RetrogeneDB - Retrocopy retro_fcat

                        
>retro_fcat_1575
ACTAGCGCCGGCGGGGGCCTCAGGAGGTCTAACAGCGCCCCCCTGATCCACGGCCTCAGTGACACTTCGCCGGTGTTCCA

GGCCGAGGCGCCGAGCGCCAGGCGGAACAGCACAACGTTCCCGAACCGCCACGGCCTGCTGCTGCCGGCCTCCCCCGTCC

GCATGCACAGCAGCCGCTTGCACCAGATCAAACAGGAGGAAGGCATGGACTTGATCAACCGAGAGACGGTCCACGAGCGC

GAGGTGCAGAACGCAATGCAGATAAGCCACTCCTGGGAGGAAAGTTTCAGCCTGAGTGACAACGATGTGGAGAAGTCCGC

CTCCCCGAAGCGCATCGATTTCATTCCGGTGTCACCAGCACCGTCACCCACCCGGGGGATTGGGAAGCAGTGTTTCTCAC

CATCCTTGCAAAGTTTTGTGAGTAGCAATGGATTGCCTCCGAGTCCTATTCCCAGCCCAACGACTCGATTTACTACCCGG

AGAAGCCAGAGTCCCATCAACTGCATTAGACCAAGCGTTCTTGGACCATTGAAAAGAAAATGTGAAATGGAAACTGAGTA

TCAGCCAAAGAGATTTTTCCAGGGCATCACCAACATGCTTTCTTCTGACGTTGCACAGCTGTCAGATCCCGGTGTGTGTG

TATCTTCTGATACCCTTGATGGAAACAGTAGCAGTGCCGGATCTTCTTGTAACTCACCAGCGAAAGTCAGCACTACCACC

GACTCTCCTGTGTCGCCTGCCCAAGCGGCCTCTCCATTTATTCCAGTAGATGAACTTTCATCTAAG

ORF - retro_fcat_1575 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	69.81 %
Parental protein coverage:	95.27 %
Number of stop codons detected:	0
Number of frameshifts detected:	0

Retrocopy - Parental Gene Alignment:

                                ParentalTSDGGALRRSSSAPLIHGLSDLSQVFQPYTFRTRRNSTTIMSRHTLLLSSSPNRVPSSRLHQIKREEGMD
TS.GG.LRRS.SAPLIHGLSD.S.VFQ......RRNSTT...RH.LLL..SP.R..SSRLHQIK.EEGMD
RetrocopyTSAGGGLRRSNSAPLIHGLSDTSPVFQAEAPSARRNSTTFPNRHGLLLPASPVRMHSSRLHQIKQEEGMD
ParentalMMNRETAHEREVQTAMQISQSWDESLSLSDSDFEKPEKLYSPKRIDFTPVSPAPSPTRGFGKQCFSPSLQ
..NRET.HEREVQ.AMQIS.SW.ES.SLSD.D.EK.....SPKRIDF.PVSPAPSPTRG.GKQCFSPSLQ
RetrocopyLINRETVHEREVQNAMQISHSWEESFSLSDNDVEKSA---SPKRIDFIPVSPAPSPTRGIGKQCFSPSLQ
ParentalMFVSSSGLPPSPVHSP-RRFSSRRSQSPVKCIRPSVLGPLKRKGEMETESQPKRLFQGTTNMLSPEAAQL
.FVSS.GLPPSP..SP..RF..RRSQSP..CIRPSVLGPLKRK.EMETE.QPKR.FQG.TNMLS...AQL
RetrocopySFVSSNGLPPSPIPSPTTRFTTRRSQSPINCIRPSVLGPLKRKCEMETEYQPKRFFQGITNMLSSDVAQL
ParentalSDLSSC--SDILDGSSSSSGLSSDSLAKGSTTAESPVACTNSCSSFILMDDLSPK
SD...C..SD.LDG.SSS.G.S..S.AK.STT..SPV......S.FI..D.LS.K
RetrocopySDPGVCVSSDTLDGNSSSAGSSCNSPAKVSTTTDSPVSPAQAASPFIPVDELSSK

                            

                            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	4 .48 RPM	28 .81 RPM
SRP017611_kidney	3 .92 RPM	24 .53 RPM
SRP017611_liver	3 .03 RPM	9 .40 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_1575 retrocopy.

TSS - click to see more details

Felis catus was not studied using FANTOM5 data.

Lab - click to see more details

retro_fcat_1575 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 14 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001311	1 retrocopy	retro_amel_105,
Bos taurus	ENSBTAG00000001886	1 retrocopy	retro_btau_103,
Canis familiaris	ENSCAFG00000018882	1 retrocopy	retro_cfam_181,
Callithrix jacchus	ENSCJAG00000004313	1 retrocopy	retro_cjac_594,
Cavia porcellus	ENSCPOG00000011218	1 retrocopy	retro_cpor_80,
Equus caballus	ENSECAG00000018643	1 retrocopy	retro_ecab_91,
Felis catus	ENSFCAG00000024842	1 retrocopy	retro_fcat_1575 ,
Myotis lucifugus	ENSMLUG00000007988	1 retrocopy	retro_mluc_382,
Macaca mulatta	ENSMMUG00000016948	1 retrocopy	retro_mmul_185,
Mustela putorius furo	ENSMPUG00000012690	1 retrocopy	retro_mputfur_64,
Mus musculus	ENSMUSG00000036022	1 retrocopy	retro_mmus_22,
Rattus norvegicus	ENSRNOG00000050146	1 retrocopy	retro_rnor_651,
Sus scrofa	ENSSSCG00000012685	1 retrocopy	retro_sscr_60,
Ictidomys tridecemlineatus	ENSSTOG00000006261	1 retrocopy	retro_itri_61,

	RetrogeneDB ID:	retro_fcat_1575
Retrocopy location	Organism:	*Cat (Felis catus)*
	Coordinates:	D4:11331752..11332538(+)
	Located in intron of:	ENSFCAG00000008812
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	FAM122B
	Ensembl ID:	ENSFCAG00000024842
	Aliases:	None
	Description:	family with sequence similarity 122B [Source:HGNC Symbol;Acc:30490]

Parental	TSDGGALRRSSSAPLIHGLSDLSQVFQPYTFRTRRNSTTIMSRHTLLLSSSPNRVPSSRLHQIKREEGMD
	TS.GG.LRRS.SAPLIHGLSD.S.VFQ......RRNSTT...RH.LLL..SP.R..SSRLHQIK.EEGMD
Retrocopy	TSAGGGLRRSNSAPLIHGLSDTSPVFQAEAPSARRNSTTFPNRHGLLLPASPVRMHSSRLHQIKQEEGMD

Parental	MMNRETAHEREVQTAMQISQSWDESLSLSDSDFEKPEKLYSPKRIDFTPVSPAPSPTRGFGKQCFSPSLQ
	..NRET.HEREVQ.AMQIS.SW.ES.SLSD.D.EK.....SPKRIDF.PVSPAPSPTRG.GKQCFSPSLQ
Retrocopy	LINRETVHEREVQNAMQISHSWEESFSLSDNDVEKSA---SPKRIDFIPVSPAPSPTRGIGKQCFSPSLQ

Parental	MFVSSSGLPPSPVHSP-RRFSSRRSQSPVKCIRPSVLGPLKRKGEMETESQPKRLFQGTTNMLSPEAAQL
	.FVSS.GLPPSP..SP..RF..RRSQSP..CIRPSVLGPLKRK.EMETE.QPKR.FQG.TNMLS...AQL
Retrocopy	SFVSSNGLPPSPIPSPTTRFTTRRSQSPINCIRPSVLGPLKRKCEMETEYQPKRFFQGITNMLSSDVAQL

Parental	SDLSSC--SDILDGSSSSSGLSSDSLAKGSTTAESPVACTNSCSSFILMDDLSPK
	SD...C..SD.LDG.SSS.G.S..S.AK.STT..SPV......S.FI..D.LS.K
Retrocopy	SDPGVCVSSDTLDGNSSSAGSSCNSPAKVSTTTDSPVSPAQAASPFIPVDELSSK

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

RetrogeneDB ID:

retro_fcat_1575