RetrogeneDB ID: retro_xtro_69

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL187592.1:2183..2942(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: nubpl
• Ensembl ID: ENSXETG00000014129
• Aliases: None
• Description: nucleotide binding protein-like [Source:Jamboree;Acc:XB-GENE-971259]

Sequence

>retro_xtro_69
CCGTTGCCGGGGGTGAAAAACATCATCGCCGTGGCCTCGGGCAAGGGCGGTGTGGGCAAGAGCACCACGGCTGTCAATCT
GGCCCTGGCGCTGGTGGCCGAGGGCGCGCGCGTGGGCCTGCTGGATGCCGATATCTACGGCCCCAGCCAGCCCATGATGA
CCGGCACTTCGGGCGAATTGGAAAGCCTGGATGGCAAGCTGATGGAGCCCAAGCGCGCCATGGGGCTGCAAATCAATTCC
ATCGGCTTCCTCGTCAAGGACGAACAGGCCATGATCTGGCGCGGCCCCATGGCCAGTCAGGCGCTGGAGCAACTCGTTAC
GCAGACGCGCTGGGACGATCTGGACTACCTGCTGGTGGATATGCCCCCCGGCACCGGCGACATCCAGCTCACCATGGCGC
AGAAGGTGCCGCTGACTGGCGCGATCATCGTCACTACGCCGCAGGATATTGCGCTGCTCGACGCCAGGAAGGGCATCACC
ATGTTCCAGAAGGTGAACGTGCCCATCCTCGGCATCGTCGAGAACATGGCTGTGCACGTGTGCAGCCACTGCGGCCATGT
GGAGCACATTTTCGGCCAGGACGGTGGCAAGAAGATGGCGCAAAGCCAGGGCATGGACTACCTGGGCGCGCTGCCGCTGC
GCCTGTCGATCCGCGAGCAGGCCGACAGTGGCTGCCCCACCGTGGCCGCCGAGCCCGACGGCGACGTGGCGCGCATCTAC
AAAACCATCGCCCGCGCGGTGGCGGTGAAGATCGCGCAG

Alignment

ORF - retro_xtro_69 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.76 %
• Parental protein coverage: 79.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PIPGVKHVVVVASGKGGVGKSTTAVNLALGIAASDQVKAVGLLDADVYGPSIPRMMNLKGNPEVSNKNLM
          P.PGVK....VASGKGGVGKSTTAVNLAL...A......VGLLDAD.YGPS.P.M....G..E.....LM
Retrocopy PLPGVKNIIAVASGKGGVGKSTTAVNLALALVAEGA--RVGLLDADIYGPSQPMMTGTSGELESLDGKLM

Parental  IPLFNYGIRCMSMGFLVEETAPIVWRGLMVMSAIEKLLRQVEWGELDYLVIDMPPGTGDVQLSISQNIPI
          .P....G....S.GFLV.......WRG.M...A.E.L..Q..W..LDYL..DMPPGTGD.QL...Q..P.
Retrocopy EPKRAMGLQINSIGFLVKDEQAMIWRGPMASQALEQLVTQTRWDDLDYLLVDMPPGTGDIQLTMAQKVPL

Parental  SGAVIVSTPQDIALVDARRGAEMFQKVNVPVLGFVQNMSIFQCPKCNHETHIFGEEGARRLAESLGFDIL
          .GA.IV.TPQDIAL.DAR.G..MFQKVNVP.LG.V.NM....C..C.H..HIFG..G....A.S.G.D.L
Retrocopy TGAIIVTTPQDIALLDARKGITMFQKVNVPILGIVENMAVHVCSHCGHVEHIFGQDGGKKMAQSQGMDYL

Parental  GDIPLHINIRETSDQGRPVVVSDPQSSEAKAYLKIASEVLRRISK
          G..PL...IRE..D.G.P.V...P....A..Y..IA..V...I..
Retrocopy GALPLRLSIREQADSGCPTVAAEPDGDVARIYKTIARAVAVKIAQ

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	15.85 RPM
SRP007412_heart	0.00 RPM	10.89 RPM
SRP007412_kidney	0.00 RPM	10.89 RPM
SRP007412_liver	0.00 RPM	9.12 RPM
SRP007412_skeletal_muscle	0.00 RPM	8.38 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_69 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_69 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
Mus musculus	ENSMUSG00000035142	1 retrocopy	retro_mmus_3096,
Xenopus tropicalis	ENSXETG00000014129	1 retrocopy	retro_xtro_69 ,