RetrogeneDB ID:

retro_tnig_5

Retrocopy
location
Organism:Tetraodon (Tetraodon nigroviridis)
Coordinates:3:12626975..12629309(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSTNIG00000007006
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:elfn1b
Ensembl ID:ENSTNIG00000008254
Aliases:None
Description:extracellular leucine-rich repeat and fibronectin type III domain containing 1b [Source:ZFIN;Acc:ZDB-GENE-080327-21]


Retrocopy-Parental alignment summary:






>retro_tnig_5
ATGGTGATGAGTGCCTTGTTTTGGTCTGTAGCCATTGTTTATTTGAGTCAGATTGGCAGAGTGAATGCAGACTGCTGGTT
AATTGAGGGTGAAAAGGGCTTTGTGTGGCTTGCAATTTGTAGCCAAAACCAACCACCTTATGAGGCCATCCCTCAGCATA
TCAACAGCACCATTGTGGACCTTCGTCTGAATGAAAACAAAATCAAGAGTATTCACTATTCAGCCCTTAGCCGCTTTGCC
AACTTAACCTACCTTAACCTGACGAAGAATGAAATCTCCTACATTGAAGACGGGGCCTTTTCTGCTCAGTTTAACCTACA
AGTCCTTCAAATGGGCTTCAACAAGTTGCGAAACTTGACCGAAGGCATCCTCAGGGGTTTAGGAAAGCTGCAGTACCTCT
ACCTCCAGGCAAATTTGATTGAGACTGTGACACCTAATGCCTTTTGGGAATGCCCCAACATTGAGAACATCGACCTCTCC
ATGAACCGAATCCAGCAGTTAGATGGGTCCACATTCTCCAGTTTGGCCAAACTGACCACCTGCGAGCTGTACACCAATCC
TTTCAACTGCTCCTGTGAGCTACTTGGATTTGTCAAATGGCTGTCGGTCTTCCCCAACAGAACAAACGAGCGGATGGTCT
GCGACTCCCCGTCTGGAGTCTCTGGTTATAGTTTACTAAGCCAGAATCCGAACAACCCAACGTACAAAAATGCTCTCTAC
ATGCTCACCACCGTGTGCACTGATGACTATGTCACTCCGTATACCCCAATCCCCACTGAGTCCATCACCCCCCCACCAGA
CTTAACACTGTGCGGTCTGGAGGATTGTCCCTCAGGGACAGAACCGGAGGAGATAATTATCAGTACGACATATAACGATG
TGGAGGTCAACCCTGTCATGAAGCTGAAACAGGTTTCAAATACAGGCGCCACCATCACCGTTCAGATTCCATACCCTTTT
AAGAAGATGTACATCCTGGTTCTCTACAACAACAGTTTTTTCACGGACATTCAGAACCTGAACAAAATAAAAGAGGACAT
TGATCTGAAAAACCTAAATCCCCACACTAACTACACATACTGTGTTGCTTCAATACGCAACTCCCTTCGCCACAATCACA
CTTGTCTGACAATCACCACTGGCCCCTGGAATGGGAAGGAGCGAAGTGTGAACAATGCAACTGCGACTCACTACATTATG
ACCATTTTAGGCTGCCTCTTCAGCATGGTGATCTTTCTGGGCATCGTCTACTATTGTTTGCGTAGAAAGCGGCAGCAAGA
CGAAAAGCACAAAAAGTCAGGTAGCCTAAAGAAGAACATAATGGAGCTTAAATACGGACAGGAACTGGAGGGGGGGACTA
TTTCTAGAATGTCGCAAAAACAGTTGCTTGCCGGGGACAGCATGGCGCGCATGCCGTACTTACCGTCTGCTGCTGAGATG
GAGCAGTACAAATTTCAAGAGATAAGTGACACCCCTAAAATGATGAAAGGGAATTACATGGAGGTGCGGAGCATGGACCA
CCACGAACGCAGGGAGTGTGAAATGGGAATGGCAGGGAACAGCCAGGGGTCGGTGGCTGAGATTTCCACCATCGCAAAAG
AGGTGGATAAAGTAAATCAGATTATTAACAACTGCATAGATGCACTGAAGTCTGAATCCACCTCTTTTCAGGGCGTAAAA
TCTGGAGCGGTGTCCACCGCAGAGCCACAGCTGGTGCTGATATCAGAACACCCACAAGGTAAACCTGGCCTTCTGTCCCC
ACCATATAAGGACAGCTACCACCACTCTCTGCAGAGGCATCGGTCATCTGACGTCTCACCAAAGAGGCCCAGCACCGCCA
CAGGAGGCCCAATGCGAAGCCCCAGGCCTTACCGCTCTGACTCCAAGTACATAGAGAAAACCTCCCCAACTGGAGAGACC
ATCGTCACTGTAACGCCTGCTGCAGCTATCCTAAGGGCTGAGGCGGACAAGATCCGTCAGTACAGCGACCATCGACACTC
GTATCCCGACGCTCAGATCGAGGAACTTGAAGGACCTGATGGCCACAAGTCCTCCTTATTAGAGCCTCTTACCCACTCCC
GTTCCAGAGACTTAGCATATTCCCAACTGCCTTCCCAGTATCACAATCTAAGCTACTCCTCCAGCCCCGAGTACTACTGC
AAACCGCCACAAAGCATCTGGGGGCGGTTCAAACTGCACCGGAAGCGGCACAAAGACGACGAGTACATGGCTGCCGGCCA
CGCATTGCGGAAAAAGGTCCAGTTCGCAAAAGACGAGGATCTGCATGATATTTTAGACTACTGGAAAGGTGTTTCAGCCC
AGCATAAATCATAA

ORF - retro_tnig_5 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.6 %
Parental protein coverage: 67.58 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalVFSTFLCWMVLLSVMRLPVVTADCWLIEGEKGFVWLAICSMNQPPYENIPAHINSTIVDLRLNENKIRSV
V.S................V.ADCWLIEGEKGFVWLAICS.NQPPYE.IP.HINSTIVDLRLNENKI.S.
RetrocopyVMSALFWSVAIVYLSQIGRVNADCWLIEGEKGFVWLAICSQNQPPYEAIPQHINSTIVDLRLNENKIKSI
ParentalHYSSLSRFGNLTYLNLTKNDISYVEDGAFSAQFNLQVLQMGFNKLRNLTEGMLRGLGKLQYLYLQANLIE
HYS.LSRF.NLTYLNLTKN.ISY.EDGAFSAQFNLQVLQMGFNKLRNLTEG.LRGLGKLQYLYLQANLIE
RetrocopyHYSALSRFANLTYLNLTKNEISYIEDGAFSAQFNLQVLQMGFNKLRNLTEGILRGLGKLQYLYLQANLIE
ParentalTVTPNTFWECPNIENIDLSMNRYGPLDLWTSKDLSKLTTCELYTNPFNCSCELLGFLRWLSAFPNRTSER
TVTPN.FWECPNIENIDLSMNR...LD..T...L.KLTTCELYTNPFNCSCELLGF..WLS.FPNRT.ER
RetrocopyTVTPNAFWECPNIENIDLSMNRIQQLDGSTFSSLAKLTTCELYTNPFNCSCELLGFVKWLSVFPNRTNER
ParentalMVCDSPQGFFGYSLLSQNPRMATQGSALHMLSVVCTEVDSSVTSFNGIGMADFTTPPPDFASPCGLEDCA
MVCDSP.G..GYSLLSQNP...T...AL.ML..VCT..D..VT....I......TPPPD....CGLEDC.
RetrocopyMVCDSPSGVSGYSLLSQNPNNPTYKNALYMLTTVCT--DDYVTPYTPI-PTESITPPPDL-TLCGLEDCP
ParentalSGTPPDEVINFSPIFSD--TNPVMTLKQVHHSSAVITVQLPLPFKKMYILALYNNSFFMDIQNLRRQRED
SGT.P.E.I..S....D...NPVM.LKQV....A.ITVQ.P.PFKKMYIL.LYNNSFF.DIQNL....ED
RetrocopySGTEPEEII-ISTTYNDVEVNPVMKLKQVSNTGATITVQIPYPFKKMYILVLYNNSFFTDIQNLNKIKED
ParentalIELKNLKPNTDYTYCVASLRNSLRFNHTCLTISTGRRSGVERAVNKSSATHYIMTILGCLFGMLLFLGLI
I.LKNL.P.T.YTYCVAS.RNSLR.NHTCLTI.TG...G.ER.VN...ATHYIMTILGCLF.M..FLG..
RetrocopyIDLKNLNPHTNYTYCVASIRNSLRHNHTCLTITTGPWNGKERSVNNATATHYIMTILGCLFSMVIFLGIV
ParentalVHCLRKRRLMEEKERKMSRIQRTLIELKYGGEDDIEGGAVGPVSQK-LSAGDSLSRIPYLPQGGEMDPYK
..CLR..R...EK..K.........ELKYG.E...EGG.....SQK.L.AGDS..R.PYLP...EM..YK
RetrocopyYYCLRRKRQQDEKHKKSGSLKKNIMELKYGQE--LEGGTISRMSQKQLLAGDSMARMPYLPSAAEMEQYK
ParentalLQEVIETPPHKPAKLNYMEVRGSGIEREREREMSPQGNPQGSVAEISTIAKEVDKVNQIINNCIDALKSE
.QE...TP..K..K.NYMEVR.......RE.EM...GN.QGSVAEISTIAKEVDKVNQIINNCIDALKSE
RetrocopyFQEISDTP--KMMKGNYMEVRSMDHHERRECEMGMAGNSQGSVAEISTIAKEVDKVNQIINNCIDALKSE
ParentalSTSFQQGIKS
STSF.QG.KS
RetrocopySTSF-QGVKS

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






RNA-Seq - click to see more details

Tetraodon nigroviridis was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Tetraodon nigroviridis was not studied using ChIP-Seq data.

EST - click to see more details

Tetraodon nigroviridis was not studied using EST data.

TSS - click to see more details

Tetraodon nigroviridis was not studied using FANTOM5 data.

Lab - click to see more details

retro_tnig_5 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_tnig_5 has 3 orthologous retrocopies within teleost group .

Species RetrogeneDB ID
Gasterosteus aculeatus retro_gacu_19
Oryzias latipes retro_olat_18
Takifugu rubripes retro_trub_13
Parental genes homology:
Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species Parental gene accession Retrocopies number
Gasterosteus aculeatus ENSGACG000000165021 retrocopy
retro_gacu_19,
Oreochromis niloticus ENSONIG000000001601 retrocopy
retro_onil_6,
Oryzias latipes ENSORLG000000097201 retrocopy
retro_olat_18,
Tetraodon nigroviridis ENSTNIG00000008254 1 retrocopy
retro_tnig_5 ,
Takifugu rubripes ENSTRUG000000151971 retrocopy
retro_trub_13,
Xiphophorus maculatus ENSXMAG000000140931 retrocopy
retro_xmac_1,




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