RetrogeneDB ID: retro_xtro_16

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL181063.1:7371..8340(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSXETG00000008436
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: taldo1
• Ensembl ID: ENSXETG00000001671
• Aliases: None
• Description: transaldolase 1 [Source:Jamboree;Acc:XB-GENE-1005380]

Sequence

>retro_xtro_16
ATGTTGTCCGGTGCGTTGCGGAATAATGGCAGCATGAACCAACTCGACACCCTCAAACTGTTCACCACCGTGGTGGCCGA
TACCGGCGACTTCAAGCAGCTGGCGCAGTTCCAGCCCCGCGACGCCACTACCAATCCCTCGCTCATCCTCAAGGCCGTGC
AAAAGCCCGAGTACGCGCCGCTCTTGCGGGAGACCGTGGCGCACTGGGGGGGCAAGCCGATGGACGAGATTGTGGATCAC
CTGCTGGTGCGTTTCGGGCGCGAGATTCTGGCCACCATTCCGGGCCGCGTCTCTACCGAGGTGGACGCGCGCCTGAGCTT
CGACACCAGCGCCACCGTGGCGCGTGCCGAGCGCATCATTGAGTTGTACCAGGCCGAGGGCATCCACATCGACCGCGTGC
TTATCAAGATTGCAGCCACCTGGGAGGGCATTCAGGCGGCCGCGCAACTGGAGCGCGAGGGTATCCATACCAACCTGACG
CTGCTGTTCTCCTTCGCCCAGGCCGTGGCCTGCGGCCAGGCCCGGGTGCAGCTGATTTCGCCCTTCGTGGGCCGTATCTA
CGACTGGTACAAAAAGCAAGCTGGCAGCGCCTGGGACGAGGCCGCCAACGCCGGTGCCAACGACCCTGGCGTGCGCTCGG
TGACGCAGATCTACCACCACTACAAGCACTTCGACATCGCCACCGAGGTGATGGGTGCGAGCTTCCGCAACCTGGGCCAG
ATTACTGCGCTGGCTGGCTGCGACCTGCTGACCATCGCCCCCGAGCTGCTGGCGCAACTGGCCGCCAGCGATGCGCCCCT
GCAACGCGCCTTGGACGCCGAGACGGCGAAGTCCCTGAACCTGCCCGCCGTGCAGTACGACGAGGCGGGCTTCCGCTACG
CGCTCAACGAGGACGCCATGGCCACCGAAAAACTGGCTGAGGGCATCCGCGCGTTTGCGGCCGATGCGGTGAAGCTGGAA
AAAATCATT

Alignment

ORF - retro_xtro_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.02 %
• Parental protein coverage: 53.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LDQLKQHTVVVADTGDFNAIEVYKPQDATTNPSLILAAAQMPDYQGLVKDAIQYGRNLGGSEEEQINNIM
          LD.LK..T.VVADTGDF.......P.DATTNPSLIL.A.Q.P.Y..L...........GG.....I....
Retrocopy LDTLKLFTTVVADTGDFKQLAQFQPRDATTNPSLILKAVQKPEYAPLLRETVAH---WGGKPMDEI---V

Parental  DKLFVLFGVEILKKIPGRVSTEVDARLSFDKDGMVKRAKRLIALYKEAGIDKERILIKLSSTWEGIQAGK
          D.L.V.FG.EIL..IPGRVSTEVDARLSFD....V.RA.R.I.LY...GI...R.LIK...TWEGIQA..
Retrocopy DHLLVRFGREILATIPGRVSTEVDARLSFDTSATVARAERIIELYQAEGIHIDRVLIKIAATWEGIQAAA

Parental  ILEEEYGIHCNMTLLFSFAQAVACAEAGVTLISPFVGRILDWH
          .LE.E.GIH.N.TLLFSFAQAVAC..A.V.LISPFVGRI.DW.
Retrocopy QLERE-GIHTNLTLLFSFAQAVACGQARVQLISPFVGRIYDWY

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	48.74 RPM
SRP007412_heart	0.00 RPM	82.35 RPM
SRP007412_kidney	0.00 RPM	82.35 RPM
SRP007412_liver	0.00 RPM	214.55 RPM
SRP007412_skeletal_muscle	0.00 RPM	5.42 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_16 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_16 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010336	1 retrocopy	retro_btau_455,
Macropus eugenii	ENSMEUG00000000841	1 retrocopy	retro_meug_756,
Mus musculus	ENSMUSG00000025503	2 retrocopies	retro_mmus_645, retro_mmus_667,
Rattus norvegicus	ENSRNOG00000018367	1 retrocopy	retro_rnor_2661,
Xenopus tropicalis	ENSXETG00000001671	1 retrocopy	retro_xtro_16 ,