RetrogeneDB - Retrocopy retro_fcat

                        
>retro_fcat_1651
CTGTACACTCTTTTAGAACCTGGGGCAGATGCTAATGCCACTACTTCAGAGAAAACCACACCACTGTTTTTAGCTGTTGA

AAATGGACAGATAGATATATTAAAGCTGTTGCTTCGACATGGAGCAAATGTTAACGGGTCCCATTCTGGGTGTGGATGCA

ACGCTTTGCATCAGGCTACTTTTCAGGAAATGCTGAGATCATAAAATTGCTTTTTTAAGAAAGGAGCAAACAAGGAATGC

CAGGATGACTTTGGAATCACACTTTTATTTGTGGCTGCTTGGCACGGCAAGCTGGAAATCTTAAACATACTTATTTCATC

AGGTGCAAAAGTCAACTGTCAAACATTGGATGAAGTTACTCCCTCATTCATTGCTGCTCAGGAGGGCCACACAGAATGTG

TAGAGCTTTTGCTGTTCAGTGGGCCAGATCCTGATCTTTACTGTAATGAGGCCTATTGGCAGTTACCTATTCATGCAGTT

GCATGAATGGTCCATATTGGACCATTAATGGACTTCTTAATACCACTTACCAACTGGGTTTGTGACATGGGCCAGACAAA

GTGAGCCCCGTTTACTCTGCAGTGTTCGGAGGGCATGAAGAGTGACTAGAAATGTTATTCCAGCATGACTACAGACAAGA

TGTCTAGATGTGCCACATCTTTGCATTTAGTTCTCCCTGTGTATGGCTTTCCAAACGGACTGTGAGTTTTTGGAATTGTG

AATATTCTTTTGAAATATGGAGCCCAACTAAATGAACTTCATTTGGCATACTGCCTAACGTATGAGAAATTTTCAGTATT

TTGCTACTTTTTGAAGAAAGGTTGTCTATTGGCATTGTGGAACCATATTTCTGAATCTATAAATCATGCAATTAAAGCAT

AGACAAAATATAAGGAATGGCTACCATCTCTCCTGCTTGCTGGATTTGACCCACTGAATCTACTCTGCAATTCTTGGATT

GACTCAGTCAGTGATGACACCCTTATCTTCACTTTGGAGTTTACTAATTGGAGGAGGCTTCTTCCAGCTGTTGAAAAGAT

GCTCTCTGCTCGTGTCTCAAACTCCTCTTGGGCTCTGCAAGCAGCATATTGCCTCTGTTCTGTCCCTTACCCACCTTTGT

TGTTTAGAAATTCGTTCA

ORF - retro_fcat_1651 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	78.66 %
Parental protein coverage:	72.35 %
Number of stop codons detected:	4
Number of frameshifts detected:	6

Retrocopy - Parental Gene Alignment:

                                ParentalVHILLEAGADPNATTSEETTPLSFAAVENGHIDVLRLLLRYGANVNGSHSMCGWNALHQATFQE-NGEII
...LLE.GAD.NATTSE.TTPL.F.AVENG.ID.L.LLLR.GANVNGSHS.CG.NALHQATFQE.N.EII
RetrocopyLYTLLEPGADANATTSEKTTPL-FLAVENGQIDILKLLLRHGANVNGSHSGCGCNALHQATFQE<NAEII
ParentalKLLL-KKGADKECQDDFGITPLFVAAQYGKLESLSILISSGANVNCQALDEATPLFIAAQEGHTECVELL
KLL..KKGA.KECQDDFGIT.LFVAA..GKLE.L.ILISSGA.VNCQ.LDE.TP.FIAAQEGHTECVELL
RetrocopyKLLF>KKGANKECQDDFGITLLFVAAWHGKLEILNILISSGAKVNCQTLDEVTPSFIAAQEGHTECVELL
ParentalLSSGADPDLYCNEDDWQLPIHAAAQMGHT-EILELLIPLTNRVCDT-GPDKVSPVYSAVFGGHEECLEML
L.SG.DPDLYCNE..WQLPIHA.A.M.H.......LIPLTN.VCD..GPDKVSPVYSAVFGGHEE.LEML
RetrocopyLFSGPDPDLYCNEAYWQLPIHAVA*MVHIGPLMDFLIPLTNWVCDM<GPDKVSPVYSAVFGGHEE*LEML
ParentalLQHGYSPDAQMCLIFGFSSP-MCMAFQKDWSCEF-FGIVNILLKYGAQLNELHLAYCLKYEKFLVFRYFL
.QH.Y..D..MC.IF.FSSP..CMAFQ.D..CEF.FGIVNILLKYGAQLNELHLAYCL.YEKF.VF.YFL
RetrocopyFQHDYRQDV*MCHIFAFSSP<LCMAFQTD--CEF<FGIVNILLKYGAQLNELHLAYCLTYEKFSVFCYFL
ParentalKKGCPLAPWNHISEFISHAIKAQTTYKEWLPSLLLAGFDPLNLLCSSWIDSVSDDILIFTLEFTNWRTLP
KKGC.LA.WNHISE.I.HAIKA.T.YKEWLPSLLLAGFDPLNLLC.SWIDSVSDD.LIFTLEFTNWR.L.
RetrocopyKKGCLLALWNHISESINHAIKA*TKYKEWLPSLLLAGFDPLNLLCNSWIDSVSDDTLIFTLEFTNWRRLL
ParentalPAVEKMISTRASHSSRALQ-QHIACLPSLTHLCRLEIRS
PAVEKM.S.R.S.SS.ALQ.QHIA...SLTHLC.LEIRS
RetrocopyPAVEKMLSARVSNSSWALQ>QHIASVLSLTHLCCLEIRS

                            

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

                        

RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0 .11 RPM	29 .04 RPM
SRP017611_kidney	0 .10 RPM	19 .99 RPM
SRP017611_liver	0 .10 RPM	17 .89 RPM

ChIP-Seq - click to see more details

Felis catus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_fcat_1651 retrocopy.

TSS - click to see more details

Felis catus was not studied using FANTOM5 data.

Lab - click to see more details

retro_fcat_1651 was not experimentally validated.

Retrocopy orthology:

Felis catus 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000022032	1 retrocopy	retro_fcat_1651 ,

	RetrogeneDB ID:	retro_fcat_1651
Retrocopy location	Organism:	*Cat (Felis catus)*
	Coordinates:	E1:28592024..28593162(+)
	Located in intron of:	ENSFCAG00000018470
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	None
	Ensembl ID:	ENSFCAG00000022032
	Aliases:	None
	Description:	None

Parental	VHILLEAGADPNATTSEETTPLSFAAVENGHIDVLRLLLRYGANVNGSHSMCGWNALHQATFQE-NGEII
	...LLE.GAD.NATTSE.TTPL.F.AVENG.ID.L.LLLR.GANVNGSHS.CG.NALHQATFQE.N.EII
Retrocopy	LYTLLEPGADANATTSEKTTPL-FLAVENGQIDILKLLLRHGANVNGSHSGCGCNALHQATFQE<NAEII

Parental	KLLL-KKGADKECQDDFGITPLFVAAQYGKLESLSILISSGANVNCQALDEATPLFIAAQEGHTECVELL
	KLL..KKGA.KECQDDFGIT.LFVAA..GKLE.L.ILISSGA.VNCQ.LDE.TP.FIAAQEGHTECVELL
Retrocopy	KLLF>KKGANKECQDDFGITLLFVAAWHGKLEILNILISSGAKVNCQTLDEVTPSFIAAQEGHTECVELL

Parental	LSSGADPDLYCNEDDWQLPIHAAAQMGHT-EILELLIPLTNRVCDT-GPDKVSPVYSAVFGGHEECLEML
	L.SG.DPDLYCNE..WQLPIHA.A.M.H.......LIPLTN.VCD..GPDKVSPVYSAVFGGHEE.LEML
Retrocopy	LFSGPDPDLYCNEAYWQLPIHAVAMVHIGPLMDFLIPLTNWVCDM<GPDKVSPVYSAVFGGHEELEML

Parental	LQHGYSPDAQMCLIFGFSSP-MCMAFQKDWSCEF-FGIVNILLKYGAQLNELHLAYCLKYEKFLVFRYFL
	.QH.Y..D..MC.IF.FSSP..CMAFQ.D..CEF.FGIVNILLKYGAQLNELHLAYCL.YEKF.VF.YFL
Retrocopy	FQHDYRQDV*MCHIFAFSSP<LCMAFQTD--CEF<FGIVNILLKYGAQLNELHLAYCLTYEKFSVFCYFL

Parental	KKGCPLAPWNHISEFISHAIKAQTTYKEWLPSLLLAGFDPLNLLCSSWIDSVSDDILIFTLEFTNWRTLP
	KKGC.LA.WNHISE.I.HAIKA.T.YKEWLPSLLLAGFDPLNLLC.SWIDSVSDD.LIFTLEFTNWR.L.
Retrocopy	KKGCLLALWNHISESINHAIKA*TKYKEWLPSLLLAGFDPLNLLCNSWIDSVSDDTLIFTLEFTNWRRLL

Parental	PAVEKMISTRASHSSRALQ-QHIACLPSLTHLCRLEIRS
	PAVEKM.S.R.S.SS.ALQ.QHIA...SLTHLC.LEIRS
Retrocopy	PAVEKMLSARVSNSSWALQ>QHIASVLSLTHLCCLEIRS

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

RetrogeneDB ID:

retro_fcat_1651