RetrogeneDB - Retrocopy retro_pabe

                        
>retro_pabe_703
TTTCGCCTTGAGGAAGATGCGGAAAAGGCTGTGATTGACTTGTATAACCGTTGGTTTAATGGACAGCCAATCCACGCCGA

GCTGTCGCCTGTGACCGACTTCAGAGAAGCCTGCTGCGGTCAGTATGAGATGGGAGAATGCACATGAGGCGGCTTCTGCA

ACTTCATGCATTTGAAGCCCATTTCCAGAGAGCTGTGGCGGGAGCTGTATGGGCGCCATCCCAAGAAGCATAGATCAAGA

TCCCAATCCCAGGAGCGTAGTTCTCGGTCTAGAGACCATGGC

ORF - retro_pabe_703 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	88.3 %
Parental protein coverage:	54.65 %
Number of stop codons detected:	1
Number of frameshifts detected:	0

Retrocopy - Parental Gene Alignment:

                                ParentalFRREEDAEKAVIDLNNRWFNGQPIHAELSPVTDFREACCRQYEMGECTRGGFCNFMHLKPISRELRRELY
FR.EEDAEKAVIDL.NRWFNGQPIHAELSPVTDFREACC.QYEMGECT.GGFCNFMHLKPISREL.RELY
RetrocopyFRLEEDAEKAVIDLYNRWFNGQPIHAELSPVTDFREACCGQYEMGECT*GGFCNFMHLKPISRELWRELY
ParentalGRRRKKHRSRSRSRERRSRSRDRG
GR..KKHRSRS.S.ER.SRSRD.G
RetrocopyGRHPKKHRSRSQSQERSSRSRDHG

                            

                            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	26 .26 RPM
SRP007412_cerebellum	0 .00 RPM	30 .28 RPM
SRP007412_heart	0 .00 RPM	13 .79 RPM
SRP007412_kidney	0 .00 RPM	30 .73 RPM
SRP007412_liver	0 .00 RPM	29 .26 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_703 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_703 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_pabe_703 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_790
Pan troglodytes	retro_ptro_549
Macaca mulatta	retro_mmul_1071

Parental genes homology:

Parental genes homology involve 8 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000015558	1 retrocopy	retro_ecab_1081,
Homo sapiens	ENSG00000160201	2 retrocopies	retro_hsap_1478, retro_hsap_790,
Loxodonta africana	ENSLAFG00000011460	1 retrocopy	retro_lafr_1135,
Macaca mulatta	ENSMMUG00000022769	2 retrocopies	retro_mmul_1071, retro_mmul_2126,
Mus musculus	ENSMUSG00000061613	3 retrocopies	retro_mmus_1602, retro_mmus_1787, retro_mmus_2955,
Nomascus leucogenys	ENSNLEG00000014737	1 retrocopy	retro_nleu_2382,
Otolemur garnettii	ENSOGAG00000016504	1 retrocopy	retro_ogar_241,
Pongo abelii	ENSPPYG00000011463	2 retrocopies	retro_pabe_1227, retro_pabe_703 ,

	RetrogeneDB ID:	retro_pabe_703
Retrocopy location	Organism:	*Orangutan (Pongo abelii)*
	Coordinates:	11:67608504..67608786(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	U2AF1
	Ensembl ID:	ENSPPYG00000011463
	Aliases:	None
	Description:	U2 small nuclear RNA auxiliary factor 1 [Source:HGNC Symbol;Acc:12453]

Parental	FRREEDAEKAVIDLNNRWFNGQPIHAELSPVTDFREACCRQYEMGECTRGGFCNFMHLKPISRELRRELY
	FR.EEDAEKAVIDL.NRWFNGQPIHAELSPVTDFREACC.QYEMGECT.GGFCNFMHLKPISREL.RELY
Retrocopy	FRLEEDAEKAVIDLYNRWFNGQPIHAELSPVTDFREACCGQYEMGECT*GGFCNFMHLKPISRELWRELY

Parental	GRRRKKHRSRSRSRERRSRSRDRG
	GR..KKHRSRS.S.ER.SRSRD.G
Retrocopy	GRHPKKHRSRSQSQERSSRSRDHG

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

RetrogeneDB ID:

retro_pabe_703