RetrogeneDB - Retrocopy retro_rnor

						
>retro_rnor_2189
AAGAAAGACAAGGACAAATCAGATGACAGAATGGCACAGCCCAGTGGTCGGTCAGGGCACAGCACTCGAGGAACTGGGTT

TTCTTCATCTGGAGTTTTAATGGTTGGACCTAACTTTAGAGGTGGGAAAAAAAATTAGATGTGGCAATTTTAGAGAATTA

TGATTAGGGAAAAGTTCATATACAAATGAATATGTGGCAATTAAACTGGAGCCCATGAAATCCAGAGCACCAAAGCTGCA

TTTGGAATACACATTCTATAAGAGGTTAGCATCTGGAGGTGGTATACCTCAAGTTTACTGTTTTGGCCCTTGTGGTAAAT

ACAAACGGTATGGTGCTTGAACTGCTGGGACCTACTTTGGAAGATTTGTTTGACCTCTGTGATAGAACACTTTTTCTTAA

AACAGTTCTCTTGATAGCTATACAACCGATTTCTCGCATGAAGTATGCCCACTCAAAGACCTTGATATTCAGAGATATGA

AGCCTGAGAACTTCTTAATAGGACGGCCAGGAAACAAAGCCCAGCAACTCATTCATATCATAGATTTTGTTTTGGTAAAT

GAATATATTGATCCAGAGACAAAGAAACATATACCATACAGAGAACACAAATCCTTACTGGAACAGTCAGAACATGAGCA

TAAACACACATCTAGGAAAAGAACAGAGTAGAAGAGCTGATTTAGAAACTTTAAGCCATATGTTCGTGTACTTCTTGAGA

GGCGGTCTTCCTTGGCAAGGCTTAAAGGTGCATATGTCAAAAGAGAGATCAGAAAATTGGAAACACGAAATGAGCCACAA

CGTTAGAAGTGGTTTGTGAAAACTTGCCAGAAATGGCAACATATCTTTGTTACATAGGAACGCTAGATTTTTTTGAAAAG

CCAGACTATGATTACCTAAGAAAGCTTTTTACTGACTTGTTCGATTACAAAGGGTATATGTTTGATTATGAATGTGACTG

GATTGGTAAACAGTTGCCTACTCCTCTAGGTGCAGTTCAGCAGACCCCACTCTGTCATCGAACAGAAAAGCACACCAACA

CCGAATCAAGATACAGCAGTCTACAAACCAG

ORF - retro_rnor_2189 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	78.42 %
Parental protein coverage:	80.13 %
Number of stop codons detected:	2
Number of frameshifts detected	7

Retrocopy - Parental Gene Alignment:

									ParentalKKDKDKSDDRMARPSGRSGHSTRGTGSSSSGVLMVGPNFRVGKKI-GCGNFGELRLGKNLYTNEYVAIKL
		KKDKDKSDDRMA.PSGRSGHSTRGTG.SSSGVLMVGPNFR.G.....CGNF.EL.LGK..YTNEYVAIKL
RetrocopyKKDKDKSDDRMAQPSGRSGHSTRGTGFSSSGVLMVGPNFRGGXXX>RCGNFREL*LGKSSYTNEYVAIKL
ParentalEPMKSRAPQLHLEYRFYKQLGSGALSEDRYSWNTCLKY-NAMVLELLGPSLEDLFDLCDRTFSLKTVLMI
		EPMKSRAP.LHLEY.FYK.L.SG......Y....C.KY.N.MVLELLGP.LEDLFDLCDRT..LKTVL.I
RetrocopyEPMKSRAPKLHLEYTFYKRLASGGGIPQVYCFGPCGKY>NGMVLELLGPTLEDLFDLCDRTLFLKTVLLI
ParentalAIQLISRMEYVHSKNLIYRDVKPENFLIGRPGNKAQQVIHIIDFGLAKEYIDPETKKHIPYREHKSL-TG
		AIQ.ISRM.Y.HSK.LI.RD.KPENFLIGRPGNKAQQ.IHIIDF.L..EYIDPETKKHIPYREHKSL.TG
RetrocopyAIQPISRMKYAHSKTLIFRDMKPENFLIGRPGNKAQQLIHIIDFVLVNEYIDPETKKHIPYREHKSL<TG
ParentalTARY-MSINTHLGKEQSRRDDLEALGHMFMYFLRGSLPWQG-LKADTLK-ERYQKIGDTKRATPIEVLCE
		T.R..MSINTHLGKEQSRR.DLE.L.HMF.YFLRG.LPWQG.LK....K..R.QKIG.TK.AT..EV.CE
RetrocopyTVRT<MSINTHLGKEQSRRADLETLSHMFVYFLRGGLPWQG<LKGAYVK<KRDQKIGNTK*ATTLEVVCE
ParentalNFPEEMATYLRYVRRLDFFEKPDYDYLRKLFTDLFDRKGYMFDYEYDWIGKQLPTPVGAVQQ-DPALSSN
		N.PE.MATYL.Y...LDFFEKPDYDYLRKLFTDLFD.KGYMFDYE.DWIGKQLPTP.GAVQQ.DP.LSSN
RetrocopyNLPE-MATYLCYIGTLDFFEKPDYDYLRKLFTDLFDYKGYMFDYECDWIGKQLPTPLGAVQQ<DPTLSSN
ParentalREAHQHRDKIQQSKNQ
		R.AHQHR.KIQQS.NQ
RetrocopyRKAHQHRIKIQQSTNQ

							

							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	58 .09 RPM
SRP017611_kidney	0 .00 RPM	41 .52 RPM
SRP017611_liver	0 .00 RPM	18 .29 RPM

ChIP-Seq - click to see more details

Rattus norvegicus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_rnor_2189 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_2189 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_rnor_2189 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017550	1 retrocopy	retro_btau_1659,
Callithrix jacchus	ENSCJAG00000017348	2 retrocopies	retro_cjac_2695, retro_cjac_3279,
Macaca mulatta	ENSMMUG00000006646	1 retrocopy	retro_mmul_1040,
Mus musculus	ENSMUSG00000073563	1 retrocopy	retro_mmus_3454,
Otolemur garnettii	ENSOGAG00000011587	1 retrocopy	retro_ogar_246,
Rattus norvegicus	ENSRNOG00000016620	1 retrocopy	retro_rnor_2267,
Rattus norvegicus	ENSRNOG00000016677	1 retrocopy	retro_rnor_2189 ,

	RetrogeneDB ID:	retro_rnor_2189
Retrocopy location	Organism:	*Rat (Rattus norvegicus)*
	Coordinates:	5:167521111..167522182(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	Csnk1g3
	Ensembl ID:	ENSRNOG00000016677
	Aliases:	None
	Description:	Casein kinase I isoform gamma-3 [Source:UniProtKB/Swiss-Prot;Acc:Q62763]

Parental	KKDKDKSDDRMARPSGRSGHSTRGTGSSSSGVLMVGPNFRVGKKI-GCGNFGELRLGKNLYTNEYVAIKL
	KKDKDKSDDRMA.PSGRSGHSTRGTG.SSSGVLMVGPNFR.G.....CGNF.EL.LGK..YTNEYVAIKL
Retrocopy	KKDKDKSDDRMAQPSGRSGHSTRGTGFSSSGVLMVGPNFRGGXXX>RCGNFREL*LGKSSYTNEYVAIKL

Parental	EPMKSRAPQLHLEYRFYKQLGSGALSEDRYSWNTCLKY-NAMVLELLGPSLEDLFDLCDRTFSLKTVLMI
	EPMKSRAP.LHLEY.FYK.L.SG......Y....C.KY.N.MVLELLGP.LEDLFDLCDRT..LKTVL.I
Retrocopy	EPMKSRAPKLHLEYTFYKRLASGGGIPQVYCFGPCGKY>NGMVLELLGPTLEDLFDLCDRTLFLKTVLLI

Parental	AIQLISRMEYVHSKNLIYRDVKPENFLIGRPGNKAQQVIHIIDFGLAKEYIDPETKKHIPYREHKSL-TG
	AIQ.ISRM.Y.HSK.LI.RD.KPENFLIGRPGNKAQQ.IHIIDF.L..EYIDPETKKHIPYREHKSL.TG
Retrocopy	AIQPISRMKYAHSKTLIFRDMKPENFLIGRPGNKAQQLIHIIDFVLVNEYIDPETKKHIPYREHKSL<TG

Parental	TARY-MSINTHLGKEQSRRDDLEALGHMFMYFLRGSLPWQG-LKADTLK-ERYQKIGDTKRATPIEVLCE
	T.R..MSINTHLGKEQSRR.DLE.L.HMF.YFLRG.LPWQG.LK....K..R.QKIG.TK.AT..EV.CE
Retrocopy	TVRT<MSINTHLGKEQSRRADLETLSHMFVYFLRGGLPWQG<LKGAYVK<KRDQKIGNTK*ATTLEVVCE

Parental	NFPEEMATYLRYVRRLDFFEKPDYDYLRKLFTDLFDRKGYMFDYEYDWIGKQLPTPVGAVQQ-DPALSSN
	N.PE.MATYL.Y...LDFFEKPDYDYLRKLFTDLFD.KGYMFDYE.DWIGKQLPTP.GAVQQ.DP.LSSN
Retrocopy	NLPE-MATYLCYIGTLDFFEKPDYDYLRKLFTDLFDYKGYMFDYECDWIGKQLPTPLGAVQQ<DPTLSSN

Parental	REAHQHRDKIQQSKNQ
	R.AHQHR.KIQQS.NQ
Retrocopy	RKAHQHRIKIQQSTNQ

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

RetrogeneDB ID:

retro_rnor_2189