RetrogeneDB - Retrocopy retro_trub

                        
>retro_trub_46
CAGTGTGACGCAGTGGCCTTCAATGCTTCCAAACGCGAGTTGTTTACTATCAACTCCAGGTACAAATCCATGCAGCGCAG

GCTGAGAGTGCAGTGGAGCGTCCAAAGCATGAGCGGCACGCTGTCACTGGAGAGACTGAAGAGGGTCAGGTTGTGGATAA

CTGTTGGACCAAGGGAGAAGTTCACAGCGTCAGAGCTGGAGGTGTTGAAGGAATACCTGGATGGGGGAGGACATGTGATG

GTTTTGCTTGGTGAAGGAGGAGAAACCAAATATAAGACCAACATCAACTTTCTCCTGGAGGAACTTGGAATAGTGGTCAA

CAAAGACGCGGTTGTGAGGAACGTGTACCACAGGTACTTGCATCCCAAAGAGGCACTTGTGTCTGACGGTGTGTTGAATA

GAGAAATTAGTCGAGCTGCCGATAAAGAGGTCAAGGGAACCTTTGAGGAGCCTCCTGGAAATGACCCAAAGGCTCTGGCG

TTTCTATATCCATACGGAGCCACGTTGAATGTGATGAAACCTGCTGTGGCGGTTCTCTCCACTGGTTCACTGTGCTTCCC

TTTCAACCGGCCTGTGATGGCCTTCCGTGAAGGTAAGGGGACTGGAAAACTGGTCGTGCTGGGTTCCTGCCACATGTTCA

GCGATCAATACATAGACAAAGAGGAAAACAGCAAAATCCTGGACGCTGTCCTCCAGTGGATCATGACGGATGACGCTGGC

ATGAACGGGACTGACGCCGCAGTGCCGGCGATTTCAGAATACACCATGATACCGGACACTCAGGTCCTGTCAGAGAAGCT

CCAGCTGTGTTTCCAGCACAACGAGGACCATTCCAGAATTTCACGTCTCTTTTCGATATGTCACTGTTTAACTTTTCTTC

TGCGTCCCTACCCCGCATCGTCAGCGCTTACAAGGAGCTTAACGTCAAATACGAGCCGCTCCACCGGGCGATCAGGCCAA

ACTTTGAGGCTCTGCTGCCTCCGCTTCAGCCGGCCGTCTTCCCACCTATTATCAGAGATTTGTCTCCGCCTGTGTTGGAG

CAGTTCGACCTCGATGAAGCCTTTCCCTCTGACAGAGAAGACGCCAGTAACTCCACCGACGACAATTTCGAATTC

ORF - retro_trub_46 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	70.63 %
Parental protein coverage:	84.88 %
Number of stop codons detected:	0
Number of frameshifts detected:	1

Retrocopy - Parental Gene Alignment:

                                ParentalQCSLAVFNASKRELFTTNSGYKSMQKRLRAQWKIQSLKDELSPEKLKGVKLWITVGPREKFTASELEMLK
QC....FNASKRELFT.NS.YKSMQ.RLR.QW..QS....LS.E.LK.V.LWITVGPREKFTASELE.LK
RetrocopyQCDAVAFNASKRELFTINSRYKSMQRRLRVQWSVQSMSGTLSLERLKRVRLWITVGPREKFTASELEVLK
ParentalDYMDGGGNVMVLLGEGGETKYETNINFLLEEFGIMVNNDVVVRNVYYKYLHPKEALVSDGVLNREISRAA
.Y.DGGG.VMVLLGEGGETKY.TNINFLLEE.GI.VN.D.VVRNVY..YLHPKEALVSDGVLNREISRAA
RetrocopyEYLDGGGHVMVLLGEGGETKYKTNINFLLEELGIVVNKDAVVRNVYHRYLHPKEALVSDGVLNREISRAA
ParentalGKMATGTYDETLENDAKALTFLYPYGATLNVMKPAVAVLSTGSECFPFNRPILAFHQGKETGKLAVLGSC
.K...GT..E...ND.KAL.FLYPYGATLNVMKPAVAVLSTGS.CFPFNRP..AF..GK.TGKL.VLGSC
RetrocopyDKEVKGTFEEPPGNDPKALAFLYPYGATLNVMKPAVAVLSTGSLCFPFNRPVMAFREGKGTGKLVVLGSC
ParentalHIFSDQYIDKEENSKLMDVVLQWLTTDSIEMNQIDAEEPEITEYTIIPDSKGLSEKLHVCLQDGEENPR-
H.FSDQYIDKEENSK..D.VLQW..TD...MN..DA..P.I.EYT.IPD...LSEKL..C.Q..E...R.
RetrocopyHMFSDQYIDKEENSKILDAVLQWIMTDDAGMNGTDAAVPAISEYTMIPDTQVLSEKLQLCFQHNEDHSR<
ParentalDFTSLFNTSLFNLSSSLSLPDIISAYKELNVKYEPL-QLITPQFETPLPPLQPAVFPPAVRDLPPPMLDL
.FTSLF..SLFN.SS..SLP.I.SAYKELNVKYEPL...I.P.FE..LPPLQPAVFPP..RDL.PP.L..
RetrocopyNFTSLFDMSLFNFSSA-SLPRIVSAYKELNVKYEPLHRAIRPNFEALLPPLQPAVFPPIIRDLSPPVLEQ
ParentalFDLDEAFSSEKVRLAQLTNKCTDDDLEF
FDLDEAF.S........T....DD..EF
RetrocopyFDLDEAFPSDREDASNST----DDNFEF

                            

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

                        

RNA-Seq - click to see more details

Takifugu rubripes was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Takifugu rubripes was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_trub_46 retrocopy.

TSS - click to see more details

Takifugu rubripes was not studied using FANTOM5 data.

Lab - click to see more details

retro_trub_46 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_trub_46 has 0 orthologous retrocopies within teleost group .

Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000027175	1 retrocopy	retro_cpor_301,
Microcebus murinus	ENSMICG00000015182	1 retrocopy	retro_mmur_400,
Myotis lucifugus	ENSMLUG00000016664	1 retrocopy	retro_mluc_990,
Otolemur garnettii	ENSOGAG00000007699	1 retrocopy	retro_ogar_2343,
Takifugu rubripes	ENSTRUG00000014953	1 retrocopy	retro_trub_46 ,

	RetrogeneDB ID:	retro_trub_46
Retrocopy location	Organism:	*Fugu rubripes (Takifugu rubripes)*
	Coordinates:	scaffold_77:845795..846910(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ENSTRUG00000012705
	Aliases:	None
	Status:	KNOWN_PSEUDOGENE
Parental gene information	Parental gene summary:
	Parental gene symbol:	IFT52
	Ensembl ID:	ENSTRUG00000014953
	Aliases:	None
	Description:	None

Parental	QCSLAVFNASKRELFTTNSGYKSMQKRLRAQWKIQSLKDELSPEKLKGVKLWITVGPREKFTASELEMLK
	QC....FNASKRELFT.NS.YKSMQ.RLR.QW..QS....LS.E.LK.V.LWITVGPREKFTASELE.LK
Retrocopy	QCDAVAFNASKRELFTINSRYKSMQRRLRVQWSVQSMSGTLSLERLKRVRLWITVGPREKFTASELEVLK

Parental	DYMDGGGNVMVLLGEGGETKYETNINFLLEEFGIMVNNDVVVRNVYYKYLHPKEALVSDGVLNREISRAA
	.Y.DGGG.VMVLLGEGGETKY.TNINFLLEE.GI.VN.D.VVRNVY..YLHPKEALVSDGVLNREISRAA
Retrocopy	EYLDGGGHVMVLLGEGGETKYKTNINFLLEELGIVVNKDAVVRNVYHRYLHPKEALVSDGVLNREISRAA

Parental	GKMATGTYDETLENDAKALTFLYPYGATLNVMKPAVAVLSTGSECFPFNRPILAFHQGKETGKLAVLGSC
	.K...GT..E...ND.KAL.FLYPYGATLNVMKPAVAVLSTGS.CFPFNRP..AF..GK.TGKL.VLGSC
Retrocopy	DKEVKGTFEEPPGNDPKALAFLYPYGATLNVMKPAVAVLSTGSLCFPFNRPVMAFREGKGTGKLVVLGSC

Parental	HIFSDQYIDKEENSKLMDVVLQWLTTDSIEMNQIDAEEPEITEYTIIPDSKGLSEKLHVCLQDGEENPR-
	H.FSDQYIDKEENSK..D.VLQW..TD...MN..DA..P.I.EYT.IPD...LSEKL..C.Q..E...R.
Retrocopy	HMFSDQYIDKEENSKILDAVLQWIMTDDAGMNGTDAAVPAISEYTMIPDTQVLSEKLQLCFQHNEDHSR<

Parental	DFTSLFNTSLFNLSSSLSLPDIISAYKELNVKYEPL-QLITPQFETPLPPLQPAVFPPAVRDLPPPMLDL
	.FTSLF..SLFN.SS..SLP.I.SAYKELNVKYEPL...I.P.FE..LPPLQPAVFPP..RDL.PP.L..
Retrocopy	NFTSLFDMSLFNFSSA-SLPRIVSAYKELNVKYEPLHRAIRPNFEALLPPLQPAVFPPIIRDLSPPVLEQ

Parental	FDLDEAFSSEKVRLAQLTNKCTDDDLEF
	FDLDEAF.S........T....DD..EF
Retrocopy	FDLDEAFPSDREDASNST----DDNFEF

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

RetrogeneDB ID:

retro_trub_46