RetrogeneDB - Retrocopy retro_stub

                        
>retro_stub_33
ATGGAGAAATCGAGCCCAACGCTTGAGAGCAGAAAGAGGAAGACAGCCGGTGAAGACGAAGACGAAGATGTTAAGTTCAA

GGGAAAGCGTACTGAACAAGTTGAAAAATTAAGGAAAGTTTCAAGGCAGGAGTATTTGAAGAATAGGGAGAAGAAGAAAT

TAAAGCAACTCAGAGATGATATAGAAGATGAGCAATTTTTGTTTGAGAAAATCGAAAAATTGAGCGAACCAGAAAAACGT

GAACATTTATACAAGCAACAAATTGTTGAATTGGTTAGTAAGGAGCAGCAGTGCGACGACGCCGGTGAGGAACGTGAGAT

TCATCCACAACAAGCTTGGGAGGAAAATCAGATCAGCAATGCGAAACTTAATTTTGGATCTAAAGACAGAAAACAGAAGG

ATTATCAATTTGTGTTTGAAGATCAAATTGAATTCATCAAATCAACTATAATTGATTCAGATTCAGATGTTGATAATGAG

AAGCTGCAATGTACCAGAAATTCGAAACTTAACGAGGATAGGAAGGATTTACCAATTTATCCGTACAAGGATGCTTTGCT

CCAAGCTGTTCATGATCATCAAGTTCTTATCATAGTTGGAGAAACTGGCTCCGGGAAGACAACTCAAATACCTCAATATC

TACATGAAGCAGGTTTTACTAGAAGCGGTGGGAAGATGATTGGTTGTACTCAGCCTCGAAGAGTTGCGGCAATGAGAGTT

GCTGCGCGTGTTTCACATGAAATGGGGGTTAAACTTGGTCATGAGGTTGGTTATTCTATTCGTTTCGAGGATTGTACTTC

TGAGAAAACTATTCTCAAGTATATGACTGACGGAATGTTGCTGAGAGAGTTCCTTACCGAGCCTGATTTAGCAAGCTATA

GTGTTATAATGATTGACGAGGCTCATGAAAGAACATTGTCAACGGATATCCTGTTTGGGTTAATAAAAGATGTAGCTCGT

GCTCGACCCCGACTCAAGTTACTTATATCTAGCGCCACCCTTGATGCAAAGAAGTTTAGTGATTATTTTGACCGTGCTCC

GATTTTTAATATACCTGGAAGGCGATTTCCGGTTGAGAAACATCATTCAAAAGCACCAATCTCTGATTACTTGGATGCAG

CAGTAGTTACTGCACTTCAGATTCATGCAACTCAACCACAGGGTGATGGTGATATATTAATCTTTTTGACGGGGCAGGAG

GAGATTGAAACAGCTGAGAATATTATTAATCGCCGAATAAGAGCTTTGGGAACGAAAATAGCTGAGTTGATAACCTGTCC

AATATATGCAAACTTACCAACTGAACTACAAGCCAAGATATTTGAGCCTACTCCTGAAGGGGTTCGTAAAGTTGTCCTGG

CTACAAATATAGCAGAGACATCATTGACGATTGATGGAATCAAGTATGTTATTGATACAGGGTTTTGTAAGATCAATTGT

TACAACCCTCGAACAGGAACTGAGTCATTGATGGTTGCTCCTATCTCGAAGGCATCTGCCAACCAACGTGCTGGTCGATC

AGGACGAACAGGTCCTGGAAAGTGCTTCCGGTTATATACTGAACATAGCTACATGAATGATTTGGAAGATAACACAATTC

CAGAAATACAAAGGACTAACCTTGCAAATGTCGTGCTCTTACTCAAGAGTGTAGGGATTACCGACTTGCTGAACTTTGAC

TTCATGGATCCTCCACCAGCTGAAGCTCTACTTAAAGCCCTGGAATTGTTATTTGCACTTGGTTCCCTTGATAAGGATGG

TAAGTTAACCAAAGTGGGTGAAAGAATGTCCGAGTTTCCTTTGGATCCAATGCTTTCCAAGATGATAGTTGCATCTGATA

AGTACAAGTGCTCAGCTGAGATAATAAGTATTGCTGCAATGCTTTCTGTCGGGAATTCAATCTTCTATCGTCCAAAGGAC

AGACAAGTCCAAGCTGACAATGCGTGGATGAACTTTCATGTTGGCAATGTGGGAGATCATATTGCTTTGCTTAAGGTTTA

CAATTCCTGGAAGGAAACAAAATTTTCAACTCAGTGGTGCTATGAGAATTACATCCAGGTCAGAAGCATGAAAAAAGCTA

GAGATATCCGAGATCAGTTAGAAGGTCGGCTTGAAAGGGTTGGAATTGATTTGACTTCAAATGTTAATGACTTGGAAGCT

ATTAAGAAGTCTATAATATCAGGATTTTTTCCCCACTCAGCAAGGCTACAGAAGAATGGAGCTTATCGAACTGTTAAACA

TCCCCAGACAGGTCACATTCATCCCAGCTCGGGTTTATCACAGGTACTTCCTAGATGGGTTGTCTACCATGAGCTGGTCC

TGACAACTAAGGAGTACATGCGGCAGGTATCTGAATTGAAACCAGAATGGCTTGTAGAAGTAGCTCCTCACTATTATCAG

TTGAAAGACGTTGAAGACTCAAGCTCGAAGAAAATGCCTCGTGGAATTGGCCTTGCATCTTCTAAATAG

ORF - retro_stub_33 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	84.23 %
Parental protein coverage:	73.71 %
Number of stop codons detected:	0
Number of frameshifts detected:	0

Retrocopy - Parental Gene Alignment:

                                ParentalVDQEPSIDSIEKTMAKSAFEKLQEDRKTLPMYPYRDDLLQAINDHQVLVIVGETGSGKTTQIPQYLHEAG
.D.....D............KL.EDRK.LP.YPY.D.LLQA..DHQVL.IVGETGSGKTTQIPQYLHEAG
RetrocopyIDSDSDVDNEKLQCTRNS--KLNEDRKDLPIYPYKDALLQAVHDHQVLIIVGETGSGKTTQIPQYLHEAG
ParentalYTKRG--KIGCTQPRRVAAMSVAARVSQEMGVKLGHEVGYSIRFEDCTSEKTILKYMTDGMLLREFLGEP
.T..G...IGCTQPRRVAAM.VAARVS.EMGVKLGHEVGYSIRFEDCTSEKTILKYMTDGMLLREFL.EP
RetrocopyFTRSGGKMIGCTQPRRVAAMRVAARVSHEMGVKLGHEVGYSIRFEDCTSEKTILKYMTDGMLLREFLTEP
ParentalDLASYSVIMVDEAHERTLSTDILFGLVKDISRFRPDLKLLISSATLDAEKFSDYFDCAPIFKIPGRRFPV
DLASYSVIM.DEAHERTLSTDILFGL.KD..R.RP.LKLLISSATLDA.KFSDYFD.APIF.IPGRRFPV
RetrocopyDLASYSVIMIDEAHERTLSTDILFGLIKDVARARPRLKLLISSATLDAKKFSDYFDRAPIFNIPGRRFPV
ParentalEIHYTKAPEADYLDAAVVTALQIHVTQPPGDGDILIFLTGQEEIETAEEIIKHRIKGLGTKIAELIICPI
E.H..KAP..DYLDAAVVTALQIH.TQP.GDGDILIFLTGQEEIETAE.II..RI..LGTKIAELI.CPI
RetrocopyEKHHSKAPISDYLDAAVVTALQIHATQPQGDGDILIFLTGQEEIETAENIINRRIRALGTKIAELITCPI
ParentalYANLPTELQAKIFEPTPEGARKVVLATNIAETSLTIDGIKYVIDPGFSKMKSYNPRTGMESLLVAPISKA
YANLPTELQAKIFEPTPEG.RKVVLATNIAETSLTIDGIKYVID.GF.K...YNPRTG.ESL.VAPISKA
RetrocopyYANLPTELQAKIFEPTPEGVRKVVLATNIAETSLTIDGIKYVIDTGFCKINCYNPRTGTESLMVAPISKA
ParentalSANQRAGRSGRTGPGKCFRLYTAYNYMNDLEDNTVPEIQRTNLANVVLSLKSLGIHDLLNFDFMDPPPAE
SANQRAGRSGRTGPGKCFRLYT...YMNDLEDNT.PEIQRTNLANVVL.LKS.GI.DLLNFDFMDPPPAE
RetrocopySANQRAGRSGRTGPGKCFRLYTEHSYMNDLEDNTIPEIQRTNLANVVLLLKSVGITDLLNFDFMDPPPAE
ParentalALLKALELLFALSALNKLGELTKVGRRMAEFPLDPMLSKMIVASDKYKCSDEIISIAAMLSVGNSIFYRP
ALLKALELLFAL..L.K.G.LTKVG.RM.EFPLDPMLSKMIVASDKYKCS.EIISIAAMLSVGNSIFYRP
RetrocopyALLKALELLFALGSLDKDGKLTKVGERMSEFPLDPMLSKMIVASDKYKCSAEIISIAAMLSVGNSIFYRP
ParentalKDKQVHADNARMNFHVGNVGDHIALLKVYSSWRETDFSTQWCYENYIQVRSMKRARDIRDQLEGLLERVE
KD.QV.ADNA.MNFHVGNVGDHIALLKVY.SW.ET.FSTQWCYENYIQVRSMK.ARDIRDQLEG.LERV.
RetrocopyKDRQVQADNAWMNFHVGNVGDHIALLKVYNSWKETKFSTQWCYENYIQVRSMKKARDIRDQLEGRLERVG
ParentalIELTSNDNDYEAIKKAITSGFFPHSAKLQKNGSYRTIKHPQTVNVHPSSGLAQVLPRWVVYHELVLTTKE
I.LTSN.ND.EAIKK.I.SGFFPHSA.LQKNG.YRT.KHPQT...HPSSGL.QVLPRWVVYHELVLTTKE
RetrocopyIDLTSNVNDLEAIKKSIISGFFPHSARLQKNGAYRTVKHPQTGHIHPSSGLSQVLPRWVVYHELVLTTKE
ParentalYMRQVTELKPDWLVEIAPHYYQLKDVEDSSSKKMPRGTGRAS
YMRQV.ELKP.WLVE.APHYYQLKDVEDSSSKKMPRG.G.AS
RetrocopyYMRQVSELKPEWLVEVAPHYYQLKDVEDSSSKKMPRGIGLAS

                            

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

                        

RNA-Seq - click to see more details

Solanum tuberosum was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Solanum tuberosum was not studied using ChIP-Seq data.

EST - click to see more details

Solanum tuberosum was not studied using EST data.

TSS - click to see more details

Solanum tuberosum was not studied using FANTOM5 data.

Lab - click to see more details

retro_stub_33 was not experimentally validated.

Retrocopy orthology:

Solanum tuberosum 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 12 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA027162	1 retrocopy	retro_oind_65,
Brachypodium distachyon	BRADI1G61220	1 retrocopy	retro_bdis_4,
Leersia perrieri	LPERR08G09260	1 retrocopy	retro_lper_14,
Hordeum vulgare	MLOC_5589	1 retrocopy	retro_hvul_14,
Oryza meridionalis	OMERI08G09070	1 retrocopy	retro_omer_5,
Oryza nivara	ONIVA08G11780	1 retrocopy	retro_oniv_26,
Oryza punctata	OPUNC08G10350	1 retrocopy	retro_opun_23,
Oryza glaberrima	ORGLA08G0098600	1 retrocopy	retro_ogla_26,
Oryza rufipogon	ORUFI08G12410	1 retrocopy	retro_oruf_44,
Solanum tuberosum	PGSC0003DMG402024649	1 retrocopy	retro_stub_33 ,
Sorghum bicolor	Sb04g022460	1 retrocopy	retro_sbic_37,
Setaria italica	Si021302m.g	1 retrocopy	retro_sita_41,

	RetrogeneDB ID:	retro_stub_33
Retrocopy location	Organism:	*Potato (Solanum tuberosum)*
	Coordinates:	12:11429704..11432173(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	PGSC0003DMG400002239
	Aliases:	None
	Status:	KNOWN_PROTEIN_CODING
Parental gene information	Parental gene summary:
	Parental gene symbol:	None
	Ensembl ID:	PGSC0003DMG402024649
	Aliases:	None
	Description:	None

Parental	VDQEPSIDSIEKTMAKSAFEKLQEDRKTLPMYPYRDDLLQAINDHQVLVIVGETGSGKTTQIPQYLHEAG
	.D.....D............KL.EDRK.LP.YPY.D.LLQA..DHQVL.IVGETGSGKTTQIPQYLHEAG
Retrocopy	IDSDSDVDNEKLQCTRNS--KLNEDRKDLPIYPYKDALLQAVHDHQVLIIVGETGSGKTTQIPQYLHEAG

Parental	YTKRG--KIGCTQPRRVAAMSVAARVSQEMGVKLGHEVGYSIRFEDCTSEKTILKYMTDGMLLREFLGEP
	.T..G...IGCTQPRRVAAM.VAARVS.EMGVKLGHEVGYSIRFEDCTSEKTILKYMTDGMLLREFL.EP
Retrocopy	FTRSGGKMIGCTQPRRVAAMRVAARVSHEMGVKLGHEVGYSIRFEDCTSEKTILKYMTDGMLLREFLTEP

Parental	DLASYSVIMVDEAHERTLSTDILFGLVKDISRFRPDLKLLISSATLDAEKFSDYFDCAPIFKIPGRRFPV
	DLASYSVIM.DEAHERTLSTDILFGL.KD..R.RP.LKLLISSATLDA.KFSDYFD.APIF.IPGRRFPV
Retrocopy	DLASYSVIMIDEAHERTLSTDILFGLIKDVARARPRLKLLISSATLDAKKFSDYFDRAPIFNIPGRRFPV

Parental	EIHYTKAPEADYLDAAVVTALQIHVTQPPGDGDILIFLTGQEEIETAEEIIKHRIKGLGTKIAELIICPI
	E.H..KAP..DYLDAAVVTALQIH.TQP.GDGDILIFLTGQEEIETAE.II..RI..LGTKIAELI.CPI
Retrocopy	EKHHSKAPISDYLDAAVVTALQIHATQPQGDGDILIFLTGQEEIETAENIINRRIRALGTKIAELITCPI

Parental	YANLPTELQAKIFEPTPEGARKVVLATNIAETSLTIDGIKYVIDPGFSKMKSYNPRTGMESLLVAPISKA
	YANLPTELQAKIFEPTPEG.RKVVLATNIAETSLTIDGIKYVID.GF.K...YNPRTG.ESL.VAPISKA
Retrocopy	YANLPTELQAKIFEPTPEGVRKVVLATNIAETSLTIDGIKYVIDTGFCKINCYNPRTGTESLMVAPISKA

Parental	SANQRAGRSGRTGPGKCFRLYTAYNYMNDLEDNTVPEIQRTNLANVVLSLKSLGIHDLLNFDFMDPPPAE
	SANQRAGRSGRTGPGKCFRLYT...YMNDLEDNT.PEIQRTNLANVVL.LKS.GI.DLLNFDFMDPPPAE
Retrocopy	SANQRAGRSGRTGPGKCFRLYTEHSYMNDLEDNTIPEIQRTNLANVVLLLKSVGITDLLNFDFMDPPPAE

Parental	ALLKALELLFALSALNKLGELTKVGRRMAEFPLDPMLSKMIVASDKYKCSDEIISIAAMLSVGNSIFYRP
	ALLKALELLFAL..L.K.G.LTKVG.RM.EFPLDPMLSKMIVASDKYKCS.EIISIAAMLSVGNSIFYRP
Retrocopy	ALLKALELLFALGSLDKDGKLTKVGERMSEFPLDPMLSKMIVASDKYKCSAEIISIAAMLSVGNSIFYRP

Parental	KDKQVHADNARMNFHVGNVGDHIALLKVYSSWRETDFSTQWCYENYIQVRSMKRARDIRDQLEGLLERVE
	KD.QV.ADNA.MNFHVGNVGDHIALLKVY.SW.ET.FSTQWCYENYIQVRSMK.ARDIRDQLEG.LERV.
Retrocopy	KDRQVQADNAWMNFHVGNVGDHIALLKVYNSWKETKFSTQWCYENYIQVRSMKKARDIRDQLEGRLERVG

Parental	IELTSNDNDYEAIKKAITSGFFPHSAKLQKNGSYRTIKHPQTVNVHPSSGLAQVLPRWVVYHELVLTTKE
	I.LTSN.ND.EAIKK.I.SGFFPHSA.LQKNG.YRT.KHPQT...HPSSGL.QVLPRWVVYHELVLTTKE
Retrocopy	IDLTSNVNDLEAIKKSIISGFFPHSARLQKNGAYRTVKHPQTGHIHPSSGLSQVLPRWVVYHELVLTTKE

Parental	YMRQVTELKPDWLVEIAPHYYQLKDVEDSSSKKMPRGTGRAS
	YMRQV.ELKP.WLVE.APHYYQLKDVEDSSSKKMPRG.G.AS
Retrocopy	YMRQVSELKPEWLVEVAPHYYQLKDVEDSSSKKMPRGIGLAS

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

RetrogeneDB ID:

retro_stub_33