RetrogeneDB - Retrocopy retro_tsyr

                        
>retro_tsyr_342
ACCCACAGAGAGCACGAAAAGCCGGTTGTCCCGTCGAGTGTCCGCAATCAGCTACGCGACAGAAACAATGTGTTAAACAT

GTCGAGAAAGATGAACGCAAATACTGAGGAGCTCCTGAAACGCAGCCGCGACCACCTCCGGCTGCAGCCCTGCCACCTGT

CGGACATCATGGGGAAGGGCCTGAGGGTGGCGCCCCTCTCCTACTACACCGGGATCATGGAGGACGCTACGGACAGTGAG

AAAAGATATGATTCATTGCCCAGTTTTACGGCTGCTGGCTGTCTAAGGCTTCTTGGCATAGGAAGAAACCAGTATATTGA

TCTTATGAATCAGTGTAGGTCATCAAAAAAGTTTTTCAGAAGGAAAACAGCCCGTGATCTTCTGCCCGTGGAAATTGCCA

TCAAGGCCTGGTGGGTGGTGCAGGCTGGCTACATCACCGAAGATGACATCAAGAAATGCACTTTACCTGAGAAATGTGCT

ATTGATGTGATCATCGATTCAGGCCCTCAACTCTCTGGATCACCAGATTACCATGTAGTACATATTTTATATGACAAAGG

ATTTATTTATCTGGATGTACCAATATCTGATGACAACTGTACAGCAGTTCCCTCTCTTGAAGGCTTTGTAAAGGATCGAG

TACAAGGTGATTATTTTGAAACTCTGCTCTATAAGATATTTGTTTCAATAGATGAGCACACTAATGTTGCAGAGCTTGCA

AATGTCCTTAAGATACACTTATCCCTGGTTAAGAATGCTGTTTCAATGTATTGCCACTTGGGCTTTGCCCATAGGAAGGG

ACAAGTCATCAATCTGGATCGACTTCATTCATCGTGGAAGAATGTACCATCCGTGAACAGATTAAAGAGCACTTTAGATC

TGCAGAAGATGCTCTTATCCTGGGACAGCGGGGAACGACGGAGACCCATTCAAGAAGCTTCATCGGCTACCAACACTGAT

ACGAACAGCCAAGAAGATCCAGCTGACACAGCCAATGTGGTAGTGTGAGCCTGTCCACAGAATACACAAAGCGAATTGCA

TTCCTGTTTGACTCAACTCTTATGGCCTTCTTAATGATGGGAAACCTTTCACCAAACTTGAAAATTTGTGCCATCACAAT

GTTTGAAGGAGGCAAGCTCTCAGATGAGTTTCTGGAAAGCTTTCTCATAGAACTGGAAAAGGTTCAGAGCACTGGTGAAG

GAGAAACTCTGAGATACTTTGATCATCCGCTTACTTTGAGAAACACCATTCTGTTTCTGCGTCATAATAAAGACCTAGTT

GCACAAACTGCACAGCCAGACCAACCCAATTATGATTTTCCTCTGGATCTCTTGTGCTGTGAGAGCCTTCTTGTCCTGAA

CCCCACAACTTGCAGGAGAGTTCTGAACAAAAACTAC

ORF - retro_tsyr_342 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	83.93 %
Parental protein coverage:	57.74 %
Number of stop codons detected:	0
Number of frameshifts detected:	3

Retrocopy - Parental Gene Alignment:

                                ParentalSQREYEKQVVLYSIRNQLRYRNNL-VKHVKKDERKYY-EELLKYSRDHLLLYPYHLSDIMVKGLRVTPFS
..RE.EK.VV..S.RNQLR.RNN..VKHV.K.....Y.EELLK.SRDHL.L.P.HLSDIM.KGLRV.P.S
RetrocopyTHREHEKPVVPSSVRNQLRDRNNV<VKHVEK-DERKY>EELLKRSRDHLRLQPCHLSDIMGKGLRVAPLS
ParentalYYTGIMEDIMNSEKSYDSLPNFTAADCLRLLGIGRNQYIDLMNQCRSSKKFFRRKTARDLLPVKPVEIAI
YYTGIMED...SEK.YDSLP.FTAA.CLRLLGIGRNQYIDLMNQCRSSKKFFRRKTARDLL...PVEIAI
RetrocopyYYTGIMEDATDSEKRYDSLPSFTAAGCLRLLGIGRNQYIDLMNQCRSSKKFFRRKTARDLL---PVEIAI
ParentalEAWWVVQAGYITEDDIKICTLPEKCAIDKIIDSGPQLSGSLDYHVVHSLYNKGFIYLDVPISDDSCIAVP
.AWWVVQAGYITEDDIK.CTLPEKCAID.IIDSGPQLSGS.DYHVVH.LY.KGFIYLDVPISDD.C.AVP
RetrocopyKAWWVVQAGYITEDDIKKCTLPEKCAIDVIIDSGPQLSGSPDYHVVHILYDKGFIYLDVPISDDNCTAVP
ParentalPLEGFVMNRVQGDYFETLLYKIFVSIDEHTNVAELANVLEIDLSLVKNAVSMYCRLGFAHKKGQVINLDQ
.LEGFV..RVQGDYFETLLYKIFVSIDEHTNVAELANVL.I.LSLVKNAVSMYC.LGFAH.KGQVINLD.
RetrocopySLEGFVKDRVQGDYFETLLYKIFVSIDEHTNVAELANVLKIHLSLVKNAVSMYCHLGFAHRKGQVINLDR
ParentalLHSSWKNVPSVNRLKSTLDPQKMLLSWDGGERRSPVQEASSATDTDTNSQEDPADTASV-SSLSLSTGYT
LHSSWKNVPSVNRLKSTLD.QKMLLSWD.GERR.P.QEASSAT.TDTNSQEDPADTA.V..S.SLST.YT
RetrocopyLHSSWKNVPSVNRLKSTLDLQKMLLSWDSGERRRPIQEASSATNTDTNSQEDPADTANV<GSVSLSTEYT
ParentalKRIAFLFDSTLTAFLMMGNLSPNLKSHAVTMFEVGKLSDESLDSFLVELEKVQSTGEGEAQRYFDHALTL
KRIAFLFDSTL.AFLMMGNLSPNLK..A.TMFE.GKLSDE.L.SFL.ELEKVQSTGEGE..RYFDH.LTL
RetrocopyKRIAFLFDSTLMAFLMMGNLSPNLKICAITMFEGGKLSDEFLESFLIELEKVQSTGEGETLRYFDHPLTL
ParentalRNTILFLRHNKDLVAQTAQPDQPNYGFPLDLLRCESLLGLDPATCSRVLNKNY
RNTILFLRHNKDLVAQTAQPDQPNY.FPLDLL.CESLL.L.P.TC.RVLNKNY
RetrocopyRNTILFLRHNKDLVAQTAQPDQPNYDFPLDLLCCESLLVLNPTTCRRVLNKNY

                            

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

                        

RNA-Seq - click to see more details

Tarsius syrichta was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Tarsius syrichta was not studied using ChIP-Seq data.

EST - click to see more details

Tarsius syrichta was not studied using EST data.

TSS - click to see more details

Tarsius syrichta was not studied using FANTOM5 data.

Lab - click to see more details

retro_tsyr_342 was not experimentally validated.

Retrocopy orthology:

Tarsius syrichta 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000176853	2 retrocopies	retro_hsap_225, retro_hsap_226,
Nomascus leucogenys	ENSNLEG00000005385	1 retrocopy	retro_nleu_3035,
Sus scrofa	ENSSSCG00000024424	2 retrocopies	retro_sscr_470, retro_sscr_507,
Tarsius syrichta	ENSTSYG00000004376	1 retrocopy	retro_tsyr_342 ,

	RetrogeneDB ID:	retro_tsyr_342
Retrocopy location	Organism:	*Tarsier (Tarsius syrichta)*
	Coordinates:	scaffold_100768:3301..4698(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	FAM91A1
	Ensembl ID:	ENSTSYG00000004376
	Aliases:	None
	Description:	family with sequence similarity 91, member A1 [Source:HGNC Symbol;Acc:26306]

Parental	SQREYEKQVVLYSIRNQLRYRNNL-VKHVKKDERKYY-EELLKYSRDHLLLYPYHLSDIMVKGLRVTPFS
	..RE.EK.VV..S.RNQLR.RNN..VKHV.K.....Y.EELLK.SRDHL.L.P.HLSDIM.KGLRV.P.S
Retrocopy	THREHEKPVVPSSVRNQLRDRNNV<VKHVEK-DERKY>EELLKRSRDHLRLQPCHLSDIMGKGLRVAPLS

Parental	YYTGIMEDIMNSEKSYDSLPNFTAADCLRLLGIGRNQYIDLMNQCRSSKKFFRRKTARDLLPVKPVEIAI
	YYTGIMED...SEK.YDSLP.FTAA.CLRLLGIGRNQYIDLMNQCRSSKKFFRRKTARDLL...PVEIAI
Retrocopy	YYTGIMEDATDSEKRYDSLPSFTAAGCLRLLGIGRNQYIDLMNQCRSSKKFFRRKTARDLL---PVEIAI

Parental	EAWWVVQAGYITEDDIKICTLPEKCAIDKIIDSGPQLSGSLDYHVVHSLYNKGFIYLDVPISDDSCIAVP
	.AWWVVQAGYITEDDIK.CTLPEKCAID.IIDSGPQLSGS.DYHVVH.LY.KGFIYLDVPISDD.C.AVP
Retrocopy	KAWWVVQAGYITEDDIKKCTLPEKCAIDVIIDSGPQLSGSPDYHVVHILYDKGFIYLDVPISDDNCTAVP

Parental	PLEGFVMNRVQGDYFETLLYKIFVSIDEHTNVAELANVLEIDLSLVKNAVSMYCRLGFAHKKGQVINLDQ
	.LEGFV..RVQGDYFETLLYKIFVSIDEHTNVAELANVL.I.LSLVKNAVSMYC.LGFAH.KGQVINLD.
Retrocopy	SLEGFVKDRVQGDYFETLLYKIFVSIDEHTNVAELANVLKIHLSLVKNAVSMYCHLGFAHRKGQVINLDR

Parental	LHSSWKNVPSVNRLKSTLDPQKMLLSWDGGERRSPVQEASSATDTDTNSQEDPADTASV-SSLSLSTGYT
	LHSSWKNVPSVNRLKSTLD.QKMLLSWD.GERR.P.QEASSAT.TDTNSQEDPADTA.V..S.SLST.YT
Retrocopy	LHSSWKNVPSVNRLKSTLDLQKMLLSWDSGERRRPIQEASSATNTDTNSQEDPADTANV<GSVSLSTEYT

Parental	KRIAFLFDSTLTAFLMMGNLSPNLKSHAVTMFEVGKLSDESLDSFLVELEKVQSTGEGEAQRYFDHALTL
	KRIAFLFDSTL.AFLMMGNLSPNLK..A.TMFE.GKLSDE.L.SFL.ELEKVQSTGEGE..RYFDH.LTL
Retrocopy	KRIAFLFDSTLMAFLMMGNLSPNLKICAITMFEGGKLSDEFLESFLIELEKVQSTGEGETLRYFDHPLTL

Parental	RNTILFLRHNKDLVAQTAQPDQPNYGFPLDLLRCESLLGLDPATCSRVLNKNY
	RNTILFLRHNKDLVAQTAQPDQPNY.FPLDLL.CESLL.L.P.TC.RVLNKNY
Retrocopy	RNTILFLRHNKDLVAQTAQPDQPNYDFPLDLLCCESLLVLNPTTCRRVLNKNY

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

RetrogeneDB ID:

retro_tsyr_342