RetrogeneDB - Retrocopy retro_fcat

						
>retro_fcat_721
AATAAGCTGATAGATAAACTTAGTACCAATGCTGAAATGGAAGAAGTAATGAATGATTACAACATGCTTAAAGCTCAAAA

TGAGCTATCCACACAACATATGGATATCATATTTACTGAAAGACAAGCGAAGGAAAAACAAACTAGAAGAGTAGAAGTAG

TTGAATAGGAAAAGCAAGCAGCAGATGACATTATCAGAAACACATCTCCTGAAAAACAAGTCAGGTACATAGAAATGAAA

ACCACAAATGAGAAACTGTTGCAGGAATTAGATACACTTCAGCAACAGCTAGATTCACTGAACATAAAAAAAAGAGAGCT

TGGAAGCTGAAATAGCACACTCCCAGGTTAAATAGGAGGCTGTACTGCTGCACGAAAAACTTTATGAGTTGGAGTCCCAT

CAAGACCAAATGATTGCTGAAGGCAAAAGCATGGGATCTCCAATGAAAGAAAGAGAGAGATTACTCAAGCAAGTTAAAGA

AGATAATCAGGAAATAGGCAGCAAGGAGCAACAGCTAATAGACATAAAAGAAAAAATAAAGCAATTTAATGAAGAAATTA

GACAACTAGACATGGATTTAGAAGAACACCATGGTGAAATGAGTCAGAAGTATAAGGAACTAAAACAGGGAGAGGAAAAT

ACGGACACTTTTATTGAGACTTTTGAGGAAACTAAGAATCAAGAACTGGAACAGAAGGCACAGATAGAAGCCAACATTGT

TACACTTTTGGAGCACAGTAGTAGAAATATAAATTGTATAAAACAGATATCCTCTATCACCAACCAAGAGCTGAAGATGA

TGTAGGATGATCTCAACTTTAAATCTACTGAAATGCAGAAATCACAAAGTGCAACTAGAAATTTGACCTCAGATAGCCAA

TGTCTACAGTTGGATCTACAGAAAATGGAGCTTCTGCAAAGTAAGATGACTGAGGAACAGTATTCTCTGAAAAGCAAAAT

TAAGCAAATGACAGCTGATTTGAAAACATATAATGATTTTCCAGCTTTAAAATCATCAGGTGAAGAAAAAAAAGAAATTA

CATCACGAGAGAACAGTATTAACAACCCGTAGAAATGCCTTTAAGAAAATAACAGAA

ORF - retro_fcat_721 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	75.88 %
Parental protein coverage:	60.93 %
Number of stop codons detected:	3
Number of frameshifts detected	2

Retrocopy - Parental Gene Alignment:

									ParentalNPCVCNIQRNLVITEIKNKSKVLRASKVIEIQSEDITLSSSETKEKQIRSVEEEVEQEKQAADGI-KNMS
		N........N....E..N....L.A......Q..DI.......KEKQ.R.VE..VE.EKQAAD.I..N.S
RetrocopyNKLIDKLSTNAEMEEVMNDYNMLKAQNELSTQHMDIIFTERQAKEKQTRRVEV-VE*EKQAADDIIRNTS
ParentalPEKQVKYTEMKTTNEKLLQELDTLQQQLDSLNMKK-ESLEAEIAHSQVKQEAVLLHEKLYELESHRDQMI
		PEKQV.Y.EMKTTNEKLLQELDTLQQQLDSLN....ESLEAEIAHSQVK.EAVLLHEKLYELESH.DQMI
RetrocopyPEKQVRYIEMKTTNEKLLQELDTLQQQLDSLNXXX>ESLEAEIAHSQVK*EAVLLHEKLYELESHQDQMI
ParentalAEDKSMGSPMEERERLLKQVKEDNQEIASMERQLTDIKEKIKQFNDEIRQLDMDLEEHQGEMNQKYKEKK
		AE.KSMGSPM.ERERLLKQVKEDNQEI.S.E.QL.DIKEKIKQFN.EIRQLDMDLEEH.GEM.QKYKE.K
RetrocopyAEGKSMGSPMKERERLLKQVKEDNQEIGSKEQQLIDIKEKIKQFNEEIRQLDMDLEEHHGEMSQKYKELK
ParentalR-EENMDTFIETFEETKNQELERKAQIEANIVTLLEHSSRNINRMKQISSITNQELKMMQDDLNFKSTEM
		..EEN.DTFIETFEETKNQELE.KAQIEANIVTLLEHSSRNIN..KQISSITNQELKMM.DDLNFKSTEM
RetrocopyQGEENTDTFIETFEETKNQELEQKAQIEANIVTLLEHSSRNINCIKQISSITNQELKMM*DDLNFKSTEM
ParentalQKSQSTARNLTSDSQRLQLDLQKMELLESKMTEEQHSLKSKIKHMTADLETYNDLPALKSSGE-EKKKKL
		QKSQS..RNLTSDSQ.LQLDLQKMELL.SKMTEEQ.SLKSKIK.MTADL.TYND.PALKSSGE....K..
RetrocopyQKSQSATRNLTSDSQCLQLDLQKMELLQSKMTEEQYSLKSKIKQMTADLKTYNDFPALKSSGE>XXXKLH
ParentalHQERTVLTTRRNAFKKITE
		H......T.RRNAFKKITE
RetrocopyHERTVLTT-RRNAFKKITE

							

							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	14 .12 RPM
SRP017611_kidney	0 .00 RPM	19 .58 RPM
SRP017611_liver	0 .20 RPM	4 .35 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_721 retrocopy.

TSS - click to see more details

Felis catus was not studied using FANTOM5 data.

Lab - click to see more details

retro_fcat_721 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000021030	1 retrocopy	retro_ecab_167,
Felis catus	ENSFCAG00000026070	1 retrocopy	retro_fcat_721 ,

	RetrogeneDB ID:	retro_fcat_721
Retrocopy location	Organism:	*Cat (Felis catus)*
	Coordinates:	B2:96575227..96576324(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	IFT74
	Ensembl ID:	ENSFCAG00000026070
	Aliases:	None
	Description:	intraflagellar transport 74 homolog (Chlamydomonas) [Source:HGNC Symbol;Acc:21424]

Parental	NPCVCNIQRNLVITEIKNKSKVLRASKVIEIQSEDITLSSSETKEKQIRSVEEEVEQEKQAADGI-KNMS
	N........N....E..N....L.A......Q..DI.......KEKQ.R.VE..VE.EKQAAD.I..N.S
Retrocopy	NKLIDKLSTNAEMEEVMNDYNMLKAQNELSTQHMDIIFTERQAKEKQTRRVEV-VE*EKQAADDIIRNTS

Parental	PEKQVKYTEMKTTNEKLLQELDTLQQQLDSLNMKK-ESLEAEIAHSQVKQEAVLLHEKLYELESHRDQMI
	PEKQV.Y.EMKTTNEKLLQELDTLQQQLDSLN....ESLEAEIAHSQVK.EAVLLHEKLYELESH.DQMI
Retrocopy	PEKQVRYIEMKTTNEKLLQELDTLQQQLDSLNXXX>ESLEAEIAHSQVK*EAVLLHEKLYELESHQDQMI

Parental	AEDKSMGSPMEERERLLKQVKEDNQEIASMERQLTDIKEKIKQFNDEIRQLDMDLEEHQGEMNQKYKEKK
	AE.KSMGSPM.ERERLLKQVKEDNQEI.S.E.QL.DIKEKIKQFN.EIRQLDMDLEEH.GEM.QKYKE.K
Retrocopy	AEGKSMGSPMKERERLLKQVKEDNQEIGSKEQQLIDIKEKIKQFNEEIRQLDMDLEEHHGEMSQKYKELK

Parental	R-EENMDTFIETFEETKNQELERKAQIEANIVTLLEHSSRNINRMKQISSITNQELKMMQDDLNFKSTEM
	..EEN.DTFIETFEETKNQELE.KAQIEANIVTLLEHSSRNIN..KQISSITNQELKMM.DDLNFKSTEM
Retrocopy	QGEENTDTFIETFEETKNQELEQKAQIEANIVTLLEHSSRNINCIKQISSITNQELKMM*DDLNFKSTEM

Parental	QKSQSTARNLTSDSQRLQLDLQKMELLESKMTEEQHSLKSKIKHMTADLETYNDLPALKSSGE-EKKKKL
	QKSQS..RNLTSDSQ.LQLDLQKMELL.SKMTEEQ.SLKSKIK.MTADL.TYND.PALKSSGE....K..
Retrocopy	QKSQSATRNLTSDSQCLQLDLQKMELLQSKMTEEQYSLKSKIKQMTADLKTYNDFPALKSSGE>XXXKLH

Parental	HQERTVLTTRRNAFKKITE
	H......T.RRNAFKKITE
Retrocopy	HERTVLTT-RRNAFKKITE

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

RetrogeneDB ID:

retro_fcat_721