RetrogeneDB - Retrocopy retro_shar

                        
>retro_shar_665
AAACTGAAGAAGCTACTAAAACATCTGAAGAAACCCTCAGACTTACCTATCACTGTGGACATTCTGGCGGAAACAGGTGT

TGGGAAAACAGTGAATGGCTGGTGGAAACATGAGCAAGTAGGAGGCTTTGCCAAAGATTTAGTGGCCCGATGGAAGAAGT

TAGTCCCTGTTGCTTAGGAGGTTGAAAGGAATATTGAGCCTGAGGAGCAAATGCTTGAGAGAAGTAGCTCTAGAAAACAT

CCCCGAGATGTTTTTCCCAAGGAGGAGGAAATGGAGGAGGAATATCAGGAAAGCTGGAAGGACTCTTGTAGCCAGTCATA

CTGACTCCCAGGAGAAAAAGCATGGAAAACTTTCAGAGTTTGGTAGAGTGCCCAAGGCCTCACACAGTAGTAAGACAAGA

GAAGAGAGAAGGCCATGGAAGAAAACCTCCTCATTGTACACATACGATCAGGAACCATTCAACAGAAGTCATGTTCACTC

ACCTCAGCCTTCCACAAGCCCTTAGCAATTATCCATGATCAACTCCCTGAAGAGGAGGAGGAGCAGCTGATACCACATCA

GAAGGCTGGCAAAAGCCATAGATAGTCATGCCTTTCAGGACCAAGGCTAAAATAGCCAAGAGAGATACGTAGGTGAACCC

CGGGACAAAGGCCTTGTGAGTCAGAGCAAAAAGCACAAGACTTCCCAGAAAGAAAAGCATCGCTTGGATAAAAGAGAGGA

AAAGAACTTTAGTTTGGGTTGAGGCAAAGTGTCTAAGGCTGTTTCTCGAGAAGAGGGCCAAAGTATCCCTCAGGAACCAG

TACTAAGGAGAAGCAGACATTGTCTAGTGCTGCCAAGAAAGAGAGGGACAAAGAAAGCGTCAGTAGCAAGAAGTTTTTAC

CTCCCTTGGAGGTGGCTTCTGTCAACCATATGAAAAAAACAAAGCACAAGGATGCACAGAAATCCAAATTGGAAAAGACC

AAGCTTAGTGTGGACAGCTTTGATGTAGGAAAGTGGGAGGGAGAATTTTCTCCCAAGCCAAAAGAGAAAGGGGTGTCTAA

TAGCTTAAAGGAAAATTCAAAGCCCTTAACTCAGACAGAAAACCATCGAGTCACTTTTCAGGGGCTTGAGAGACAGATAT

GGATGATGTCTATGAATAGCCCACCACGTCTTTTGAATCATACCCCAGCTACGACCAGCCCCAGAGGGGAAAAAAAAGGT

TGTTAAAACTACAAGTGGGATTCGTGCAGAGAAAAGTCACAATAAGCAGAATGGTTTCAAAGCTGATCATAAAAACTCTA

ATAATATCATTCAGAAACTCCCTAAGATGAGTGAGAGCAAGGCAGAAAAGCAACTTTCTGGAGCCAGCTCTGCCAAACTA

AAAACAGTCTCCATTGATGTGATGCCAACATTACCGGACATCCCCTTGCCTACCATTTAGGCCATTTATCACCCACTTCC

TTCTCTTAAACTGATTCCCTCCTTTTAGCCAAAGAGGAAAGAACCCTCACCCCATGAAGAAGAGGAAGCTGGATTTACTG

GATGTAGGATGAATTCAAAAATGCAAGTCTATTCTGATTCCAAGTGTGCCTACCTATCGAAGATGATGTCCATGCACCAG

CAGTGCACTGGAGTCCTCAATAATAGCATAGACTCAATTTATGAAGTTGGGGGTATTCCCTATTCTGTACTTGAACCAGT

TTTGGAAAGATGTACTCCTGAGCAACCCTATGGAATTGAGGAGTGCAGCCATGTGTTACACGAAGAGACTGATCAGCTGA

GGAAAATTCACTGCCATAGGGACTTTAAGAGAGAGAGACCAGAAGAATTTGGGTCTTGGAGGGAGGTGAGTCTTCAGCTC

CGGGATGCTCGGGAGCAGGGACTGCTCCTCTTAGCTGAGAACATTCGATCAGCTCATGCCAACAAACCCAAAGGCCGACA

AGCAAAGATGGCCTTTGTCAACTCTGTGGCCAAGTCGCCTCTGATGTCAGGAGACAGCAGGAGAAATGTGGGACTGGAGG

AGCGGCTGTTCCCAAAAAGATCAAGGTCAAACCCACCCCCTACACCTCCAGCAATAGCTACATCTGCAGCAGGGGGTGCA

GCAGCGCCAAGGAAGGGCAGCCCTACAACGGCCCC

ORF - retro_shar_665 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	74.14 %
Parental protein coverage:	90.85 %
Number of stop codons detected:	7
Number of frameshifts detected:	7

Retrocopy - Parental Gene Alignment:

                                ParentalKKKKLLKHLKRLSDLPITVDILAETGVGKTVNGLRKHEQVGGFAKDLVARWKKLVPVA----QNIEPEEQ
K.KKLLKHLK..SDLPITVDILAETGVGKTVNG..KHEQVGGFAKDLVARWKKLVPVA.....NIEPEEQ
RetrocopyKLKKLLKHLKKPSDLPITVDILAETGVGKTVNGWWKHEQVGGFAKDLVARWKKLVPVA*EVERNIEPEEQ
ParentalDLERSSSRKRPRDV-FPKEEEMEEEYQESWKASCSQPHSPDYREKKHRKLSEFDRMPKASHSGETREERK
.LERSSSRK.PRDV.FP....................H..D..EKKH.KLSEF.R.PKASHS..TREER.
RetrocopyMLERSSSRKHPRDV>FPRRRKWRRNIRKAGRTLVAS-HT-DSQEKKHGKLSEFGRVPKASHSSKTREERR
ParentalRWNKTSPLYTSDQELSDSSHVHSPQPSTSP-QQLSMDYDQLPEEEEEEQPVPH-RKAGKS-HSHAFQDRG
.W.KTS.LYT.DQE....S..H...P..S....L....DQLPEEEEE.Q..PH.R...K...SHAFQD.G
RetrocopyPWKKTSSLYTYDQEPFNRS--HVHSPQPST<KPLAIIHDQLPEEEEE-QLIPH>RRLAKAIDSHAFQDQG
ParentalLNSQERRLGEPQDRGSVSRSKEHKTSQKEKHRLDTREEKTFSLGRDKVSKAVSREEGR-RSPSGASTKEK
.NSQER..GEP.D.G.VS.SK.HKTSQKEKHRLD.REEK.FSLG..KVSKAVSREEG....PSG.STKEK
Retrocopy*NSQERYVGEPRDKGLVSQSKKHKTSQKEKHRLDKREEKNFSLG*GKVSKAVSREEGQ<KYPSGTSTKEK
ParentalQTLSSAAKKERDKESGGSKKKLLPPLEVASVNHMKKTKHKDAQKSKLEKTKLSGDSFDVGKWEGEFSPKP
QTLSSAAKKERDKES..SKK..LPPLEVASVNHMKKTKHKDAQKSKLEKTKLS.DSFDVGKWEGEFSPKP
RetrocopyQTLSSAAKKERDKESVSSKK-FLPPLEVASVNHMKKTKHKDAQKSKLEKTKLSVDSFDVGKWEGEFSPKP
ParentalKEKGGSNSLKTREGKPKASNSDRKSSSHFSG-AGETDVDDDYEQPTMSFESYLSYDQPQRK-KKKVVKTT
KEKG.SNSLK....KP............F.G.A.ETD.DD.YE.PT.SFESY.SYDQPQR.....VVKTT
RetrocopyKEKGVSNSLK-ENSKPLTQTENHRVT--FQG<A*ETDMDDVYE*PTTSFESYPSYDQPQRX<XXXVVKTT
ParentalTGVRAEKSHSKQNGSKADHKNSNNAIQKLPKMNESKAEKQHSGTSSAKLKKVSTDVTPTLPDIPLPTIQA
.G.RAEKSH.KQNG.KADHKNSNN.IQKLPKM.ESKAEKQ.SG.SSAKLK.VS.DV.PTLPDIPLPTI.A
RetrocopySGIRAEKSHNKQNGFKADHKNSNNIIQKLPKMSESKAEKQLSGASSAKLKTVSIDVMPTLPDIPLPTI*A
ParentalNYRPLPSLELIPSFQPKRKAVSSPHEEEEAGFTGRRMNSKMQVYSGSKCAYLPKMMSLHQQCIRVLNNNI
.Y.PLPSL.LIPSF.PKRK...SPHEEEEAGFTG.RMNSKMQVYS.SKCAYL.KMMS.HQQC..VLNN.I
RetrocopyIYHPLPSLKLIPSF*PKRKE-PSPHEEEEAGFTGCRMNSKMQVYSDSKCAYLSKMMSMHQQCTGVLNNSI
ParentalDSIYEVGGVPYSVLEPVLERCTPEQLYRIEECNHVLTEETDQLWKIHCHRDFKRERPEEFESWREMYLRL
DSIYEVGG.PYSVLEPVLERCTPEQ.Y.IEEC.HVL.EETDQL.KIHCHRDFKRERPEEF.SWRE..L.L
RetrocopyDSIYEVGGIPYSVLEPVLERCTPEQPYGIEECSHVLHEETDQLRKIHCHRDFKRERPEEFGSWREVSLQL
ParentalQDAREQRLLLLTENIRSAHANKPKGRQAKMAFVNSVAKPP-RDVRRRQEKFGTGGAAVPEKIKIKPAPYT
.DAREQ.LLLL.ENIRSAHANKPKGRQAKMAFVNSVAK.P..DVRR.QEK.GTGGAAVP.KIK.KP.PYT
RetrocopyRDAREQGLLLLAENIRSAHANKPKGRQAKMAFVNSVAKSP<SDVRRQQEKCGTGGAAVPKKIKVKPTPYT
ParentalSSSGYTCSSSSSSYSNSAEEGQPYDGP
SS..Y.CS...SS....A.EGQPY.GP
RetrocopySSNSYICSRGCSS----AKEGQPYNGP

                            

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

                        

RNA-Seq - click to see more details

Sarcophilus harrisii was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Sarcophilus harrisii was not studied using ChIP-Seq data.

EST - click to see more details

Sarcophilus harrisii was not studied using EST data.

TSS - click to see more details

Sarcophilus harrisii was not studied using FANTOM5 data.

Lab - click to see more details

retro_shar_665 was not experimentally validated.

Retrocopy orthology:

Sarcophilus harrisii 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000011241	1 retrocopy	retro_dnov_1854,
Loxodonta africana	ENSLAFG00000017306	1 retrocopy	retro_lafr_424,
Myotis lucifugus	ENSMLUG00000005258	1 retrocopy	retro_mluc_498,
Monodelphis domestica	ENSMODG00000012842	1 retrocopy	retro_mdom_1961,
Sarcophilus harrisii	ENSSHAG00000006165	1 retrocopy	retro_shar_665 ,

	RetrogeneDB ID:	retro_shar_665
Retrocopy location	Organism:	*Tasmanian devil (Sarcophilus harrisii)*
	Coordinates:	GL856967.1:1118231..1120346(-)
	Located in intron of:	ENSSHAG00000012329
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	None
	Ensembl ID:	ENSSHAG00000006165
	Aliases:	None
	Description:	None

Parental	KKKKLLKHLKRLSDLPITVDILAETGVGKTVNGLRKHEQVGGFAKDLVARWKKLVPVA----QNIEPEEQ
	K.KKLLKHLK..SDLPITVDILAETGVGKTVNG..KHEQVGGFAKDLVARWKKLVPVA.....NIEPEEQ
Retrocopy	KLKKLLKHLKKPSDLPITVDILAETGVGKTVNGWWKHEQVGGFAKDLVARWKKLVPVA*EVERNIEPEEQ

Parental	DLERSSSRKRPRDV-FPKEEEMEEEYQESWKASCSQPHSPDYREKKHRKLSEFDRMPKASHSGETREERK
	.LERSSSRK.PRDV.FP....................H..D..EKKH.KLSEF.R.PKASHS..TREER.
Retrocopy	MLERSSSRKHPRDV>FPRRRKWRRNIRKAGRTLVAS-HT-DSQEKKHGKLSEFGRVPKASHSSKTREERR

Parental	RWNKTSPLYTSDQELSDSSHVHSPQPSTSP-QQLSMDYDQLPEEEEEEQPVPH-RKAGKS-HSHAFQDRG
	.W.KTS.LYT.DQE....S..H...P..S....L....DQLPEEEEE.Q..PH.R...K...SHAFQD.G
Retrocopy	PWKKTSSLYTYDQEPFNRS--HVHSPQPST<KPLAIIHDQLPEEEEE-QLIPH>RRLAKAIDSHAFQDQG

Parental	LNSQERRLGEPQDRGSVSRSKEHKTSQKEKHRLDTREEKTFSLGRDKVSKAVSREEGR-RSPSGASTKEK
	.NSQER..GEP.D.G.VS.SK.HKTSQKEKHRLD.REEK.FSLG..KVSKAVSREEG....PSG.STKEK
Retrocopy	NSQERYVGEPRDKGLVSQSKKHKTSQKEKHRLDKREEKNFSLGGKVSKAVSREEGQ<KYPSGTSTKEK

Parental	QTLSSAAKKERDKESGGSKKKLLPPLEVASVNHMKKTKHKDAQKSKLEKTKLSGDSFDVGKWEGEFSPKP
	QTLSSAAKKERDKES..SKK..LPPLEVASVNHMKKTKHKDAQKSKLEKTKLS.DSFDVGKWEGEFSPKP
Retrocopy	QTLSSAAKKERDKESVSSKK-FLPPLEVASVNHMKKTKHKDAQKSKLEKTKLSVDSFDVGKWEGEFSPKP

Parental	KEKGGSNSLKTREGKPKASNSDRKSSSHFSG-AGETDVDDDYEQPTMSFESYLSYDQPQRK-KKKVVKTT
	KEKG.SNSLK....KP............F.G.A.ETD.DD.YE.PT.SFESY.SYDQPQR.....VVKTT
Retrocopy	KEKGVSNSLK-ENSKPLTQTENHRVT--FQG<AETDMDDVYEPTTSFESYPSYDQPQRX<XXXVVKTT

Parental	TGVRAEKSHSKQNGSKADHKNSNNAIQKLPKMNESKAEKQHSGTSSAKLKKVSTDVTPTLPDIPLPTIQA
	.G.RAEKSH.KQNG.KADHKNSNN.IQKLPKM.ESKAEKQ.SG.SSAKLK.VS.DV.PTLPDIPLPTI.A
Retrocopy	SGIRAEKSHNKQNGFKADHKNSNNIIQKLPKMSESKAEKQLSGASSAKLKTVSIDVMPTLPDIPLPTI*A

Parental	NYRPLPSLELIPSFQPKRKAVSSPHEEEEAGFTGRRMNSKMQVYSGSKCAYLPKMMSLHQQCIRVLNNNI
	.Y.PLPSL.LIPSF.PKRK...SPHEEEEAGFTG.RMNSKMQVYS.SKCAYL.KMMS.HQQC..VLNN.I
Retrocopy	IYHPLPSLKLIPSF*PKRKE-PSPHEEEEAGFTGCRMNSKMQVYSDSKCAYLSKMMSMHQQCTGVLNNSI

Parental	DSIYEVGGVPYSVLEPVLERCTPEQLYRIEECNHVLTEETDQLWKIHCHRDFKRERPEEFESWREMYLRL
	DSIYEVGG.PYSVLEPVLERCTPEQ.Y.IEEC.HVL.EETDQL.KIHCHRDFKRERPEEF.SWRE..L.L
Retrocopy	DSIYEVGGIPYSVLEPVLERCTPEQPYGIEECSHVLHEETDQLRKIHCHRDFKRERPEEFGSWREVSLQL

Parental	QDAREQRLLLLTENIRSAHANKPKGRQAKMAFVNSVAKPP-RDVRRRQEKFGTGGAAVPEKIKIKPAPYT
	.DAREQ.LLLL.ENIRSAHANKPKGRQAKMAFVNSVAK.P..DVRR.QEK.GTGGAAVP.KIK.KP.PYT
Retrocopy	RDAREQGLLLLAENIRSAHANKPKGRQAKMAFVNSVAKSP<SDVRRQQEKCGTGGAAVPKKIKVKPTPYT

Parental	SSSGYTCSSSSSSYSNSAEEGQPYDGP
	SS..Y.CS...SS....A.EGQPY.GP
Retrocopy	SSNSYICSRGCSS----AKEGQPYNGP

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

RetrogeneDB ID:

retro_shar_665