RetrogeneDB ID: retro_xtro_46

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL179807.1:653..1370(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: dlst
• Ensembl ID: ENSXETG00000013264
• Aliases: None
• Description: dihydrolipoamide S-succinyltransferase (E2 component of 2-oxo-glutarate complex) [Source:Jamboree;Acc:XB-GENE-1016310]

Sequence

>retro_xtro_46
GCCGCGCCAGACCTGGGTGGGCGCCCCGAGCAGCGCGTGCCCATGAGCCGCCTGCGCGCCCGCGTGGCCGAGCGCCTGCT
GCAGTCGCAATCCACCAACGCCATCCTGACCACGTTCAACGAAGTGAACATGGCCCCCGTGATGGAACTGCGCAAGAAGT
TCCAGGACGCCTTCACCAAGGAGCATGGCGTCAAGCTGGGCTTCATGTCCTTCTTCGTCAAGGCCGCCGTGCACGCGCTC
AAGAAGTACCCGGTGCTCAACGCCTCGGTGGACGGTAACGACATCGTCTACCACGGCTACTTCGACATCGGCATCGCCGT
AGGCTCGCCGCGCGGTCTGGTGGTGCCCATCCTGCGCAACGCCGACCAGATGGGCTTTGCCGACATCGAGAAGAAGATCG
CCGAGTTCGGCAAGAAGGCGGCCGAAGGCAAGCTGGGCATCGAGGAGATGAGCGGCGGCACCTTCTCCATCTCCAACGGC
GGCACCTTCGGCTCGATGATGTCCACCCCCATCATCAACCCGCCGCAGTCGGCCATCCTGGGCGTGCACGCCACCAAGGA
TCGCGCCGTGGTGGAGAACGGCCAGGTCGTGGTGCGCCCGATGAACTACCTGGCCATGAGCTACGACCACCGCATCATCG
ACGGCCGCGAAGCCGTGCTCGGCCTGGTCGCCATGAAGGACGCGCTGGAAGACCCGTCGCGCCTGCTGTTCGACCTG

Alignment

ORF - retro_xtro_46 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.43 %
• Parental protein coverage: 53.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ATQPASARSEHRVKMNRMRQRIAQRLKEAQNTCAMLTTFNEVDMSNIHQMRSMHKDSFLKKHGLKLGFMS
          A......R.E.RV.M.R.R.R.A.RL...Q.T.A.LTTFNEV.M......R....D.F.K.HG.KLGFMS
Retrocopy AAPDLGGRPEQRVPMSRLRARVAERLLQSQSTNAILTTFNEVNMAPVMELRKKFQDAFTKEHGVKLGFMS

Parental  AFVKASAFALQDQPAVNGVIDDTTKEIVYRDYIDISVAVSTPRGLVVPVLRNVESMNFADIERTIAELGE
          .FVKA...AL...P..N...D.....IVY..Y.DI..AV..PRGLVVP.LRN...M.FADIE..IAE.G.
Retrocopy FFVKAAVHALKKYPVLNASVDGN--DIVYHGYFDIGIAVGSPRGLVVPILRNADQMGFADIEKKIAEFGK

Parental  KARKNELAIEDMDGGTFTISNGGVFGSLFGTPIINPPQSAILGMHGIFDRPVAVSGKVEIRPMMYVALTY
          KA....L.IE.M.GGTF.ISNGG.FGS...TPIINPPQSAILG.H...DR.V...G.V..RPM.Y.A..Y
Retrocopy KAAEGKLGIEEMSGGTFSISNGGTFGSMMSTPIINPPQSAILGVHATKDRAVVENGQVVVRPMNYLAMSY

Parental  DHRLIDGREAVLFLRKIKSAVEDPRVLLLDL
          DHR.IDGREAVL.L...K.A.EDP..LL.DL
Retrocopy DHRIIDGREAVLGLVAMKDALEDPSRLLFDL

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.07 RPM	104.68 RPM
SRP007412_heart	0.00 RPM	302.56 RPM
SRP007412_kidney	0.00 RPM	302.56 RPM
SRP007412_liver	0.00 RPM	94.90 RPM
SRP007412_skeletal_muscle	0.00 RPM	364.58 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_46 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_46 was not experimentally validated.

Homology

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.

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000009316	1 retrocopy	retro_cpor_1089,
Homo sapiens	ENSG00000119689	1 retrocopy	retro_hsap_407,
Gorilla gorilla	ENSGGOG00000011591	1 retrocopy	retro_ggor_403,
Nomascus leucogenys	ENSNLEG00000016330	1 retrocopy	retro_nleu_1006,
Oryctolagus cuniculus	ENSOCUG00000015606	1 retrocopy	retro_ocun_322,
Pan troglodytes	ENSPTRG00000006543	1 retrocopy	retro_ptro_312,
Tursiops truncatus	ENSTTRG00000001915	1 retrocopy	retro_ttru_681,
Xenopus tropicalis	ENSXETG00000013264	1 retrocopy	retro_xtro_46 ,