RetrogeneDB - Retrocopy retro_pabe

                        
>retro_pabe_2161
TCCAAGGCCAAGTATAAGGAGCAAAGGACAGTCTTGGCTGAGGACCAGCTAGCCCAGATGTCAAACCAGTTGGGCATGTT

CAAGATCAACCTGGAGGAATTTGCCAGCAAGCCCAAGCAGGAGATCCGGAAGGATCCTGAGTTCCATGTGTAGTTCCAGG

ACATGTGTACAACCTTTAGGGTGGAGCCTTTGGCCTCTGGAAAAGGATTTTGATCTGAGATGCTGGGTGTGGGGGATTTT

TATTACGAACTAGGTGTCCACATTATCAAAGTGTGCCTGGTGCTGAGCATTGGAGTGGAGGTCCGATAACCCTGGAGGAA

CTACATCAACAGGTGTTAAAAGGAAGGGGCAAGTTCGCCCAGGATGTCAGTCAAGACGACCTGATCAGGGCCATCAAGAA

ACTAAAGGCACTTGGCACTGGCTTCAGCATCATCCCCATGAGTGGCACTTACCTCATTCAGTCTGTTCCAGCTGAATTCA

ATATGGATTACACCAAGGGGCTGCAGCTGGCAGAGAAAAATGGCTATTGACTGTCAGAGAGATCAAAGCCAGTCTTAAAT

GGGAGACCCAATGAGCGGGGCAAGTGCCAGAACCCCTGCTGAGAGAAGGGCTGGCGTGGCTGGACTTACAGGCCCCAGGG

GAGATCCACTACTGGCTGCCAGCTCTATTCACTGACCTCTACTCCCAGGAGATTACAGCTGAGGCAGCCAGAGAAGTCTT

CCCCTAAGTGTGGAAGGGCACACAGCAGCAGGCAGGGAGAAGCAGGGAGGC

ORF - retro_pabe_2161 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	80.99 %
Parental protein coverage:	93.19 %
Number of stop codons detected:	3
Number of frameshifts detected:	3

Retrocopy - Parental Gene Alignment:

                                ParentalAEAKYKERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNPEFRVQFQDMCATIGVDPLASGKGF
..AKYKE..TVLAEDQLAQMS.QL.MFK.NLEEFASK.KQEIRK.PEF.V.FQDMC.T..V.PLASGKGF
RetrocopySKAKYKEQRTVLAEDQLAQMSNQLGMFKINLEEFASKPKQEIRKDPEFHV*FQDMCTTFRVEPLASGKGF
ParentalWSEMLGVGDFYYELGVQIIEVCLAL-KHRNGGLITLEELHQQVLKGRGKFAQDVSQDDLIRAIKKLKALG
.SEMLGVGDFYYELGV.II.VCL.L..H..GG.ITLEELHQQVLKGRGKFAQDVSQDDLIRAIKKLKALG
Retrocopy*SEMLGVGDFYYELGVHIIKVCLVL<EHWSGGPITLEELHQQVLKGRGKFAQDVSQDDLIRAIKKLKALG
ParentalTGFGIIPVGGTYLIQSVPAELNMDHTVVLQLAEKNGY-VTVSEIKASLNWETERARQVLEHLLKEGLAWL
TGF.IIP..GTYLIQSVPAE.NMD.T..LQLAEKNGY..TV.EIKASL.WET..A.QV.E.LL.EGLAWL
RetrocopyTGFSIIPMSGTYLIQSVPAEFNMDYTKGLQLAEKNGY<LTVREIKASLKWETQ*AGQVPEPLLREGLAWL
ParentalDLQAPGEAHYWLPALFTDLYSQEITAEEARE-SPPLTGVVEGHTAAGREGGGG
DLQAPGE.HYWLPALFTDLYSQEITAE.ARE.S.PL...VEGHTAAGRE..GG
RetrocopyDLQAPGEIHYWLPALFTDLYSQEITAEAARE<SLPLS--VEGHTAAGREKQGG

                            

                            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 .11 RPM	25 .21 RPM
SRP007412_cerebellum	0 .12 RPM	22 .25 RPM
SRP007412_heart	0 .00 RPM	16 .86 RPM
SRP007412_kidney	0 .03 RPM	42 .86 RPM
SRP007412_liver	0 .00 RPM	23 .93 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_2161 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_2161 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_pabe_2161 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2394
Gorilla gorilla	retro_ggor_1816

Parental genes homology:

Parental genes homology involve 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005062	1 retrocopy	retro_amel_164,
Canis familiaris	ENSCAFG00000016893	1 retrocopy	retro_cfam_1488,
Choloepus hoffmanni	ENSCHOG00000013760	1 retrocopy	retro_chof_1372,
Callithrix jacchus	ENSCJAG00000007322	2 retrocopies	retro_cjac_1175, retro_cjac_1922,
Echinops telfairi	ENSETEG00000000758	1 retrocopy	retro_etel_709,
Felis catus	ENSFCAG00000008944	2 retrocopies	retro_fcat_1291, retro_fcat_574,
Homo sapiens	ENSG00000159210	1 retrocopy	retro_hsap_2394,
Gorilla gorilla	ENSGGOG00000025290	1 retrocopy	retro_ggor_1816,
Macropus eugenii	ENSMEUG00000016638	1 retrocopy	retro_meug_663,
Mustela putorius furo	ENSMPUG00000015356	1 retrocopy	retro_mputfur_1425,
Mus musculus	ENSMUSG00000006058	1 retrocopy	retro_mmus_1050,
Nomascus leucogenys	ENSNLEG00000002743	1 retrocopy	retro_nleu_2520,
Oryctolagus cuniculus	ENSOCUG00000009156	2 retrocopies	retro_ocun_814, retro_ocun_996,
Pongo abelii	ENSPPYG00000008911	1 retrocopy	retro_pabe_2161 ,
Tarsius syrichta	ENSTSYG00000004576	1 retrocopy	retro_tsyr_843,

	RetrogeneDB ID:	retro_pabe_2161
Retrocopy location	Organism:	*Orangutan (Pongo abelii)*
	Coordinates:	2b:120563934..120564705(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	SNF8
	Ensembl ID:	ENSPPYG00000008911
	Aliases:	None
	Description:	SNF8, ESCRT-II complex subunit [Source:HGNC Symbol;Acc:17028]

Parental	AEAKYKERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNPEFRVQFQDMCATIGVDPLASGKGF
	..AKYKE..TVLAEDQLAQMS.QL.MFK.NLEEFASK.KQEIRK.PEF.V.FQDMC.T..V.PLASGKGF
Retrocopy	SKAKYKEQRTVLAEDQLAQMSNQLGMFKINLEEFASKPKQEIRKDPEFHV*FQDMCTTFRVEPLASGKGF

Parental	WSEMLGVGDFYYELGVQIIEVCLAL-KHRNGGLITLEELHQQVLKGRGKFAQDVSQDDLIRAIKKLKALG
	.SEMLGVGDFYYELGV.II.VCL.L..H..GG.ITLEELHQQVLKGRGKFAQDVSQDDLIRAIKKLKALG
Retrocopy	*SEMLGVGDFYYELGVHIIKVCLVL<EHWSGGPITLEELHQQVLKGRGKFAQDVSQDDLIRAIKKLKALG

Parental	TGFGIIPVGGTYLIQSVPAELNMDHTVVLQLAEKNGY-VTVSEIKASLNWETERARQVLEHLLKEGLAWL
	TGF.IIP..GTYLIQSVPAE.NMD.T..LQLAEKNGY..TV.EIKASL.WET..A.QV.E.LL.EGLAWL
Retrocopy	TGFSIIPMSGTYLIQSVPAEFNMDYTKGLQLAEKNGY<LTVREIKASLKWETQ*AGQVPEPLLREGLAWL

Parental	DLQAPGEAHYWLPALFTDLYSQEITAEEARE-SPPLTGVVEGHTAAGREGGGG
	DLQAPGE.HYWLPALFTDLYSQEITAE.ARE.S.PL...VEGHTAAGRE..GG
Retrocopy	DLQAPGEIHYWLPALFTDLYSQEITAEAARE<SLPLS--VEGHTAAGREKQGG

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

RetrogeneDB ID:

retro_pabe_2161