RetrogeneDB ID: retro_xtro_34

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL174257.1:34190..34931(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: enosf1
• Ensembl ID: ENSXETG00000003158
• Aliases: None
• Description: enolase superfamily member 1 [Source:Jamboree;Acc:XB-GENE-940740]

Sequence

>retro_xtro_34
ACCATTACCGCGATTCGCGTCGAAGATATCCGCTTTCCTACGTCCCAGTCCCTGGACGGTTCCGACGCCATGAACCCGGA
CCCGGACTACTCGGCCGCCTATGTGATTTTGCAGACCGACAACCCGGCCCTTGAAGGCCATGGCCTGACCTTCACCATCG
GCCGTGGCAACGAGATTTGCTGTGCGGCGATCCAGGCCATGCAGCCGCTGTTGATAGGCTTGACCCTGGAATGGATCGCC
GAAGACATGGGCCGTTTCTGGCGGCATATCACCAGCGACAGCCAGTTGCGCTGGATTGGCCCGGACAAGGGCGCCATTCA
CCTGGCCACCGGCGCGATCGTCAACGCCGCGTGGGATTTGTGGGCCAAGGCCGAAGGAAAACCCTTGTGGCGCCTGGTGG
CCGACATGAGTCCGGAACAGTTGGTGCGGTGCATCGACTTCCGCTACATCACCGACTGCATCACCTCCAGCGAAGCCCTG
GCCTTGCTGCGCCAACGCGCCGAAGGCAAGGCTGAACGCATGGCCGACCTGCAAGCCAATGGCTACCCCTGCTACACCAC
CTCGGCCGGCTGGCTCGGTTATGGCGACGAAAAGCTGCGCAGGCTGTGCCAGGAAGCGGTGGATGCAGGCTTCAACCACG
TCAAGCTCAAGGTCGGCCATGACTTGCAGGACGACCTGCGCCGCGTGCGCATCGCCCGCGAAGTGCTGGGGCCGGACCGC
CAACTGATGATCGACGCCAAC

Alignment

ORF - retro_xtro_34 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.03 %
• Parental protein coverage: 55.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TITSLHVTDVRFPTSLDQHGSDAMHTDPDYSAAYIVIETDAADGLKGHGLTFTLGKGTEIVVCAVRALSR
          TIT...V.D.RFPTS....GSDAM..DPDYSAAY....TD....L.GHGLTFT.G.G.EI...A..A...
Retrocopy TITAIRVEDIRFPTSQSLDGSDAMNPDPDYSAAYVILQTDNP-ALEGHGLTFTIGRGNEICCAAIQAMQP

Parental  HVIGKALGDIVNNFRDFYRQLTSDGQLRWIGPEKGAVQLATAAVLNAVWDLWAKKEKKPLWKLLVDMDPH
          ..IG..L..I......F.R..TSD.QLRWIGP.KGA..LAT.A..NA.WDLWAK.E.KPLW.L..DM.P.
Retrocopy LLIGLTLEWIAEDMGRFWRHITSDSQLRWIGPDKGAIHLATGAIVNAAWDLWAKAEGKPLWRLVADMSPE

Parental  QLVSCIDFRYITDALTEEEALEILQNGKQGQRDREEHMLRSGYPAYTTSCAWLGYSDEQLKKLCSDALKE
          QLV.CIDFRYITD..T..EAL..L.....G...R.......GYP.YTTS..WLGY.DE.L..LC..A...
Retrocopy QLVRCIDFRYITDCITSSEALALLRQRAEGKAERMADLQANGYPCYTTSAGWLGYGDEKLRRLCQEAVDA

Parental  GWTRFKVKVGADLKDDIRRCELIRGMIGPDNIMMLDAN
          G....K.KVG.DL.DD.RR....R...GPD...M.DAN
Retrocopy GFNHVKLKVGHDLQDDLRRVRIAREVLGPDRQLMIDAN

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	2.98 RPM
SRP007412_heart	0.00 RPM	9.56 RPM
SRP007412_kidney	0.00 RPM	9.56 RPM
SRP007412_liver	0.00 RPM	16.07 RPM
SRP007412_skeletal_muscle	0.00 RPM	4.07 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_34 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_34 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Xenopus tropicalis	ENSXETG00000003158	3 retrocopies	retro_xtro_34 , retro_xtro_36, retro_xtro_44,