RetrogeneDB - Retrocopy retro_itri

						
>retro_itri_1536
CCAAGGCCATTCAGACTGTCTCCCAAAGGCTTTTCTGTGGAGCTTTGCATGAACAGGGAAGATGATACTTCACAGAAAGA

GAAGACTGATCATTTCATCTTCACATATACCCAGGAGGGGATCTTCGATATTCTGCCAAATCCCTCTTCAGCCTCGTCCT

GGGCTTCATCTCTGACAATGTTGATCACATTGATCCCCTTATTGGCTTTCTTGAGCAAATTGCTGAAAAACTGTTCTCTG

CTGCTGAAGCCAGGCAGAAATTCACAGAGCCAGGTGCAGGGCTGAGGGCTTTACAGAAATTCACTGAGGCCTATGGAAGT

CTGGTGCTGTGCTCTCTGTGCTTGCGAAATAGGTATCTGGTGATTTCAGAAAAACTTGAGGAGATTAAGTCTTTCCAGGA

GCTGACTCACCTGGACCTTTCCTGTTGTAAGCTTGGAGATAAGCATGAACTTCTAGAACATCTCACCAAGGAGGCCCTTT

CCAGTGTAACTCAGCTCCACCTGAAGGATCATTATTTATCTAATGCAGGAGTGCTGAAAACAACAGTACCAGTTCAAGTG

ATGAAAAGAAGTCTTGAGAGCCTAACACTGCTAGACTTATTCTGTAACCCTGACGTTACAGATGCAGGAATTGGATACCT

TCTTTCTTTTAGAAAATTAAACTGCTTAGATATTTCTGGGACAGGACTCAAGGATATCAACGCTGTCAAACAGAAGCTCC

AGACCCACCTAGGCCTTATTCACTCCAAAGTGCCTTTGAAGGAATTTGATCATAGTAACTGCAAAACGAGGGCTGACCAG

ATTCTTCTGCAGTGGGAATGTGTGATGGTGGAGGCCAAGAAACCCAGAAAAGTCCCCGAACCTCAAGAGGCAACTCAGTA

CTTCTATCGGAAGCAGGCTCTGATGGAAATCTTGAGGAAGTGTCCCCTGGCAGACTCCCACATGACCTCTTCTGGAAAAC

TCCAGTTCTATAAAGAAAAGCCCCAGACTGCCATGGGCCATTGTTAAAAGAAGCCACAGAGAGACAAGAGTCAAAGAAGA

GCAAGAATAGAGCTTTTGAGGAGTCAGAGAAGGAACAGAATAATTCTTCACAGTCTTCAAAGCAAAAATATGTATTTGTT

TTGCTGTGGAAGACTGGGACTTATTAAATTCCTAC

ORF - retro_itri_1536 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	87.72 %
Parental protein coverage:	90.57 %
Number of stop codons detected:	0
Number of frameshifts detected	3

Retrocopy - Parental Gene Alignment:

									ParentalPRPFRLFPKGFSVELCMNREDDTAQKEKTDHFIFTYTREG-NLRYSAKSLFSLVLGFISDNVDHIDSLIG
		PRPFRL.PKGFSVELCMNREDDT.QKEKTDHFIFTYT.EG..LRYSAKSLFSLVLGFISDNVDHID.LIG
RetrocopyPRPFRLSPKGFSVELCMNREDDTSQKEKTDHFIFTYTQEG<DLRYSAKSLFSLVLGFISDNVDHIDPLIG
ParentalFPEQIAEKLFSAAEARQKFTEPGAGLRALQKFTEAYGSLVLCSLCLRNRYLVISEKLEEIKSFRELTRLD
		F.EQIAEKLFSAAEARQKFTEPGAGLRALQKFTEAYGSLVLCSLCLRNRYLVISEKLEEIKSF.ELT.LD
RetrocopyFLEQIAEKLFSAAEARQKFTEPGAGLRALQKFTEAYGSLVLCSLCLRNRYLVISEKLEEIKSFQELTHLD
ParentalLSCCKLGDEHELLEHLTNEALSSVTQLHLKDNCLSDAGVRKMTAPVRVMKRGLENLTLLDLSCNPDITDA
		LSCCKLGD.HELLEHLT.EALSSVTQLHLKD..LS.AGV.K.T.PV.VMKR.LE.LTLLDL.CNPD.TDA
RetrocopyLSCCKLGDKHELLEHLTKEALSSVTQLHLKDHYLSNAGVLKTTVPVQVMKRSLESLTLLDLFCNPDVTDA
ParentalGIGYLLSFKKLNCLDISGTGLKDINAVKQKLQTHIGLIHSKVPLKEFDHSNCKTEGWADQIVLQWERVTV
		GIGYLLSF.KLNCLDISGTGLKDINAVKQKLQTH.GLIHSKVPLKEFDHSNCKT...ADQI.LQWE.V.V
RetrocopyGIGYLLSFRKLNCLDISGTGLKDINAVKQKLQTHLGLIHSKVPLKEFDHSNCKTR--ADQILLQWECVMV
ParentalEAKKPRKVPEPQEATQYFYRKRALMEASRKCPLADSHMNSSGKLQFYKEK-APDCHGPLLKQS---QESK
		EAKKPRKVPEPQEATQYFYRK.ALME..RKCPLADSHM.SSGKLQFYKEK.APDCHGPLLK.....QESK
RetrocopyEAKKPRKVPEPQEATQYFYRKQALMEILRKCPLADSHMTSSGKLQFYKEK<APDCHGPLLKEATERQESK
ParentalKSKKRAFEESEKEQSNSSQSS-KQKY-VCLAVEDWDLLNSY
		KSK.RAFEESEKEQ.NSSQSS.K.K...C.AVEDWDLLNSY
RetrocopyKSKNRAFEESEKEQNNSSQSS<KAKICICFAVEDWDLLNSY

							

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

						

RNA-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_itri_1536 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_1536 was not experimentally validated.

Retrocopy orthology:

Ictidomys tridecemlineatus 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000016552	1 retrocopy	retro_ogar_816,
Ochotona princeps	ENSOPRG00000005566	1 retrocopy	retro_opri_15,
Ictidomys tridecemlineatus	ENSSTOG00000022786	1 retrocopy	retro_itri_1536 ,

	RetrogeneDB ID:	retro_itri_1536
Retrocopy location	Organism:	*Squirrel (Ictidomys tridecemlineatus)*
	Coordinates:	JH393533.1:744148..745303(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ENSSTOG00000026182
	Aliases:	None
	Status:	KNOWN_PSEUDOGENE
Parental gene information	Parental gene summary:
	Parental gene symbol:	LRRC42
	Ensembl ID:	ENSSTOG00000022786
	Aliases:	None
	Description:	leucine rich repeat containing 42 [Source:HGNC Symbol;Acc:28792]

Parental	PRPFRLFPKGFSVELCMNREDDTAQKEKTDHFIFTYTREG-NLRYSAKSLFSLVLGFISDNVDHIDSLIG
	PRPFRL.PKGFSVELCMNREDDT.QKEKTDHFIFTYT.EG..LRYSAKSLFSLVLGFISDNVDHID.LIG
Retrocopy	PRPFRLSPKGFSVELCMNREDDTSQKEKTDHFIFTYTQEG<DLRYSAKSLFSLVLGFISDNVDHIDPLIG

Parental	FPEQIAEKLFSAAEARQKFTEPGAGLRALQKFTEAYGSLVLCSLCLRNRYLVISEKLEEIKSFRELTRLD
	F.EQIAEKLFSAAEARQKFTEPGAGLRALQKFTEAYGSLVLCSLCLRNRYLVISEKLEEIKSF.ELT.LD
Retrocopy	FLEQIAEKLFSAAEARQKFTEPGAGLRALQKFTEAYGSLVLCSLCLRNRYLVISEKLEEIKSFQELTHLD

Parental	LSCCKLGDEHELLEHLTNEALSSVTQLHLKDNCLSDAGVRKMTAPVRVMKRGLENLTLLDLSCNPDITDA
	LSCCKLGD.HELLEHLT.EALSSVTQLHLKD..LS.AGV.K.T.PV.VMKR.LE.LTLLDL.CNPD.TDA
Retrocopy	LSCCKLGDKHELLEHLTKEALSSVTQLHLKDHYLSNAGVLKTTVPVQVMKRSLESLTLLDLFCNPDVTDA

Parental	GIGYLLSFKKLNCLDISGTGLKDINAVKQKLQTHIGLIHSKVPLKEFDHSNCKTEGWADQIVLQWERVTV
	GIGYLLSF.KLNCLDISGTGLKDINAVKQKLQTH.GLIHSKVPLKEFDHSNCKT...ADQI.LQWE.V.V
Retrocopy	GIGYLLSFRKLNCLDISGTGLKDINAVKQKLQTHLGLIHSKVPLKEFDHSNCKTR--ADQILLQWECVMV

Parental	EAKKPRKVPEPQEATQYFYRKRALMEASRKCPLADSHMNSSGKLQFYKEK-APDCHGPLLKQS---QESK
	EAKKPRKVPEPQEATQYFYRK.ALME..RKCPLADSHM.SSGKLQFYKEK.APDCHGPLLK.....QESK
Retrocopy	EAKKPRKVPEPQEATQYFYRKQALMEILRKCPLADSHMTSSGKLQFYKEK<APDCHGPLLKEATERQESK

Parental	KSKKRAFEESEKEQSNSSQSS-KQKY-VCLAVEDWDLLNSY
	KSK.RAFEESEKEQ.NSSQSS.K.K...C.AVEDWDLLNSY
Retrocopy	KSKNRAFEESEKEQNNSSQSS<KAKICICFAVEDWDLLNSY

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

RetrogeneDB ID:

retro_itri_1536