RetrogeneDB ID: retro_xtro_40

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL174848.1:18234..18642(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: c7orf10
• Ensembl ID: ENSXETG00000015599
• Aliases: None
• Description: chromosome 7 open reading frame 10 [Source:Jamboree;Acc:XB-GENE-5750708]

Sequence

>retro_xtro_40
CTGGCCGATCTGGGGGCCGAAGTCATCAAGGTGGAGCGGCCCGGCCTGGGCGACGAAACCCGGGGCTGGGGTCCGCCCTG
GATGCCGGCCGCTGCGGGCAGCCAACGGCACGATTCGGCCTATTTCGGCTCCGCCAACCGCGGCAAGAAATCGGTCACCA
TCGACTTCACCACCGCGCAGGGCCAGGCGCTACTCAGGGATCTGGTTCGGCAGTGCGACGTGCTGGTGGAGAACTACAAG
GCGGGCACCCTGGCACGCTACGGCCTGGGGTATGGTGACCTCAAGGCCATCCACCCCGGCCTCGTGTACTGCTCCGTCAC
CGGCTTCGGGCACACCGGCCCATACAGCCACAAGCCGGGCTACGACTTCGTGTTCCAGGCCATGAGCGGACTGATGAGCA
TCACCGGC

Alignment

ORF - retro_xtro_40 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.94 %
• Parental protein coverage: 59.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LADLGAEVIKVERPGSGDDTRS----WGPPFVGSE---SAYFLSVNRNKKSIAVNMKNPNGSKIIQELAK
          LADLGAEVIKVERPG.GD.TR.....W.P...GS....SAYF.S.NR.KKS.........G......L..
Retrocopy LADLGAEVIKVERPGLGDETRGWGPPWMPAAAGSQRHDSAYFGSANRGKKSVTIDFTTAQGQALLRDLVR

Parental  ACDVFVENYIPGKLSKMGLGFEEIKEIAPHIIYCSITGYGQTGPLFQRAGYDAVACAMSGLMYITG
          .CDV.VENY..G.L...GLG....K.I.P...YCS.TG.G.TGP.....GYD.V..AMSGLM.ITG
Retrocopy QCDVLVENYKAGTLARYGLGYGDLKAIHPGLVYCSVTGFGHTGPYSHKPGYDFVFQAMSGLMSITG

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	0.07 RPM
SRP007412_heart	0.00 RPM	0.57 RPM
SRP007412_kidney	0.00 RPM	0.57 RPM
SRP007412_liver	0.00 RPM	1.19 RPM
SRP007412_skeletal_muscle	0.00 RPM	1.29 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_40 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_40 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Xenopus tropicalis	ENSXETG00000015599	1 retrocopy	retro_xtro_40 ,