RetrogeneDB - Retrocopy retro_pabe

                        
>retro_pabe_3149
TCCTCATGCCGCAGAACCTGCAGTGTAATGACACTAGTTAAGTCCAGGCCTTTTTGGGAAAAGCAAGAGAAGATACTGCT

GAAAGGTCGCAGGCTCATTGCAGACGATCTCAAGGCTGGAGCTGTGCTGAAAGGTTTCTTCTCTAGCCATCTATAATACA

TAAAGAAGCTGCTCATCGATAAGCTGAAGGGTGTCAGCCTCATTAAGATGAAATTCGAGGACATCAAGGATTGGTCCAAC

CTAGTAATGCCACGAGAATAATGGGGATTTTTGCCAAACTTGACCATGTTACATGACATATCCAAAGACTCAGCTTTAGC

AGTCACTGCCTTTATTATGGATTTGTGACAATCTCTGTGACCCTGGGAACCTGGGGACAATTCTGAGATCTCCAGCTGGG

GCAGGCTGCAGCAAAGTGTTACTCACTTTGAAAGGCTGTGTGGATGCTTGGGAGCCCAAAGTGCTACAGGCAGGTATGGG

TGCACATTTCCAGGTGCCCATTATCAATAATCTGAAAACAAAACAGTGCCAAATTACCTGCCCCCTGACACCAAGGTCTG

TGTGGCTGACAACTGAAGCCTTTATGCTCAGGCTCAGATGTCTAATAAAGCCAGTGACTATGGCTGGGTGTATGATTGGC

GATCCCTGAAGTTTCACAAGTATGAAGAAAAGGAAGGTCTAGAAACTGGAGCCAGTAAAGGTTTGCTGCCTGTTATTGAG

GTTCAGAGTTATGACTTGGACTGGACAGAGGCACCAGCAGCTGTAGTGGTTGGCGGCAAGACCTACGGCATGAGCCTGGA

ATCTCTGTAGTTGGCCGAGAGCCCTGCGGACAAGAGGCTGCTGATCCCTGTTGCACCTGGAGTGGACAGCCCCGACTTGG

CCACGGCTGCACACATCCTGCTTTTTGAAGGGAAAAGACAACTGCGGGTGAGGGCAGAACACTTGAGCGGGGACAGGAGT

TACCAC

ORF - retro_pabe_3149 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	76.69 %
Parental protein coverage:	76.67 %
Number of stop codons detected:	4
Number of frameshifts detected:	3

Retrocopy - Parental Gene Alignment:

                                ParentalSGDRRLSSVMTIVKSRPFREKQGKILLEGRRLIADALKAGAVPKMFFFSRLEYLKELPVDKLKGVSLIKV
S..RR..SVMT.VKSRPF.EKQ.KILL.GRRLIAD.LKAGAV.K.FF.S.L.Y.K.L..DKLKGVSLIK.
RetrocopySSCRRTCSVMTLVKSRPFWEKQEKILLKGRRLIADDLKAGAVLKGFFSSHL*YIKKLLIDKLKGVSLIKM
ParentalKFEDIKDWSDLVTPQG-IMGXXXXXDHVK-MTYPKTQLQHSLPLLLICDNLRDPGNLGTILRSAAGAGCS
KFEDIKDWS.LV.P...IMG.....DHV..MTYPKTQL..SLPLL.ICDNL.DPGNLGTILRS.AGAGCS
RetrocopyKFEDIKDWSNLVMPRE<IMGIFAKLDHVT<MTYPKTQL*QSLPLLWICDNLCDPGNLGTILRSPAGAGCS
ParentalKVLLT-KGCVDAWEPKVLRAGMGAHFQVPIINNL-EWETVPNYLPPDTRVYVADNCGLYAQAEMSNKASD
KVLLT.KGCVDAWEPKVL.AGMGAHFQVPIINNL.E..TVPNYLPPDT.V.VADN..LYAQA.MSNKASD
RetrocopyKVLLTLKGCVDAWEPKVLQAGMGAHFQVPIINNL<ENKTVPNYLPPDTKVCVADN*SLYAQAQMSNKASD
ParentalHGWVCDQRVLKFHKYEEEEDVETGASQDWLPDVEVQSYDSDWTEAPAAVVIGGETYGVSLESLQLAESTG
.GWV.D.R.LKFHKYEE.E..ETGAS...LP..EVQSYD.DWTEAPAAVV.GG.TYG.SLESL.LAES..
RetrocopyYGWVYDWRSLKFHKYEEKEGLETGASKGLLPVIEVQSYDLDWTEAPAAVVVGGKTYGMSLESL*LAESPA
ParentalGKRLLIPVVPGVDSLNSAMAASILLFEGKRQLRGKAEDLSRDRSYH
.KRLLIPV.PGVDS...A.AA.ILLFEGKRQLR..AE.LS.DRSYH
RetrocopyDKRLLIPVAPGVDSPDLATAAHILLFEGKRQLRVRAEHLSGDRSYH

                            

                            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 .00 RPM	13 .60 RPM
SRP007412_cerebellum	0 .00 RPM	8 .03 RPM
SRP007412_heart	0 .00 RPM	7 .22 RPM
SRP007412_kidney	0 .07 RPM	9 .25 RPM
SRP007412_liver	0 .03 RPM	7 .41 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_3149 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_3149 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_pabe_3149 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3704
Gorilla gorilla	retro_ggor_2505
Macaca mulatta	retro_mmul_1709
Callithrix jacchus	retro_cjac_3130

Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021701	1 retrocopy	retro_cjac_3130,
Homo sapiens	ENSG00000171861	1 retrocopy	retro_hsap_3704,
Gorilla gorilla	ENSGGOG00000015518	1 retrocopy	retro_ggor_2505,
Macaca mulatta	ENSMMUG00000011423	1 retrocopy	retro_mmul_1709,
Nomascus leucogenys	ENSNLEG00000000570	1 retrocopy	retro_nleu_180,
Pongo abelii	ENSPPYG00000007762	1 retrocopy	retro_pabe_3149 ,

	RetrogeneDB ID:	retro_pabe_3149
Retrocopy location	Organism:	*Orangutan (Pongo abelii)*
	Coordinates:	7:66673209..66674175(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	RNMTL1
	Ensembl ID:	ENSPPYG00000007762
	Aliases:	None
	Description:	RNA methyltransferase like 1 [Source:HGNC Symbol;Acc:18485]

Parental	SGDRRLSSVMTIVKSRPFREKQGKILLEGRRLIADALKAGAVPKMFFFSRLEYLKELPVDKLKGVSLIKV
	S..RR..SVMT.VKSRPF.EKQ.KILL.GRRLIAD.LKAGAV.K.FF.S.L.Y.K.L..DKLKGVSLIK.
Retrocopy	SSCRRTCSVMTLVKSRPFWEKQEKILLKGRRLIADDLKAGAVLKGFFSSHL*YIKKLLIDKLKGVSLIKM

Parental	KFEDIKDWSDLVTPQG-IMGXXXXXDHVK-MTYPKTQLQHSLPLLLICDNLRDPGNLGTILRSAAGAGCS
	KFEDIKDWS.LV.P...IMG.....DHV..MTYPKTQL..SLPLL.ICDNL.DPGNLGTILRS.AGAGCS
Retrocopy	KFEDIKDWSNLVMPRE<IMGIFAKLDHVT<MTYPKTQL*QSLPLLWICDNLCDPGNLGTILRSPAGAGCS

Parental	KVLLT-KGCVDAWEPKVLRAGMGAHFQVPIINNL-EWETVPNYLPPDTRVYVADNCGLYAQAEMSNKASD
	KVLLT.KGCVDAWEPKVL.AGMGAHFQVPIINNL.E..TVPNYLPPDT.V.VADN..LYAQA.MSNKASD
Retrocopy	KVLLTLKGCVDAWEPKVLQAGMGAHFQVPIINNL<ENKTVPNYLPPDTKVCVADN*SLYAQAQMSNKASD

Parental	HGWVCDQRVLKFHKYEEEEDVETGASQDWLPDVEVQSYDSDWTEAPAAVVIGGETYGVSLESLQLAESTG
	.GWV.D.R.LKFHKYEE.E..ETGAS...LP..EVQSYD.DWTEAPAAVV.GG.TYG.SLESL.LAES..
Retrocopy	YGWVYDWRSLKFHKYEEKEGLETGASKGLLPVIEVQSYDLDWTEAPAAVVVGGKTYGMSLESL*LAESPA

Parental	GKRLLIPVVPGVDSLNSAMAASILLFEGKRQLRGKAEDLSRDRSYH
	.KRLLIPV.PGVDS...A.AA.ILLFEGKRQLR..AE.LS.DRSYH
Retrocopy	DKRLLIPVAPGVDSPDLATAAHILLFEGKRQLRVRAEHLSGDRSYH

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

RetrogeneDB ID:

retro_pabe_3149