RetrogeneDB - Retrocopy retro_fcat

						
>retro_fcat_1355
TCAGCCAAGATTGTGCAGCTGTTAAAGGAGTGGACAGAGGCCTTCTCCTGTGACTTCCAGGATGAGAAGGCCATGGTTGA

ACCAAAGACCATTACCCACCAGGTCACACAGTGTGACAAGGAGAATGGCACAGTGAACAAGGCTATTTCCCAAATGACAC

AGAGCCTGCTGCTGTAGCTGGCTGCCCAGAGCCAGCTTCAGGAGCTGTGGGAAAAGCTTCACTCACCAGCCATGGACAAA

GGGTCTTTCTTCAAGGCTAAGCCGCCAGCCACTCAGAAGGACATCCTGGGTGTGTGCTTTGACCCCCTGGTGCTGGCCCA

GCAGCTGACTCATACTGAGCTGGAGAGGATCAATAGCATTCACCCTGAGGATCTGATGCAGATCGTCAGCCACATGAACT

CTCGGGACAAGCACTGGTGCCAAGGGGACCTGACCAAGACCTATAGCCTGGAGGCCTGTGACAATGGTTCAACTGCCTTA

GCATGCTAGTGGCCACTGAGGTGTGCCAGGTGGTGAAGAAGAAGCACTGGACCCACATGCTAGAGTTCTTTCTTGCTGTG

GCCCAGAAGCACTTTAATATTGGGAATTTCAACTCCATGATGGCCATCATCTCTGGCATGAACCTCATTCCTGTGGCAAG

GCTTAAGAAAACATGGTCCAAAGTCAAGATGGCCAAGTTTGACATCTTGGAGCACCACATGGACCCATCCAGCAACTTCT

GCAACTACCGCACGGCCCTGCAGGGGGCCACACAAAGGCCCCAGATGGCCAACAACAGCAGAAAGAAGATTGTTATCCCT

GTATTCAACCTTTTCATTAAGGACATTTACTTCCTGCACAAAATCCATACCAATCACTTGCCCAATGGGCATGTTAACTT

CAAGGAATTTAGGGAAATCTCCAGACAAATCCATGAGTTCATGACATGGACTCAGGTAGATTGTCCCTTCGAGAAGGACA

AGAAGATTCAGAACTACCTGCTCACGGCACCCATCTGGAGCGAGGAAGCCCTCTTCATCATCTCCTTTGAAAATGAAGGT

CCTGAAAACCACATCGAGAAGGATAGCTGGAAGACTCTTAGGATGACTCTCCTTAACAGAGCC

ORF - retro_fcat_1355 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	86.45 %
Parental protein coverage:	76.67 %
Number of stop codons detected:	1
Number of frameshifts detected	1

Retrocopy - Parental Gene Alignment:

									ParentalTAKIVQLLKEWTEAFPYDFQDEKAMAELKAITHRVTQCDEENGTVKKAIAQMTQSLLLSLAARSQLQELR
		.AKIVQLLKEWTEAF..DFQDEKAM.E.K.ITH.VTQCD.ENGTV.KAI.QMTQSLLL.LAA.SQLQEL.
RetrocopySAKIVQLLKEWTEAFSCDFQDEKAMVEPKTITHQVTQCDKENGTVNKAISQMTQSLLL*LAAQSQLQELW
ParentalDKLRSPAMDKGSVLKTKPPATQKDILGVCCDPLVLAQQLTHIELERVSSIHPEDLMQIVSHMDSRDKHRC
		.KL.SPAMDKGS..K.KPPATQKDILGVC.DPLVLAQQLTH.ELER..SIHPEDLMQIVSHM.SRDKH.C
RetrocopyEKLHSPAMDKGSFFKAKPPATQKDILGVCFDPLVLAQQLTHTELERINSIHPEDLMQIVSHMNSRDKHWC
ParentalRGDLTKTYSLEAYDN-WFNCLSMLVATEVCRVVKKKHRTRMLEFFIDVARECFNIGNFNSMMAIISGMNL
		.GDLTKTYSLEA.DN.WFNCLSMLVATEVC.VVKKKH.T.MLEFF..VA...FNIGNFNSMMAIISGMNL
RetrocopyQGDLTKTYSLEACDN<WFNCLSMLVATEVCQVVKKKHWTHMLEFFLAVAQKHFNIGNFNSMMAIISGMNL
ParentalSPVARLKKTWSKVKTAKFDVLEHHMDPSSNFCNYRTALQGATQRSQMANSSREKIVIPVFNLFVKDIYFL
		.PVARLKKTWSKVK.AKFD.LEHHMDPSSNFCNYRTALQGATQR.QMAN.SR.KIVIPVFNLF.KDIYFL
RetrocopyIPVARLKKTWSKVKMAKFDILEHHMDPSSNFCNYRTALQGATQRPQMANNSRKKIVIPVFNLFIKDIYFL
ParentalHKIHTNHLPNGHVNFKKFWEISRQIHEFMTWTQVECPFEKDKKIQNYLLTAPIYSEEALFIASFESEGPE
		HKIHTNHLPNGHVNFK.F.EISRQIHEFMTWTQV.CPFEKDKKIQNYLLTAPI.SEEALFI.SFE.EGPE
RetrocopyHKIHTNHLPNGHVNFKEFREISRQIHEFMTWTQVDCPFEKDKKIQNYLLTAPIWSEEALFIISFENEGPE
ParentalNHMEKDSWKTLRTTLLNRA
		NH.EKDSWKTLR.TLLNRA
RetrocopyNHIEKDSWKTLRMTLLNRA

							

							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 .00 RPM	47 .40 RPM
SRP017611_kidney	0 .00 RPM	1 .55 RPM
SRP017611_liver	0 .00 RPM	0 .30 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_1355 retrocopy.

TSS - click to see more details

Felis catus was not studied using FANTOM5 data.

Lab - click to see more details

retro_fcat_1355 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	ENSFCAG00000013972	1 retrocopy	retro_fcat_1355 ,

	RetrogeneDB ID:	retro_fcat_1355
Retrocopy location	Organism:	*Cat (Felis catus)*
	Coordinates:	C2:88076116..88077219(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	RASGEF1A
	Ensembl ID:	ENSFCAG00000013972
	Aliases:	None
	Description:	RasGEF domain family, member 1A [Source:HGNC Symbol;Acc:24246]

Parental	TAKIVQLLKEWTEAFPYDFQDEKAMAELKAITHRVTQCDEENGTVKKAIAQMTQSLLLSLAARSQLQELR
	.AKIVQLLKEWTEAF..DFQDEKAM.E.K.ITH.VTQCD.ENGTV.KAI.QMTQSLLL.LAA.SQLQEL.
Retrocopy	SAKIVQLLKEWTEAFSCDFQDEKAMVEPKTITHQVTQCDKENGTVNKAISQMTQSLLL*LAAQSQLQELW

Parental	DKLRSPAMDKGSVLKTKPPATQKDILGVCCDPLVLAQQLTHIELERVSSIHPEDLMQIVSHMDSRDKHRC
	.KL.SPAMDKGS..K.KPPATQKDILGVC.DPLVLAQQLTH.ELER..SIHPEDLMQIVSHM.SRDKH.C
Retrocopy	EKLHSPAMDKGSFFKAKPPATQKDILGVCFDPLVLAQQLTHTELERINSIHPEDLMQIVSHMNSRDKHWC

Parental	RGDLTKTYSLEAYDN-WFNCLSMLVATEVCRVVKKKHRTRMLEFFIDVARECFNIGNFNSMMAIISGMNL
	.GDLTKTYSLEA.DN.WFNCLSMLVATEVC.VVKKKH.T.MLEFF..VA...FNIGNFNSMMAIISGMNL
Retrocopy	QGDLTKTYSLEACDN<WFNCLSMLVATEVCQVVKKKHWTHMLEFFLAVAQKHFNIGNFNSMMAIISGMNL

Parental	SPVARLKKTWSKVKTAKFDVLEHHMDPSSNFCNYRTALQGATQRSQMANSSREKIVIPVFNLFVKDIYFL
	.PVARLKKTWSKVK.AKFD.LEHHMDPSSNFCNYRTALQGATQR.QMAN.SR.KIVIPVFNLF.KDIYFL
Retrocopy	IPVARLKKTWSKVKMAKFDILEHHMDPSSNFCNYRTALQGATQRPQMANNSRKKIVIPVFNLFIKDIYFL

Parental	HKIHTNHLPNGHVNFKKFWEISRQIHEFMTWTQVECPFEKDKKIQNYLLTAPIYSEEALFIASFESEGPE
	HKIHTNHLPNGHVNFK.F.EISRQIHEFMTWTQV.CPFEKDKKIQNYLLTAPI.SEEALFI.SFE.EGPE
Retrocopy	HKIHTNHLPNGHVNFKEFREISRQIHEFMTWTQVDCPFEKDKKIQNYLLTAPIWSEEALFIISFENEGPE

Parental	NHMEKDSWKTLRTTLLNRA
	NH.EKDSWKTLR.TLLNRA
Retrocopy	NHIEKDSWKTLRMTLLNRA

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

RetrogeneDB ID:

retro_fcat_1355