RetrogeneDB ID: retro_xtro_4

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL173409.1:348554..349700(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSXETG00000024701
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSXETG00000026344
• Aliases: None
• Description: None

Sequence

>retro_xtro_4
ATGGCAGCGAAAGATGACGTCGTCCCTGTTTTCGTTCGAGTGAAGAATTCAGTGAGAGTTGTTGCAGCTGATCCTTTGAA
CGTGGAGAAGAGCTTGATCTACGTTGTTCAAGTGATACTGGAGGAGTTCGGGAGAGTCTCCAAGAACGAAATTCTCGCGA
TCCAGGACTATCCAAGGAGAGGCATCTATGATGTTACCTTTGAAGGAGAAGGTGTTTTTCACAGTTTTGTGAGAATCCTG
GAGGAAAATCCGGCTGATCCGAGGTTAAGCGGATTTAAAGTTTTTCCGCATTTTGCAGAAGAGGAGATCTTTTTGGTGGT
TAAAACGTATTCACCATTTGTGCCTCTTAAAGAGATCAAAACGGTTCTGGGTAGGTACTGTAAAAAGTTGACCTTTGGAG
GTAAGATATTGAATGAGCTGGGAATATGGACCTCAAAGTACAGGTTCAAAGCCGTTCTGGAAAAAAAAGGTATGTACCCA
CCAGCGAGGTTCCAGCTGGGAACTGTTAACATTGATTGGTTTTTCAGTGGAATGCCGGAGTTTTGCAGAAGATGCAAACA
ATATGGACACCTGGCAGATGGATGTGTCCTATGCCAGAATTGCGGTAAGACTGGTCATGAATTTAAAAGTTGTCCTTTAC
CAAGGAAATGTAACTTTTGTTTTCAAGGAGGTCATTTATATGCAGCTTGCCCAAAAAGGAAACCAGAGGAAGTTGATGTG
GCTTTGGGTAAGTTGTTAAAACCGGTTGAGCAAAGTCAAGAACCACTGGTTCCTTTGGAGCCTTTGGTTGCTTCGCCTGA
TATGGGGGATTTAAGCGCTTCACCGGTGATGCAGTCCTCTAGTGAAAATGTGTCGGATGTTTCGAGCCACACAAGTGAAA
CGGTGCCAATCATTAAGAGGAAAAAAAGGGAAAAAAATAAACCGCTTCAGGTAACTCAGTCTGGTGTTGTGGAAGGAGAG
TATAAAACAAGAGGCGAACGGTTATACCAGTTTTGGAAAGTTAAAACGGATAAGGAAATACAGGATTTTTTGTCTACTTG
GTCTGATGAGGAGGAGCTTGATGGGGTTAATGAATGCATTAAAGAAGGTGGTGAAATTAAAATCGTTAGAAATAAAGTGT
TGAAATATATACGTAATTTGAAATAA

Alignment

ORF - retro_xtro_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.38 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEVAEETVPAFARVRNSVRIIVEDATTKESKLLHVVNTILGDFGHVRKGEILAIQDYPKRRIYDVTFDGE
          M......VP.F.RV.NSVR....D....E..L..VV..IL..FG.V.K.EILAIQDYP.R.IYDVTF.GE
Retrocopy MAAKDDVVPVFVRVKNSVRVVAADPLNVEKSLIYVVQVILEEFGRVSKNEILAIQDYPRRGIYDVTFEGE

Parental  GVFSSFWKIYSENPADPRLSGFKVFPHFAEEEIFLVVKTYSPFVPLKEIETVLGRYCKKLTFGGKILNEL
          GVF.SF..I..ENPADPRLSGFKVFPHFAEEEIFLVVKTYSPFVPLKEI.TVLGRYCKKLTFGGKILNEL
Retrocopy GVFHSFVRILEENPADPRLSGFKVFPHFAEEEIFLVVKTYSPFVPLKEIKTVLGRYCKKLTFGGKILNEL

Parental  GIWTSKYRFKAVLEKKGMYPPARFQLGTVNIDCFFSGMPDFCRRCKQYGHLADGCVLCQNCGKTGHEFKS
          GIWTSKYRFKAVLEKKGMYPPARFQLGTVNID.FFSGMP.FCRRCKQYGHLADGCVLCQNCGKTGHEFKS
Retrocopy GIWTSKYRFKAVLEKKGMYPPARFQLGTVNIDWFFSGMPEFCRRCKQYGHLADGCVLCQNCGKTGHEFKS

Parental  CPLPRKCNFCFQGGHLYAACPKRKAKPEEVDVAVEKQEKRVEVSQQELSVPLESLVASPDWGDLSASPVM
          CPLPRKCNFCFQGGHLYAACPKRK..PEEVDVA..K..K.VE.SQ..L.VPLE.LVASPD.GDLSASPVM
Retrocopy CPLPRKCNFCFQGGHLYAACPKRK--PEEVDVALGKLLKPVEQSQEPL-VPLEPLVASPDMGDLSASPVM

Parental  QTSSENVSDVSSHTSETMPNIKRKKREKNKPLQVTQSGVVEGEYETRGERLYQFWKIKTDKEIQDFLSTW
          Q.SSENVSDVSSHTSET.P.IKRKKREKNKPLQVTQSGVVEGEY.TRGERLYQFWK.KTDKEIQDFLSTW
Retrocopy QSSSENVSDVSSHTSETVPIIKRKKREKNKPLQVTQSGVVEGEYKTRGERLYQFWKVKTDKEIQDFLSTW

Parental  SDEEELDGVNECIKEGGDIKCVRNKVLKFIRNLK
          SDEEELDGVNECIKEGG.IK.VRNKVLK.IRNLK
Retrocopy SDEEELDGVNECIKEGGEIKIVRNKVLKYIRNLK

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_4 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_4 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,