RetrogeneDB ID: retro_xtro_38

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL174460.1:26773..27118(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: gstz1
• Ensembl ID: ENSXETG00000011079
• Aliases: None
• Description: glutathione transferase zeta 1 [Source:Jamboree;Acc:XB-GENE-978910]

Sequence

>retro_xtro_38
CTCTACTCCTACTTCCGCAGCTCTGCGGCCTACCGCGTGCGCATCGCCCTGGCACTCAAGGAACTGGCCTACGACACCCT
CCCCGTGCATCTGCTCAAGGATGGCGGCCAGCACCACAGCAGCACCTACCGCAACGCCAACCCGCAGGGGCTGGTGCCCG
CCCTGCAGGTGGCCGAAGAGGGGCCAGTGCTGGCGCAGTCGCTGGCCATCCTGGAATACCTCGACGAGGTGTACCCCACA
CCCGCCCTGCTGCCCACCGGCGCCCTGGCGCGCGCACGCGTGCGCGGTCTGGCGCACATGGTGGCCTGCGAAATCCACCC
ACTCAACAACCTGCGCGTGTTGAAG

Alignment

ORF - retro_xtro_38 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.43 %
• Parental protein coverage: 52.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LYGYFRSSCSWRVRIALAFKGIEYDQQVINLVKDGGMQLSNEYKQVNPMQQVPALCI--DGVTLSQSLAI
          LY.YFRSS...RVRIALA.K...YD.....L.KDGG...S..Y...NP...VPAL.....G..L.QSLAI
Retrocopy LYSYFRSSAAYRVRIALALKELAYDTLPVHLLKDGGQHHSSTYRNANPQGLVPALQVAEEGPVLAQSLAI

Parental  IEYLEETRPNPPLLPRDPKKRAQVRMISDQIASGIQPLQNLCVLQ
          .EYL.E..P.P.LLP.....RA.VR......A..I.PL.NL.VL.
Retrocopy LEYLDEVYPTPALLPTGALARARVRGLAHMVACEIHPLNNLRVLK

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	3.74 RPM
SRP007412_heart	0.00 RPM	10.82 RPM
SRP007412_kidney	0.00 RPM	10.82 RPM
SRP007412_liver	0.00 RPM	78.79 RPM
SRP007412_skeletal_muscle	0.00 RPM	11.34 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_38 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_38 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000017287	1 retrocopy	retro_dnov_116,
Monodelphis domestica	ENSMODG00000005427	1 retrocopy	retro_mdom_1030,
Xenopus tropicalis	ENSXETG00000011079	1 retrocopy	retro_xtro_38 ,