RetrogeneDB ID: retro_xtro_52

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL180723.1:8802..9705(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: hmgcl
• Ensembl ID: ENSXETG00000015336
• Aliases: None
• Description: 3-hydroxymethyl-3-methylglutaryl-CoA lyase [Source:Jamboree;Acc:XB-GENE-1002069]

Sequence

>retro_xtro_52
TCCAAAGCCCCGACCATGAACTACCCCAGCCGCGTACGCATCATCGACGTAGGCCCGCGCGACGGCCTGCAAAACGAAAA
GCAAGCCGTACCCGACAGCGTCAAAATCGGACTGGTACAGCGCCTGCAAGATGCGGGCCTGCGCGAAATTGAAGTAACCA
GCTACGTCAGCCCCAAGTGGGTACCGCAGATGGCGGACAACCACCTCGTCATGTCCGGCATAGCGCGCCGAACGGGTGTG
CGCTACAGCGTGCTCACCCCCAACCACCAGGGCTGGAAAGCCGCCGTAGCCGACCGGCCCGACGAGATCGTCGTCTTCGG
CGCTGCCAGCGAGGCGTTCAGCCAGAAGAACATCAACTGCTCCATTGCCGAAAGCATCGCGCGCTTCGCCCCGGTAGCCG
AGGCAGCGCGCGCCGCAGGCGTAGCCGTGCGCGGCGCCATGAGCTGCAGCGTAGGCTGCCCCTACGAAGGCGAGATCGCA
CCCGAACGCGTGGCCTACCTGGCGGGGCTGATGAAGGACATTGGCGTACAGCGCGTGGACGTGGCCGACACCATCGGCGT
GGGCACGCCACTGAAGGTACAGCGCGCCATTGCAGCGGCGCTACAGCACTACGCACTGGATGCCGTGTCGTGCCACTTCC
ACGACACCTACGGCCAGGCACTGTCGAACACGCTGGCGGCGCTGACGCTGGGCGTATGGAACTTCCAGTCTTCCGTAGCG
GGCCTGGGCGGCTGCCCCTACGCCAAGGGCGCCACAGGCAACGTGGCCACCGAAGACCTGGTGTACCTGCTGCACGGCAT
GGGCATCGAAACGGGCATCGACCTGGACAAACTGGTAGACGCGGGCACATACATCAGCGATTTCCTGGGCCGCAAAAGCA
ACTCGCGCGTGGCCGTGGCGCTG

Alignment

ORF - retro_xtro_52 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.48 %
• Parental protein coverage: 92.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SSLPIQSFPKEVKVVEVGPRDGLQNEKTVVPSEVKIHLINLLSEAGLQAIEATSFVSPKWVPQMADHKNV
          S..P....P..V....VGPRDGLQNEK..VP..VKI.L...L..AGL..IE.TS.VSPKWVPQMAD...V
Retrocopy SKAPTMNYPSRVRIIDVGPRDGLQNEKQAVPDSVKIGLVQRLQDAGLREIEVTSYVSPKWVPQMADNHLV

Parental  IQGIKKYPNVTYPVLTPNLTGFQAAVECGAKEVAIFGAASELFSKKNINCSIDESLQRFKDVIAAAKEAN
          ..GI.....V.Y.VLTPN..G..AAV.....E...FGAASE.FS.KNINCSI.ES..RF..V..AA..A.
Retrocopy MSGIARRTGVRYSVLTPNHQGWKAAVADRPDEIVVFGAASEAFSQKNINCSIAESIARFAPVAEAARAAG

Parental  IPVRGYVSCVLGCPYEGKVAPSKVAEVAYKMFSMGCYEISLGDTIGVGTPGGMRDMLRAVLDVVPAKALA
          ..VRG..SC..GCPYEG..AP..VA..A..M...G.......DTIGVGTP........A.L......A..
Retrocopy VAVRGAMSCSVGCPYEGEIAPERVAYLAGLMKDIGVQRVDVADTIGVGTPLKVQRAIAAALQHYALDAVS

Parental  VHCHDTYGQALANILVALQMGVQVVDASVAGLGGCPYAQGASGNVATEDVVYMLHGLGIQTGIDIKKLTE
          .H.HDTYGQAL.N.L.AL..GV.....SVAGLGGCPYA.GA.GNVATED.VY.LHG.GI.TGID..KL..
Retrocopy CHFHDTYGQALSNTLAALTLGVWNFQSSVAGLGGCPYAKGATGNVATEDLVYLLHGMGIETGIDLDKLVD

Parental  AGAFICKALGKKSNSKVAQAM
          AG..I...LG.KSNS.VA.A.
Retrocopy AGTYISDFLGRKSNSRVAVAL

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	11.91 RPM
SRP007412_heart	0.00 RPM	43.93 RPM
SRP007412_kidney	0.00 RPM	43.93 RPM
SRP007412_liver	0.00 RPM	18.32 RPM
SRP007412_skeletal_muscle	0.00 RPM	13.50 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_52 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_52 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Sorex araneus	ENSSARG00000014017	1 retrocopy	retro_sara_387,
Xenopus tropicalis	ENSXETG00000015336	1 retrocopy	retro_xtro_52 ,