RetrogeneDB ID: retro_xtro_32

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL173660.1:187656..188544(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSXETG00000024706
• Aliases: None
• Description: None

Sequence

>retro_xtro_32
TCTGCTGAGGGTGTTCCAGTTTATGCGAGAGTGAAGAACTCGGTTTGGATTCTGTCCCTGGATGTTGCAGATGAAGGCAA
ACGGCTGGCTTATGTGGTGAAGACAATCCTTGGTGCTGTCAGCAAAGTCAAGAAGGAGGATATCCTTGCTTTGCAGGATT
ACCCAAAGAAGGGGATTTATGATGTGTCCTTCGTGGGAGAAAGACCTTTTTTGGAGTTTCTTAAGGCTGTGAAAGTGAAG
GATGTTCGTTTGGAGGGTTTTAAAGTGATCCCTCACTTTGACCAAGAAGAGGTAGTTCTGGTGGTCAAAACTTTCTCACC
ACTGGTGCCGTTAAAGGAAATTGAATTTGTGCTTCGTCGGTATTGTGAGAAGTTATCATTTGCCGGTAAAGTCCTCAATG
AGTTTGGGTTATGGACATCGAAGTATAAGTTCAAAGCGGTGTTCCTGAAAGGGATGTTCCCTCCGGCAAGGTTTCGGCTG
GGTAAGGTGAATATTGATATTTTTTTCAACGGGATGCCTGATTTTTGTAAGAAATGTCGGAATTATGGACATTTGGCGGA
TACGTGTAAGGCATGTCGTTTTTGTGGGGATGTGCAACATGAAGCTAAGGATTGCCTAAGTCCGAGAAAATGCAATTTAT
GTCTGCAAGAAGGGCATTTGTATAATTTGTGTCCTGTGAGAAAGCAGAAAGTGGCGGAAGTGGAGGAGGCAGCGGTATTG
GATGAGATGTTGCTGGGAATGGAAATTCCGAGTGAAAGTGAAACTGTGGAGAGCGGGGCTAAGAGAGTGCTTTCGGATGT
GGAGTCATCAGAGGTGGCTGTGGTAGAGGAGACTGGTTCGGAGACAATGCAGTCAGAGGAGGAGGTGGTGAATGATGGAG
GAAAAGGA

Alignment

ORF - retro_xtro_32 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.5 %
• Parental protein coverage: 84.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SEDSVPVFVRVRNSIRIVAVDPSNAEQNLKYVVQKVLEEFGRVSRREILAIQDYPKRGVYDVTFDGEGVF
          S...VPV..RV.NS..I...D.......L.YVV...L.....V....ILA.QDYPK.G.YDV.F.GE..F
Retrocopy SAEGVPVYARVKNSVWILSLDVADEGKRLAYVVKTILGAVSKVKKEDILALQDYPKKGIYDVSFVGERPF

Parental  RSFMSILEGNLADPRLEGFKLFPHFAEEEVFLVVKSYSPFVPLKEIEAVIGRYCKKLSFAGKVLNELGIW
          ..F.........D.RLEGFK..PHF..EEV.LVVK..SP.VPLKEIE.V..RYC.KLSFAGKVLNE.G.W
Retrocopy LEFLKAVK--VKDVRLEGFKVIPHFDQEEVVLVVKTFSPLVPLKEIEFVLRRYCEKLSFAGKVLNEFGLW

Parental  TSKYRFKAVFEKGTFPPARFRLGTVNIDCFFKGMPEFCRRCRQYGHVLEGCTACQNCGKTGHEVMNCVLP
          TSKY.FKAVF.KG.FPPARFRLG.VNID.FF.GMP.FC..CR.YGH....C.AC..CG...HE...C..P
Retrocopy TSKYKFKAVFLKGMFPPARFRLGKVNIDIFFNGMPDFCKKCRNYGHLADTCKACRFCGDVQHEAKDCLSP

Parental  KKCNFCLQEGHLYVRCPQRKVEPVEVSADLAESEVQLRQSLVGTARSLSLQEESVTSGEESEPRQVSQEG
          .KCN.CLQEGHLY..CP.RK....EV.......E..L.................V.S..ES....V..E.
Retrocopy RKCNLCLQEGHLYNLCPVRKQKVAEVEEAAVLDEMLLGMEIPSESETVESGAKRVLSDVESSEVAVVEET

Parental  PTVKRTKKEEKTKEDGSSG
          ........EE....DG..G
Retrocopy GS-ETMQSEEEVVNDGGKG

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	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_skeletal_muscle	0.00 RPM	0.00 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_32 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_32 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Xenopus tropicalis	ENSXETG00000024706	1 retrocopy	retro_xtro_32 ,
Xenopus tropicalis	ENSXETG00000026344	1 retrocopy	retro_xtro_4,
Xenopus tropicalis	ENSXETG00000033956	2 retrocopies	retro_xtro_22, retro_xtro_71,