RetrogeneDB - Retrocopy retro_itri

                        
>retro_itri_1893
TCTCCCTGGTTTATCTACATCTGGAGCTACACTTAAAATAAGAGAGAAGAAATCCAGATTAGGTGGTCCTGCATCCATGT

GCCAAAAGTGACAATTAAGATCCAGCTCAGAGCATCAGAGAAGAGCCAGGTGGGTGAGACAAATAAAGTATCTGAAACAC

TTAAGGACATTTCAAACCACGTTGTGGGTTCCACCTTTCTTTCGTGGTTCTGAGCACCAAGCCCACAGACATAAAGTAAG

CTCAGAATCTACAGTGCACTTCATCTACTGCTCAGGAATCCTGTCCTCCTAAATCTCCAAGGGCTCATGTACTAAAGCCA

CTGGTGAAGAACTTCTGCACCTTACTGCTAAATGATCCTGGGACTCTGGGCAGCATTAACCCTTTGTGTATTGCCCAGGT

GAATGATCCTGTCCAGAGGTTCATCAGCACCCTAGCCAAGAACACTACTCACCTTGCTTTGGGAGGAAGAGTTCACCTTT

GAGTGGAACACCAGGTCCAAGGATTTACACCTGCAGATTACAGAGGACTGGCAATCCTCAGAAGGTCTGCTGGCCCTGTC

CTGTCCTCTGTTCAAGAAACAGCCTTCCAGGATGTAGAGCTTCTTTCTGATCAGTGGGCCCACCCTCAGTAGATCAGCAC

TGGGCTCTGTCATTGCAGAGCTTTCTTACATAGAACCCAGTGAATTGAAATCCTGACAAATCCCTTACCCTGTTGCTTCT

GCCAAGATAGAAAAGGATCACACAGTGATGCCATGGGGTACCATGGTCACTACTTTTACTACTGTGAAGACCAAGCCTTA

CTATGATGTGGGGAGGGTGTCCTGGCTGAGTTCTGAATCCCCACTGAAGACATCCATCAAGGTGAAGGTCATTAAGAAGG

ACATCTTCATCCAGGTCATTCATGCCATGAGGCAACTGTCAGGAAGATATTCTTTTCTTCAGATATGGAACTGCTGGTGT

TGAATGGTTTCAGTCAGGTCATTGAAGTTGCCATTCAGCAGCTCACTGAATCTTCAAAGCTGAAACTCAAGTCATCACAG

AAGAATAACACTATCATCATATCAGGGATCTCCAATACCTTGCTCTCTCAGGACAATACTGCTCTCATGCAGGAT

ORF - retro_itri_1893 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	69.21 %
Parental protein coverage:	52.88 %
Number of stop codons detected:	4
Number of frameshifts detected:	3

Retrocopy - Parental Gene Alignment:

                                ParentalSPVHLQLELHMKEKREDIQIRWSYIHVPELTIKIQPRAPGEGQVGETNAISETLKDILKHLVSSTSPS-V
SP...........KRE.IQIRWS.IHVP..TIKIQ.RA....QVGETN..SETLKDI..H.V.ST..S.V
RetrocopySPWFIYIWSYT*NKREEIQIRWSCIHVPKVTIKIQLRASEKSQVGETNKVSETLKDISNHVVGSTFLS<V
ParentalVLSTKPTDIKEAQNLQRASSPAQESCPPKPPRAHELKLLVKNIRVSLLNDPGASGSVSPVCIAQLNDPVQ
VLSTKPTDIK.AQNLQ..SS.AQESCPPK.PRAH.LK.LVKN....LLNDPG..GS..P.CIAQ.NDPVQ
RetrocopyVLSTKPTDIK*AQNLQCTSSTAQESCPPKSPRAHVLKPLVKNFCTLLLNDPGTLGSINPLCIAQVNDPVQ
ParentalRFTSTQAKSTTQLT-WEEEFTFELNAKSKELHLQIAENGRSSEGLLAMTTVPLDLFKKQPSGLQSFTLIG
RF.ST.AK.TT.L..WEEEFTFE.N..SK.LHLQI.E...SSEGLLA.......LFKKQPS...SF.LI.
RetrocopyRFISTLAKNTTHLA>WEEEFTFEWNTRSKDLHLQITEDWQSSEGLLALSC---PLFKKQPSRM*SFFLIS
ParentalGPTLSSSALGSVTAEFSYIEPGELKSWQTPPPVAAAKIEKDRTVMPCGTVVTTVTAVKTKPRYDVGRASP
GPTLS.SALGSV.AE.SYIEP.ELKS.Q.P.PVA.AKIEKD.TVMP.GT.VTT.T.VKTKP.YDVGR.S.
RetrocopyGPTLSRSALGSVIAELSYIEPSELKS*QIPYPVASAKIEKDHTVMPWGTMVTTFTTVKTKPYYDVGRVSW
ParentalLSSAESPVKTPVKVKVIEKDISIQAI-SCHGAPVSKTFSSSDTELLVLNGSDPVAEVAIRQLSESSKLKL
LSS.ESP.KT..KVKVI.KDI.IQ.I.SCH.A.V.K.F.SSD.ELLVLNG...V.EVAI.QL.ESSKLKL
RetrocopyLSS-ESPLKTSIKVKVIKKDIFIQVI<SCHEATVRKIFFSSDMELLVLNGFSQVIEVAIQQLTESSKLKL
ParentalKSPRKKSTIIISGISKTSLSQDHEAALMQD
KS..K..TIIISGIS.T.LSQD...ALMQD
RetrocopyKSSQKNNTIIISGISNTLLSQDN-TALMQD

                            

                            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_1893 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_1893 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000015690	1 retrocopy	retro_itri_1893 ,

	RetrogeneDB ID:	retro_itri_1893
Retrocopy location	Organism:	*Squirrel (Ictidomys tridecemlineatus)*
	Coordinates:	JH395499.1:396..1511(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	C2CD2
	Ensembl ID:	ENSSTOG00000015690
	Aliases:	None
	Description:	C2 calcium-dependent domain containing 2 [Source:HGNC Symbol;Acc:1266]

Parental	SPVHLQLELHMKEKREDIQIRWSYIHVPELTIKIQPRAPGEGQVGETNAISETLKDILKHLVSSTSPS-V
	SP...........KRE.IQIRWS.IHVP..TIKIQ.RA....QVGETN..SETLKDI..H.V.ST..S.V
Retrocopy	SPWFIYIWSYT*NKREEIQIRWSCIHVPKVTIKIQLRASEKSQVGETNKVSETLKDISNHVVGSTFLS<V

Parental	VLSTKPTDIKEAQNLQRASSPAQESCPPKPPRAHELKLLVKNIRVSLLNDPGASGSVSPVCIAQLNDPVQ
	VLSTKPTDIK.AQNLQ..SS.AQESCPPK.PRAH.LK.LVKN....LLNDPG..GS..P.CIAQ.NDPVQ
Retrocopy	VLSTKPTDIK*AQNLQCTSSTAQESCPPKSPRAHVLKPLVKNFCTLLLNDPGTLGSINPLCIAQVNDPVQ

Parental	RFTSTQAKSTTQLT-WEEEFTFELNAKSKELHLQIAENGRSSEGLLAMTTVPLDLFKKQPSGLQSFTLIG
	RF.ST.AK.TT.L..WEEEFTFE.N..SK.LHLQI.E...SSEGLLA.......LFKKQPS...SF.LI.
Retrocopy	RFISTLAKNTTHLA>WEEEFTFEWNTRSKDLHLQITEDWQSSEGLLALSC---PLFKKQPSRM*SFFLIS

Parental	GPTLSSSALGSVTAEFSYIEPGELKSWQTPPPVAAAKIEKDRTVMPCGTVVTTVTAVKTKPRYDVGRASP
	GPTLS.SALGSV.AE.SYIEP.ELKS.Q.P.PVA.AKIEKD.TVMP.GT.VTT.T.VKTKP.YDVGR.S.
Retrocopy	GPTLSRSALGSVIAELSYIEPSELKS*QIPYPVASAKIEKDHTVMPWGTMVTTFTTVKTKPYYDVGRVSW

Parental	LSSAESPVKTPVKVKVIEKDISIQAI-SCHGAPVSKTFSSSDTELLVLNGSDPVAEVAIRQLSESSKLKL
	LSS.ESP.KT..KVKVI.KDI.IQ.I.SCH.A.V.K.F.SSD.ELLVLNG...V.EVAI.QL.ESSKLKL
Retrocopy	LSS-ESPLKTSIKVKVIKKDIFIQVI<SCHEATVRKIFFSSDMELLVLNGFSQVIEVAIQQLTESSKLKL

Parental	KSPRKKSTIIISGISKTSLSQDHEAALMQD
	KS..K..TIIISGIS.T.LSQD...ALMQD
Retrocopy	KSSQKNNTIIISGISNTLLSQDN-TALMQD

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

RetrogeneDB ID:

retro_itri_1893