RetrogeneDB ID: retro_xtro_20

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL172805.1:1714982..1715384(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ppia
• Ensembl ID: ENSXETG00000018981
• Aliases: None
• Description: peptidylprolyl isomerase A (cyclophilin A) [Source:Jamboree;Acc:XB-GENE-5778000]

Sequence

>retro_xtro_20
ATGGGCCTTATAATCATGGAGCTCAGGAGTGATGTGGTTCCAAAGACTGCAGAGAACTTCCGTGCCCTTTGCACACATGA
GAAGGGGTTTGGCTACAAGAACTCTGGCTTCCACAGAATTATCCCTGAATTCATGTGCCAGGGAGGTGACTTCACCAACC
ACAATGGAACTGGTGGGAAATCTATCTACGGAAATAAGTTTGCTGATGAGAACTTCCAGCTGAGGCACACTGGCCCTGGA
ATCCTCTCTATGGCCAATGCTGGAGCAAATACAAACGGCTCCCAGTTTTTCATCTGCACTGCTAAGACCTCCTGGCTTGA
TGGAAAGCATGTCGTGTTCGGGACCGTTATTGATGGCATGGATGTCGTGAAAAATACGGAGAAACTAGGTTCTCAGTCTG
GA

Alignment

ORF - retro_xtro_20 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.01 %
• Parental protein coverage: 70.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGRIIMELRSDVVPKTAENFRALCTNEKGFGYKNSGFHRIIPEFMCQGGDFTNHNGTGGKSIYGNKFADE
          MG.IIMELRSDVVPKTAENFRALCT.EKGFGYKNSGFHRIIPEFMCQGGDFTNHNGTGGKSIYGNKFADE
Retrocopy MGLIIMELRSDVVPKTAENFRALCTHEKGFGYKNSGFHRIIPEFMCQGGDFTNHNGTGGKSIYGNKFADE

Parental  NFQLRHTGPGILSMANAGANTNGSQFFICTAKTSWLDGKHVVFGTVIDGMDVVRNMEKLGSQSG
          NFQLRHTGPGILSMANAGANTNGSQFFICTAKTSWLDGKHVVFGTVIDGMDVV.N.EKLGSQSG
Retrocopy NFQLRHTGPGILSMANAGANTNGSQFFICTAKTSWLDGKHVVFGTVIDGMDVVKNTEKLGSQSG

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	1.73 RPM	602.55 RPM
SRP007412_heart	0.32 RPM	512.45 RPM
SRP007412_kidney	0.32 RPM	512.45 RPM
SRP007412_liver	0.67 RPM	1377.11 RPM
SRP007412_skeletal_muscle	0.12 RPM	92.35 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_20 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_20 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 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000007365	1 retrocopy	retro_cpor_560,
Equus caballus	ENSECAG00000008796	3 retrocopies	retro_ecab_507, retro_ecab_649, retro_ecab_732,
Homo sapiens	ENSG00000108179	1 retrocopy	retro_hsap_1436,
Microcebus murinus	ENSMICG00000007086	8 retrocopies	retro_mmur_1266, retro_mmur_218, retro_mmur_515, retro_mmur_568, retro_mmur_605, retro_mmur_694, retro_mmur_769, retro_mmur_87,
Myotis lucifugus	ENSMLUG00000016233	1 retrocopy	retro_mluc_339,
Nomascus leucogenys	ENSNLEG00000010567	1 retrocopy	retro_nleu_70,
Procavia capensis	ENSPCAG00000009406	1 retrocopy	retro_pcap_275,
Pan troglodytes	ENSPTRG00000002669	1 retrocopy	retro_ptro_979,
Pteropus vampyrus	ENSPVAG00000001713	2 retrocopies	retro_pvam_380, retro_pvam_623,
Tupaia belangeri	ENSTBEG00000015457	1 retrocopy	retro_tbel_1906,
Tursiops truncatus	ENSTTRG00000014385	1 retrocopy	retro_ttru_1314,
Vicugna pacos	ENSVPAG00000010049	2 retrocopies	retro_vpac_261, retro_vpac_86,
Xenopus tropicalis	ENSXETG00000018981	1 retrocopy	retro_xtro_20 ,