RetrogeneDB ID: retro_xtro_22

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL172997.1:23343..23829(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSXETG00000033956
• Aliases: None
• Description: None

Sequence

>retro_xtro_22
TTGGTGGTTAAGATGTATAACCCCAATGTACCCCAAGAAAATATTACCACATGGCTCTCTCTATACTGTGAAAAAGTTAA
ATTCCTGCATAATGTGGTAAACCAGTTTGGACTCTGGACTGGTAAGCGCAAGTACCTGGTCACTTTTAAAAAGGGGATTT
TACCACCAGCCCATTTTAATATCGGAAAGTTTAATGGGGACTTGTTCTTTGATGGCATGGGCAGTTTCTGTCGCGTGTGT
CATGAATATGGACATTCTACTAATGATTGCCAGCAAGTTTGCAGATGCAGAAACTGTAATTCTTTTGAGCACGCGACAAA
AGAGTGCCCCAAGGCTAAACGCTGTAATTTCTGCCTTGGGGAAGGTCATGTTTATCACAACTGCCCAAGCAGAAGTAAAG
TGCAAAATGCTGCTCCTGGTGGGGGGGATCGAGTGAAGCCTGCAGCCAAACCTGTGTGGAAGGCGGTTCGAGAGCAGCGG
TTCCAG

Alignment

ORF - retro_xtro_22 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.97 %
• Parental protein coverage: 60.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LVIMSYSPFVPLGEIEAFLWRYCKKVSFVGHVLNKLGIWTSKYRFKVVLRKKGILPPARFSIGKYNGDLF
          LV...Y.P.VP...I...L..YC.KV.F...V.N..G.WT.K....V...KKGILPPA.F.IGK.NGDLF
Retrocopy LVVKMYNPNVPQENITTWLSLYCEKVKFLHNVVNQFGLWTGKRKYLVTF-KKGILPPAHFNIGKFNGDLF

Parental  YDGMGSFCRLCHEYGHTIEDCKQVCRCRNCDSFKHTTKECSKEKRCNFCFNTGHVYFNCPNRSREKMRHA
          .DGMGSFCR.CHEYGH...DC.QVCRCRNC.SF.H.TKEC.K.KRCNFC...GHVY.NCP.RS..K...A
Retrocopy FDGMGSFCRVCHEYGHSTNDCQQVCRCRNCNSFEHATKECPKAKRCNFCLGEGHVYHNCPSRS--KVQNA

Parental  VPEGKPSVERHATPVLVLAAKQASQ
          .P.G...V...A.PV......Q..Q
Retrocopy APGGGDRVKPAAKPVWKAVREQRFQ

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	0.07 RPM	0.00 RPM
SRP007412_heart	0.13 RPM	0.00 RPM
SRP007412_kidney	0.13 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_22 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_22 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,