RetrogeneDB ID: retro_xtro_29

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL173212.1:244753..245230(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSXETG00000031345
• Aliases: None
• Description: None

Sequence

>retro_xtro_29
GTTATATCTAATATTCTGGCCAAACAAAGGAAGTTGACTTACAATATCAGTATCCAGGAGAAACAGGCTATACGGGCTTT
GAAAAGCAACAAAGACTTGATAAAAAAACCAACTGATAAAGGGGGTGCCGTGGTAATAATGGACACTACCAATTACATAA
AAGAAGCCAATAGACATGTGGTTGTCTAACACCACATATTATGAAAGGCTGGAAGAGGATCCAACTCATAAATATACAAA
GAAACTTAAACAGGTCATCAGTAGCTTCTCCCCCCACAGACACACTTAATGGATTTGATGCCAGTTAACCCCAGAATTGG
TACTTTTTACATGTTACCCAAAATACATAAGGAAGGCAACCCAGGACGACCCATCATCTCTGGTATTGGAACATTAACCG
AGGGCATATCTGGCTGGGTAGAAGACATTCTGAAGCCAACTGTCAAGAGAACACCCAGTTTCATACAGGACACCACT

Alignment

ORF - retro_xtro_29 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.05 %
• Parental protein coverage: 94.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LLSEKTKKKKKIKTTKISIQEKNAIWALKNNKDLIIKPADKGGSVVIMDTTDYIKEANRQL-SNTTYY-R
          ..S....K..K..T..ISIQEK.AI.ALK.NKDLI.KP.DKGG.VVIMDTT.YIKEANR......T.Y..
Retrocopy VISNILAKQRKL-TYNISIQEKQAIRALKSNKDLIKKPTDKGGAVVIMDTTNYIKEANRHV>LSNTTYYE

Parental  RLEVDP--KHTKELKQVISGLSPQ-QTHLMDLMPVNPRIGTFYMLPKIHKEGNPGRPIISGIGTLTKGIS
          RLE.DP..K.TK.LKQVIS..SP..QTHLMDLMPVNPRIGTFYMLPKIHKEGNPGRPIISGIGTLT.GIS
Retrocopy RLEEDPTHKYTKKLKQVISSFSPH<QTHLMDLMPVNPRIGTFYMLPKIHKEGNPGRPIISGIGTLTEGIS

Parental  GACQYFLEKCHMPTMPTVQTTS
          G.....L......T....Q.T.
Retrocopy GWVEDILKPTVKRTPSFIQDTT

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	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.37 RPM	0.00 RPM
SRP007412_skeletal_muscle	0.06 RPM	0.00 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_29 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_29 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Xenopus tropicalis	ENSXETG00000031345	1 retrocopy	retro_xtro_29 ,
Xenopus tropicalis	ENSXETG00000032448	1 retrocopy	retro_xtro_19,