RetrogeneDB ID: retro_xtro_17

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL172686.1:1761392..1761903(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: mrpl10
• Ensembl ID: ENSXETG00000014749
• Aliases: None
• Description: mitochondrial ribosomal protein L10 [Source:Jamboree;Acc:XB-GENE-947066]

Sequence

>retro_xtro_17
GTGGCCCCTCAGCCCAAACCCAGCGACATGGTTAAGGAGCACGCCTTGGAGCAGCTTCTGTGCAGCCAGTTGTGGACTAT
CCTACAGGAATGCACAATGGTGGCCATGTTTCAGCACAGTCAGTGGGGGTGGAAGACTTGGTACATTTGTGGCTCTAGCT
CCTAATACACTACATTCACATGAAGCATTTCCCTCTCCAGGTTGTGAGGAAAACCTTAGCCGATTCCCATCTAAGTTCTA
TGTTGCCTCTCTTTATGGGGCACACATTCCTAATAGTTAGCCCCCAACTGAAGGAAATGTTGCAGTGTGTCCAGAGCCTG
CCCCTGCCCCAAGTCCACCTTTTGAGTGCCTGCATTGAGAATAGACTCTCAGTCACCAGGTAGTGGTAAACTACCCGAGA
CTGCCAAGCTTAGAGGTTCTGCAGGGCTAGGTGCTGGCAGGACTGGCACTGATGGCATCACTGACCCCTTCCTTGTTCAA
ACAGCACTTAGTAAAGCTGGGCGCTATGTTG

Alignment

ORF - retro_xtro_17 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.14 %
• Parental protein coverage: 74.03 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VAPQPKPSEM--ENPLEQLLCSQLRTVLQDCKMVAVFQRS-AAGAEDLLHLRHRLLKHDIHMKHFPLQVV
          VAPQPKPS.M..E..LEQLLCSQL.T.LQ.C.MVA.FQ.S...G.EDL.HL...LL.H.IHMKHFPLQVV
Retrocopy VAPQPKPSDMVKEHALEQLLCSQLWTILQECTMVAMFQHS<SVGVEDLVHLWL*LLIHYIHMKHFPLQVV

Parental  RKTLADSHLSSMLPLFIGHTFLIVSHEVKVKEMLQCVRSLPQVQLLAPGACVENRL-LSRQGVVNYSRLP
          RKTLADSHLSSMLPLF.GHTFLIVS.....KEMLQCV.SLP..Q.....AC.ENRL.LS.Q.VVNY.RLP
Retrocopy RKTLADSHLSSMLPLFMGHTFLIVSPQ--LKEMLQCVQSLPLPQVHLLSACIENRL<LSHQVVVNYPRLP

Parental  SLEVLRGQVVAGLALMASLTPSLLTQHSVKLGALL
          SLEVL.G.V.AGLALMASLTPSL..QH.VKLGA.L
Retrocopy SLEVLQG*VLAGLALMASLTPSLFKQHLVKLGAML

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	16.82 RPM
SRP007412_heart	0.06 RPM	9.94 RPM
SRP007412_kidney	0.06 RPM	9.94 RPM
SRP007412_liver	0.00 RPM	6.71 RPM
SRP007412_skeletal_muscle	0.00 RPM	11.03 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_17 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_17 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000159111	1 retrocopy	retro_hsap_3234,
Nomascus leucogenys	ENSNLEG00000001803	1 retrocopy	retro_nleu_952,
Otolemur garnettii	ENSOGAG00000006173	1 retrocopy	retro_ogar_989,
Pongo abelii	ENSPPYG00000008881	1 retrocopy	retro_pabe_2680,
Pan troglodytes	ENSPTRG00000009337	1 retrocopy	retro_ptro_2186,
Xenopus tropicalis	ENSXETG00000014749	1 retrocopy	retro_xtro_17 ,