RetrogeneDB - Retrocopy retro_xtro

                        
>retro_xtro_55
ATTGAGGTGCTGAAGAAGACCCTGGCGCAGAAGGCGCAGGACTTCGACGGTATCGTCAAGATCGGCCGCACCCACCTGCA

GGACGCGACGCCGCTCACGCTGGGCCAGGAGATCTCGGGCTGGGTCGCGCAGCTTGAGCACGGCGCGCGGCACGTGAAGG

ATGCGCTGCCCCACCTGTACGAACTGGCGCTGGGTGGCACCGCCGTGGGCACGGGTCTGAACGCGCCCAAGGGCTATGCC

GAAGGCGTGGCCAAGGAACTGGCGGCCATGACTGGCCTGCCCTTCGTCACCTCGCCCAACAAGTTCGAATCGCTGGCCAC

CCAGGATGCGCTGGTGCACGCCCATGGCGCGCTCAAGACCCTGGCGGCCAGCCTGAACAAGATCGCCAATGACGTGCGTT

GGCTCGCCAGCGGCCCGCGCAGCGGCATCGGCGAGCTCAGCATTCCCGAGAACGAGCCTGGCTCGTCCATCATGCCCGGC

AAGGTCAATCCCACGCAGAGCGAGGCCGTCACCATGCTGGCCGCACAGGTCATGGGCAACGACGTGGCGATCAACATCGG

CGGCATGTCGGGCAACTTCGAATTGAACGTGTTCCGCCCCGTGGTGGCGCACAACTTCCTGCAGAGCGTGCGCCTGCTGG

CCGACGGCATCGTGAGCTTCAACAACCACTGTGCCGTGGGCATCGAACCCAACCGCGAGCGCATCGACCATCTTGTCCAG

CAGTCGCTGATGCTGGTGACGGCGCTCAACCCGCACATTGGCTACGACAAGGCCGCCTACATCGCCAAGAAGGGCCACAA

GGAGGGCACCAGCCTGCGCGCGGCGGCCATCGCCTCGGGCCACGTCACGGCTGAGCAGTTCGACCAGTGGGTGGTGCCAG

AGAAGATGGTTGGT

ORF - retro_xtro_55 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	59.0 %
Parental protein coverage:	58.74 %
Number of stop codons detected:	0
Number of frameshifts detected:	0

Retrocopy - Parental Gene Alignment:

                                ParentalLQKLHDALEEKSKEFENIIKIGRTHTQDAVPLTLGQEFGGYVQQIKYSVSRIKAALPRVYELAAGGTAVG
...L...L..K...F..I.KIGRTH.QDA.PLTLGQE..G.V.Q........K.ALP..YELA.GGTAVG
RetrocopyIEVLKKTLAQKAQDFDGIVKIGRTHLQDATPLTLGQEISGWVAQLEHGARHVKDALPHLYELALGGTAVG
ParentalTGLNTRIGFAEKVAAKVAELTGLPFITAPNKFESLAAHDALVELSGALNTLACSLMKIANDIRFLGSGPR
TGLN...G.AE.VA...A..TGLPF.T.PNKFESLA..DALV...GAL.TLA.SL.KIAND.R.L.SGPR
RetrocopyTGLNAPKGYAEGVAKELAAMTGLPFVTSPNKFESLATQDALVHAHGALKTLAASLNKIANDVRWLASGPR
ParentalSGLGELILPENEPGSSIMPAGKVNPTQCEAVTMVALRLMAHH-AYEIRTSGNAYPMLFLKNLQIKNVLQS
SG.GEL..PENEPGSSIMP.GKVNPTQ.EAVTM.A...M....A..I..................N.LQS
RetrocopySGIGELSIPENEPGSSIMP-GKVNPTQSEAVTMLAAQVMGNDVAINIGGMSGNFELNVFRPVVAHNFLQS
ParentalIRLLGDAAVSFTDNCIVGVQANTERINKLMSESLMLVTALNPHIAGYDKAAKIAKTAHKEGTTLKETAIK
.RLL.D..VSF...C.VG...N.ERI..L...SLMLVTALNPHI.GYDKAA.IAK..HKEGT.L...AI.
RetrocopyVRLLADGIVSFNNHCAVGIEPNRERIDHLVQQSLMLVTALNPHI-GYDKAAYIAKKGHKEGTSLRAAAIA
ParentalLGFLTSDQFDQWVKPEDMLG
.G..T..QFDQWV.PE.M.G
RetrocopySGHVTAEQFDQWVVPEKMVG

                            

                            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	0 .00 RPM	25 .76 RPM
SRP007412_heart	0 .00 RPM	128 .49 RPM
SRP007412_kidney	0 .00 RPM	128 .49 RPM
SRP007412_liver	0 .00 RPM	57 .47 RPM
SRP007412_skeletal_muscle	0 .00 RPM	116 .70 RPM

ChIP-Seq - click to see more details

Xenopus tropicalis was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_xtro_55 retrocopy.

TSS - click to see more details

Xenopus tropicalis was not studied using FANTOM5 data.

Lab - click to see more details

retro_xtro_55 was not experimentally validated.

Retrocopy orthology:

Xenopus tropicalis does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017359	1 retrocopy	retro_cjac_2339,
Echinops telfairi	ENSETEG00000018721	2 retrocopies	retro_etel_1069, retro_etel_1457,
Microcebus murinus	ENSMICG00000003451	2 retrocopies	retro_mmur_1215, retro_mmur_720,
Mus musculus	ENSMUSG00000026526	1 retrocopy	retro_mmus_3600,
Oryctolagus cuniculus	ENSOCUG00000021494	1 retrocopy	retro_ocun_50,
Otolemur garnettii	ENSOGAG00000009936	1 retrocopy	retro_ogar_322,
Rattus norvegicus	ENSRNOG00000003653	1 retrocopy	retro_rnor_2979,
Xenopus tropicalis	ENSXETG00000032112	1 retrocopy	retro_xtro_55 ,

	RetrogeneDB ID:	retro_xtro_55
Retrocopy location	Organism:	*Xenopus (Xenopus tropicalis)*
	Coordinates:	GL181302.1:9366..10260(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	FH
	Ensembl ID:	ENSXETG00000032112
	Aliases:	None
	Description:	fumarate hydratase [Source:HGNC Symbol;Acc:3700]

Parental	LQKLHDALEEKSKEFENIIKIGRTHTQDAVPLTLGQEFGGYVQQIKYSVSRIKAALPRVYELAAGGTAVG
	...L...L..K...F..I.KIGRTH.QDA.PLTLGQE..G.V.Q........K.ALP..YELA.GGTAVG
Retrocopy	IEVLKKTLAQKAQDFDGIVKIGRTHLQDATPLTLGQEISGWVAQLEHGARHVKDALPHLYELALGGTAVG

Parental	TGLNTRIGFAEKVAAKVAELTGLPFITAPNKFESLAAHDALVELSGALNTLACSLMKIANDIRFLGSGPR
	TGLN...G.AE.VA...A..TGLPF.T.PNKFESLA..DALV...GAL.TLA.SL.KIAND.R.L.SGPR
Retrocopy	TGLNAPKGYAEGVAKELAAMTGLPFVTSPNKFESLATQDALVHAHGALKTLAASLNKIANDVRWLASGPR

Parental	SGLGELILPENEPGSSIMPAGKVNPTQCEAVTMVALRLMAHH-AYEIRTSGNAYPMLFLKNLQIKNVLQS
	SG.GEL..PENEPGSSIMP.GKVNPTQ.EAVTM.A...M....A..I..................N.LQS
Retrocopy	SGIGELSIPENEPGSSIMP-GKVNPTQSEAVTMLAAQVMGNDVAINIGGMSGNFELNVFRPVVAHNFLQS

Parental	IRLLGDAAVSFTDNCIVGVQANTERINKLMSESLMLVTALNPHIAGYDKAAKIAKTAHKEGTTLKETAIK
	.RLL.D..VSF...C.VG...N.ERI..L...SLMLVTALNPHI.GYDKAA.IAK..HKEGT.L...AI.
Retrocopy	VRLLADGIVSFNNHCAVGIEPNRERIDHLVQQSLMLVTALNPHI-GYDKAAYIAKKGHKEGTSLRAAAIA

Parental	LGFLTSDQFDQWVKPEDMLG
	.G..T..QFDQWV.PE.M.G
Retrocopy	SGHVTAEQFDQWVVPEKMVG

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

RetrogeneDB ID:

retro_xtro_55