RetrogeneDB - Retrocopy retro_pabe

						
>retro_pabe_3021
ATAGAGAGCGCTCTCCCCGCTGCCAGCTTCCTGTACTGGGTAGGTGCAGGCACCGTGGCCTACCTAGCCCTGTGCATCTG

CTACTCGCTCTTCAGGGCCCTCTGGGTCTGGGGAGTGGGGAACGAATCGGAGGTCGGCCCAGGGCTCGGGGAATGGGCAC

ATCAGGTAGTACTGATGGAAATGGAAAATTGTCTGCAGAAGAGTTAGCAAAGCATGGAATGACGGTTGTCCTTATCAGCA

GATTACAGGATAAACTCGACCAGGTTTCCAGGGAAATAAAAGAAAAATTCAAAGTGGAGACAAGAACCATTGCTGTTGAC

TTTGCTTCAGAAGATATTTATGATAAAATTAAAACAGACTTGGCTGGTCTTGAAATCGGCGTGTTAGTGAACAACGTGGG

AATGTCATATGAGGATCCCAAATACTTTTTGGACATTCCTGACTTGGACAATATGATCAAGAAAATGATAAATATTAATA

TTCTTTCTGTTTGTAAGATGACACAATTGGTGCACCTGGCATGATGGAAAGATCTAAAGGGGCGAATCTGAACCTCTCAG

CTGGCAGAGGCATGTTCCCCGTCCCACTGTTGATGATCTGTTCTGCAACCAAGACTTTTGTTGATTTCTTCTCTCAGTGC

CTCCATGGGGAGTATAGGAGCAAGGGCATCTTTGTGCAGAGTGTCCTGCCATACTTTGTAGCTATAAAACTGGCTAAAAT

CCAAAAGCCAACTTTGGATAAGCCCTCTTCGGAGACATTTTGAAGTCTGCAATTAAAACAGTTGGCCTGCAATCCCAAAC

CAATGGATACCTGATCCATGCTCTTATGGGCTTGATAATCTCAATCCTGCCATCTTGGATTTATTTTAAAATAACCATGG

CTATGAAAAGTCTACACAGGATCGCTATTTGAAGAAAACCAAGAAGAAC

ORF - retro_pabe_3021 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	78.8 %
Parental protein coverage:	100. %
Number of stop codons detected:	0
Number of frameshifts detected	4

Retrocopy - Parental Gene Alignment:

									ParentalMESALPAAGFLYWVGAGTVAYLALRISYSLFTALRVW-GMGNEAGVGPGLGEWAVVTGSTDGIGKSYAEE
		.ESALPAA.FLYWVGAGTVAYLAL.I.YSLF.AL.VW.G.G...G.G..........GSTDG.GK..AEE
RetrocopyIESALPAASFLYWVGAGTVAYLALCICYSLFRALWVW<GSGERIG-GRPRARGMGTSGSTDGNGKLSAEE
ParentalLAKHGMKVVLISRSQDKLDQVSSEIKEKFKVETRTIAVDFASEDIYDKIKMGLSGLEIGILVNNVGMSYE
		LAKHGM.VVLISR.QDKLDQVS.EIKEKFKVETRTIAVDFASEDIYDKIK..L.GLEIG.LVNNVGMSYE
RetrocopyLAKHGMTVVLISRLQDKLDQVSREIKEKFKVETRTIAVDFASEDIYDKIKTDLAGLEIGVLVNNVGMSYE
ParentalYPEYFLDVPDLDNVIKKNDNINILSVCKMTQLV-LPGMVERSKGAILNISSGSGMLPVPLLTIYSATKTF
		.P.YFLD.PDLDN.IKK..NINILSVCKMTQLV..PGM.ERSKGA.LN.S.G.GM.PVPLL.I.SATKTF
RetrocopyDPKYFLDIPDLDNMIKKMININILSVCKMTQLV<APGMMERSKGANLNLSAGRGMFPVPLLMICSATKTF
ParentalVDFFSRCLHEEYRSKGVFVQSVLPYFVATKLAKIRKPTLDKPSPETF-VKSAIKTVGLQSRTNGYLIHAL
		VDFFS.CLH.EYRSKG.FVQSVLPYFVA.KLAKI.KPTLDKPS.ETF..KSAIKTVGLQS.TNGYLIHAL
RetrocopyVDFFSQCLHGEYRSKGIFVQSVLPYFVAIKLAKIQKPTLDKPSSETF<LKSAIKTVGLQSQTNGYLIHAL
ParentalMGSIISNLPSWIYFKIVMNM-NKSTRAHHLKKTKKN
		MG.IIS.LPSWIYFKI.M.M..KST....LKKTKKN
RetrocopyMGLIISILPSWIYFKITMAM<EKSTQDRYLKKTKKN

							

							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
SRP007412_brain_prefrontal_cortex	0 .83 RPM	11 .61 RPM
SRP007412_cerebellum	3 .04 RPM	8 .88 RPM
SRP007412_heart	0 .45 RPM	9 .00 RPM
SRP007412_kidney	0 .40 RPM	14 .25 RPM
SRP007412_liver	0 .58 RPM	17 .01 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_3021 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_3021 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_pabe_3021 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2491
Pan troglodytes	retro_ptro_2499

Parental genes homology:

Parental genes homology involve 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011325	1 retrocopy	retro_cjac_2489,
Dipodomys ordii	ENSDORG00000004834	1 retrocopy	retro_dord_561,
Homo sapiens	ENSG00000149084	1 retrocopy	retro_hsap_3684,
Gorilla gorilla	ENSGGOG00000002003	1 retrocopy	retro_ggor_2491,
Nomascus leucogenys	ENSNLEG00000017959	1 retrocopy	retro_nleu_2273,
Oryctolagus cuniculus	ENSOCUG00000016351	1 retrocopy	retro_ocun_1335,
Otolemur garnettii	ENSOGAG00000009102	1 retrocopy	retro_ogar_3391,
Pongo abelii	ENSPPYG00000003343	1 retrocopy	retro_pabe_3021 ,
Pan troglodytes	ENSPTRG00000003522	1 retrocopy	retro_ptro_2499,
Ictidomys tridecemlineatus	ENSSTOG00000005473	1 retrocopy	retro_itri_1099,
Tursiops truncatus	ENSTTRG00000005103	1 retrocopy	retro_ttru_772,

	RetrogeneDB ID:	retro_pabe_3021
Retrocopy location	Organism:	*Orangutan (Pongo abelii)*
	Coordinates:	6:160736492..160737421(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	HSD17B12
	Ensembl ID:	ENSPPYG00000003343
	Aliases:	None
	Description:	hydroxysteroid (17-beta) dehydrogenase 12 [Source:HGNC Symbol;Acc:18646]

Parental	MESALPAAGFLYWVGAGTVAYLALRISYSLFTALRVW-GMGNEAGVGPGLGEWAVVTGSTDGIGKSYAEE
	.ESALPAA.FLYWVGAGTVAYLAL.I.YSLF.AL.VW.G.G...G.G..........GSTDG.GK..AEE
Retrocopy	IESALPAASFLYWVGAGTVAYLALCICYSLFRALWVW<GSGERIG-GRPRARGMGTSGSTDGNGKLSAEE

Parental	LAKHGMKVVLISRSQDKLDQVSSEIKEKFKVETRTIAVDFASEDIYDKIKMGLSGLEIGILVNNVGMSYE
	LAKHGM.VVLISR.QDKLDQVS.EIKEKFKVETRTIAVDFASEDIYDKIK..L.GLEIG.LVNNVGMSYE
Retrocopy	LAKHGMTVVLISRLQDKLDQVSREIKEKFKVETRTIAVDFASEDIYDKIKTDLAGLEIGVLVNNVGMSYE

Parental	YPEYFLDVPDLDNVIKKNDNINILSVCKMTQLV-LPGMVERSKGAILNISSGSGMLPVPLLTIYSATKTF
	.P.YFLD.PDLDN.IKK..NINILSVCKMTQLV..PGM.ERSKGA.LN.S.G.GM.PVPLL.I.SATKTF
Retrocopy	DPKYFLDIPDLDNMIKKMININILSVCKMTQLV<APGMMERSKGANLNLSAGRGMFPVPLLMICSATKTF

Parental	VDFFSRCLHEEYRSKGVFVQSVLPYFVATKLAKIRKPTLDKPSPETF-VKSAIKTVGLQSRTNGYLIHAL
	VDFFS.CLH.EYRSKG.FVQSVLPYFVA.KLAKI.KPTLDKPS.ETF..KSAIKTVGLQS.TNGYLIHAL
Retrocopy	VDFFSQCLHGEYRSKGIFVQSVLPYFVAIKLAKIQKPTLDKPSSETF<LKSAIKTVGLQSQTNGYLIHAL

Parental	MGSIISNLPSWIYFKIVMNM-NKSTRAHHLKKTKKN
	MG.IIS.LPSWIYFKI.M.M..KST....LKKTKKN
Retrocopy	MGLIISILPSWIYFKITMAM<EKSTQDRYLKKTKKN

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

RetrogeneDB ID:

retro_pabe_3021