEVQG..L.AF.DSALFDHFTCQKPKIRNRKLQQV.AREGQ
RetrocopyLACDCRLLWILQRRKTLNFDGASPVCMSPVEVQGRALNAFSDSALFDHFTCQKPKIRNRKLQQVSAREGQ
ParentalPVSFLCRAEGEPAPAIIWISPQRRRITAKSLGRITVLSSGTLEIRYAQLTDSGTYICIASNAGGNDTYFA
.VSF.CRAEGEPAP.I.WISPQRRRIT.KS.GR.TVL..GTLEIRYAQ.TDSGTYICIASNAGGNDTYFA
RetrocopyVVSFVCRAEGEPAPVIFWISPQRRRITTKSSGRLTVLPEGTLEIRYAQVTDSGTYICIASNAGGNDTYFA
ParentalTLTVRGQPLDAASAFFLNRSLYSGDFFNDTNLNNTRVFLKFTLDLTTILVSTAMGCITFLGVVLFCFLLL
TLTV.G.PLDA..A...NR..Y.GD..NDTNLN.TRVFLKFTLDL.TIL.STAMGCI.FLGVVLFCF.LL
RetrocopyTLTVSGLPLDA--ALLANRTYYAGD-LNDTNLNDTRVFLKFTLDLKTILISTAMGCIMFLGVVLFCFILL
ParentalFVWSRGRGQRKNNFTVEYSFRKSE-PVTGSSSGGTRKFNMKMI
FVWSRGRGQ.KNNF.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

Gasterosteus aculeatus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Gasterosteus aculeatus was not studied using ChIP-Seq data.

EST - click to see more details

Gasterosteus aculeatus was not studied using EST data.

TSS - click to see more details

Gasterosteus aculeatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_gacu_3 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_gacu_3 has 2 orthologous retrocopies within teleost group .

Species RetrogeneDB ID
Tetraodon nigroviridis retro_tnig_4
Danio rerio retro_drer_4
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 ENSGACG00000015271 1 retrocopy
retro_gacu_3 ,
Oreochromis niloticus ENSONIG000000101991 retrocopy
retro_onil_14,
Tetraodon nigroviridis ENSTNIG000000153191 retrocopy
retro_tnig_4,
Xiphophorus maculatus ENSXMAG000000193161 retrocopy
retro_xmac_14,


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