RetrogeneDB - Retrocopy retro_fcat

                        
>retro_fcat_30
ATGGCCCTGCAGGATGTGTGCAAGTGGCAGGCCCCCAACACCCAGGGACCATCACCTCACCTGCCTCAGCCTGGGGCCTG

GGCTGTGCCCCCAGGCTGCGATCCTCAAACCTTCTTGCAGATCCACGGCCCCAGGCTGGCCCATGGCACCACCACCTTGG

CCTTCCTCTTCCGGCATGGAGTCATCGCTGCTGCTGACACACGTTCCTCCTGCGGCAACTATGTGGAGTGTCCAACCTCA

CGCAAGATCATCCCTGTGCACCAGCACCTCCTGGGCACCACCTCCGGCACCTCGGCCGACTGTGCCGTATGGTACCGCGT

GCTACGACGGGAGCTGCGGCTTCGGGCACTGAGGGAGGGTCAGCTGCCCAGCGTGGCCGGTGCCGCCAAGCTCTTGTCGA

CCATGATGTCCTGCTACCGGGGCCTGGATCTGTGTGTGGCCACGGCCCTGTGTGGCTGGGACCGCTCTGGCCCTGCCCTC

TTCTATGTCTACAGTGACGGCACCCGCCTGCAAGGGAACATCTTCTCCGTGGGTTCTGGATCTCCCTATGCCTACGGCGT

GCTAGACCGCGGCTACCGCTATGACATGACCCCCCAGGAAGCCTATGCCCTGGCTCGCTGTGCCGTGGCCCACGCCACCC

ACCGCGATGCCTACTCCGGGGGTTCTGTAGACCTTTTCCACGTGCGGGAGAGCGGATGGGAGTATGTGTCACGCAACGAT

GCCTGTGTGCTGTACTCGGAACTGCAGAAGCTTCCGGAGCCAGACAAGGAAGAGGAGGAGGCCAGCCGGGACCATCCGGA

GCCCGCCAGCCGGCACAGAGACTCTAGGATGCCCGCAGAGACTGAGATTCTCTGA

ORF - retro_fcat_30 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	53.85 %
Parental protein coverage:	70.65 %
Number of stop codons detected:	0
Number of frameshifts detected:	0

Retrocopy - Parental Gene Alignment:

                                ParentalMAHGTTTLAFKFQHGVVVAVDSRASAGTYIATLRCNKVIEINPYLLGTMSGSAADCQYWERLLAKECRLY
.AHGTTTLAF.F.HGV..A.D.R.S.G.Y.......K.I.....LLGT.SG..ADC..W.R.L..E.RL.
RetrocopyLAHGTTTLAFLFRHGVIAAADTRSSCGNYVECPTSRKIIPVHQHLLGTTSGTSADCAVWYRVLRRELRLR
ParentalYLRNGERISVSAASKLLSNMVFQYRGMGLSMGSMICGWDKKGPGLYYVNSDGTRLSGNMFSTGSGNTYAY
.LR.G...SV..A.KLLS.M...YRG..L......CGWD..GP.L.YV.SDGTRL.GN.FS.GSG..YAY
RetrocopyALREGQLPSVAGAAKLLSTMMSCYRGLDLCVATALCGWDRSGPALFYVYSDGTRLQGNIFSVGSGSPYAY
ParentalGVMDSGYRPDLSPEEAYELGRRAIVYATHRDSYSGGVVNMYHMKEDGWVKLESTD
GV.D.GYR.D..P.EAY.L.R.A...ATHRD.YSGG.V...H..E.GW......D
RetrocopyGVLDRGYRYDMTPQEAYALARCAVAHATHRDAYSGGSVDLFHVRESGWEYVSRND

                            

                            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	0 .46 RPM
SRP017611_kidney	0 .00 RPM	3 .71 RPM
SRP017611_liver	0 .20 RPM	11 .22 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_30 retrocopy.

TSS - click to see more details

Felis catus was not studied using FANTOM5 data.

Lab - click to see more details

retro_fcat_30 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 16 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002026	1 retrocopy	retro_amel_27,
Bos taurus	ENSBTAG00000003039	1 retrocopy	retro_btau_11,
Canis familiaris	ENSCAFG00000000829	1 retrocopy	retro_cfam_75,
Equus caballus	ENSECAG00000018887	1 retrocopy	retro_ecab_18,
Felis catus	ENSFCAG00000023131	1 retrocopy	retro_fcat_30 ,
Loxodonta africana	ENSLAFG00000003213	1 retrocopy	retro_lafr_65,
Microcebus murinus	ENSMICG00000015254	1 retrocopy	retro_mmur_33,
Myotis lucifugus	ENSMLUG00000013876	1 retrocopy	retro_mluc_285,
Monodelphis domestica	ENSMODG00000014366	1 retrocopy	retro_mdom_179,
Otolemur garnettii	ENSOGAG00000013830	1 retrocopy	retro_ogar_256,
Procavia capensis	ENSPCAG00000016741	1 retrocopy	retro_pcap_21,
Pan troglodytes	ENSPTRG00000018022	2 retrocopies	retro_ptro_1102, retro_ptro_97,
Pteropus vampyrus	ENSPVAG00000002800	1 retrocopy	retro_pvam_20,
Sus scrofa	ENSSSCG00000026951	1 retrocopy	retro_sscr_90,
Tupaia belangeri	ENSTBEG00000007794	1 retrocopy	retro_tbel_2055,
Tarsius syrichta	ENSTSYG00000007730	1 retrocopy	retro_tsyr_1639,

	RetrogeneDB ID:	retro_fcat_30
Retrocopy location	Organism:	*Cat (Felis catus)*
	Coordinates:	B3:75336189..75337044(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ENSFCAG00000008111
	Aliases:	None
	Status:	KNOWN_PROTEIN_CODING
Parental gene information	Parental gene summary:
	Parental gene symbol:	PSMB8
	Ensembl ID:	ENSFCAG00000023131
	Aliases:	None
	Description:	proteasome (prosome, macropain) subunit, beta type, 8 [Source:HGNC Symbol;Acc:9545]

Parental	MAHGTTTLAFKFQHGVVVAVDSRASAGTYIATLRCNKVIEINPYLLGTMSGSAADCQYWERLLAKECRLY
	.AHGTTTLAF.F.HGV..A.D.R.S.G.Y.......K.I.....LLGT.SG..ADC..W.R.L..E.RL.
Retrocopy	LAHGTTTLAFLFRHGVIAAADTRSSCGNYVECPTSRKIIPVHQHLLGTTSGTSADCAVWYRVLRRELRLR

Parental	YLRNGERISVSAASKLLSNMVFQYRGMGLSMGSMICGWDKKGPGLYYVNSDGTRLSGNMFSTGSGNTYAY
	.LR.G...SV..A.KLLS.M...YRG..L......CGWD..GP.L.YV.SDGTRL.GN.FS.GSG..YAY
Retrocopy	ALREGQLPSVAGAAKLLSTMMSCYRGLDLCVATALCGWDRSGPALFYVYSDGTRLQGNIFSVGSGSPYAY

Parental	GVMDSGYRPDLSPEEAYELGRRAIVYATHRDSYSGGVVNMYHMKEDGWVKLESTD
	GV.D.GYR.D..P.EAY.L.R.A...ATHRD.YSGG.V...H..E.GW......D
Retrocopy	GVLDRGYRYDMTPQEAYALARCAVAHATHRDAYSGGSVDLFHVRESGWEYVSRND

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

RetrogeneDB ID:

retro_fcat_30