RetrogeneDB ID: retro_xtro_54

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL181088.1:2800..3550(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: etfb
• Ensembl ID: ENSXETG00000022222
• Aliases: None
• Description: electron-transfer-flavoprotein, beta polypeptide [Source:Jamboree;Acc:XB-GENE-956098]

Sequence

>retro_xtro_54
ATGAAGATGAAAGTTCTGATCTCCGTAAAACGCGTAGTGGACTACAACGTGAAGGTTCGCGTGAAATCGGACAGCACGGG
CGTAGACATCGCCAACGTCAAGATGAGCATGAACCCCTTCGACGAAATCGCCGTCGAGGAGGCCGTGCGCCTCAAAGAAA
AGGGTGTGGCCACCGAGGTCATCGCCGTGAGCTGTGGCGTGGCGCAATGCCAGGAGACGCTACGCACCGCCATGGCCATA
GGCGCCGACCGCGCGGTTCTTGTGGAAACCGACGCCGAACTACAGCCCCTGGCCGTGGCCAAACTCCTGAAGGCCCTGAT
GAACAAGGAACAGCCCGACCTCATCATCCTGGGCAAACAGGCCATCGACGACGACGCCAACCAGACCGGCCAGATGCTCG
CCGCGCTGGCCGATCTGCCGCAAGCCACGTTCGCTTCCAAGGTGGAACTGAGTGCCGACGCCGCGACCGTGACGCGCGAG
GTCGACGGCGGCCTGGAGACGCTGCAATTGACCCTGCCAGCCGTGATTACCACCGACCTGCGCCTGAACGAGCCGCGCTA
CGTCACGCTGCCCAACATCATGAAGGCCAAGAAGAAGACGCTGGATACCGTCAGGCCCGCCGATTTGGGCGTGGACGTGG
CTCCGCGCCTCAAGACCCTCAAGGTGAGCGAGCCCGCCAAGCGCGGCGCTGGCGTCAAGGTGCCCGATGTGGCCGCCCTG
GTTGAGAAACTCAAGAACGAAGCCAAGGTC

Alignment

ORF - retro_xtro_54 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.81 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALRALVGVKRVIDYAVKVRVKPDKTGVVTDGVKHSMNPFCEIAVEEAVRLKEKKIVSEIIAVSCGPQQC
          M....L..VKRV.DY.VKVRVK.D.TGV....VK.SMNPF.EIAVEEAVRLKEK....E.IAVSCG..QC
Retrocopy MKMKVLISVKRVVDYNVKVRVKSDSTGVDIANVKMSMNPFDEIAVEEAVRLKEKGVATEVIAVSCGVAQC

Parental  QETIRTALAMGADRGIHVEVAAKDAESLGPFQVSKIMAALAKKENVNLVLMGKQAIDDDCNQTGQMTAAL
          QET.RTA.A.GADR...VE....DAE.L.P..V.K...AL..KE...L...GKQAIDDD.NQTGQM.AAL
Retrocopy QETLRTAMAIGADRAVLVET---DAE-LQPLAVAKLLKALMNKEQPDLIILGKQAIDDDANQTGQMLAAL

Parental  LDWPQGTFASEVKVEGEKLTVVREVDGGLETISVKLPAVVTADLRLNEPRYATLPNIMKAKKKKIETVKP
          .D.PQ.TFAS.V.......TV.REVDGGLET....LPAV.T.DLRLNEPRY.TLPNIMKAKKK...TV.P
Retrocopy ADLPQATFASKVELSADAATVTREVDGGLETLQLTLPAVITTDLRLNEPRYVTLPNIMKAKKKTLDTVRP

Parental  SDLGVDITSRIRVLSVEDPPQRLAGVKVETVQDLVSKLKESGRI
          .DLGVD...R...L.V..P..R.AGVKV..V..LV.KLK.....
Retrocopy ADLGVDVAPRLKTLKVSEPAKRGAGVKVPDVAALVEKLKNEAKV

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	0.00 RPM	12.46 RPM
SRP007412_heart	0.00 RPM	87.03 RPM
SRP007412_kidney	0.00 RPM	87.03 RPM
SRP007412_liver	0.00 RPM	26.10 RPM
SRP007412_skeletal_muscle	0.00 RPM	50.86 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_54 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_54 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014360	1 retrocopy	retro_amel_1039,
Tursiops truncatus	ENSTTRG00000003974	1 retrocopy	retro_ttru_1158,
Xenopus tropicalis	ENSXETG00000022222	1 retrocopy	retro_xtro_54 ,