RetrogeneDB ID: retro_xtro_41

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL174887.1:2033..3212(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: cat.2
• Ensembl ID: ENSXETG00000003981
• Aliases: None
• Description: catalase, gene 2 [Source:Jamboree;Acc:XB-GENE-976955]

Sequence

>retro_xtro_41
CTCACGACCGCCGCTGGCGCCCCCGTCGCCAACAACCAGGATGCACTCACCGCTGGCCCGCGCGGCCCGATGCTGCTGCA
GGACCTATGGCACCTGGAGAAGCTCGCGCACTTCCACCGCGAAGTCATCCCCGAGCGCCGCATGCACGCCAAGGGCTCGG
GCGCCTACGGCAGCTTCACCGTCACGGGTGACATCACGCGCTACACGCGCGCCAAGGTGTTCTCCGGCATCGGCAGGCAA
ACGCCGCTGTTCGTGCGTTTTTCCACCGTCGCTGGCGAGCGCGGCGCGGCCGACGCTGAGCGTGACATCCGCGGCTTCGC
CGTGAAGATGTACACCGAGGAAGGCAACTGGGATCTGGTGGGCAACAACACGCCGGTGTTCTTCTTCCGCGACCCGCTCA
AGTTCCCCGACCTGAACAAAGCCGTCAAACGCGACCCATACACCAACCTGCGCAGCCCCGAGAGCAACTGGGACTTCTGG
ACCAGCCTGCCCGAAGCGCTGCACCAGATCACCATTGTGATGAGCGACCGTGGCATACCCAAGAGCTACCGCCACATGCA
CGGTTTCGGCTCGCACACTTACAGCCTCATCAACCAGGCTGGCGAGCGCCACTACGTCAAGTTCCACTGGGTGAGCCAGC
AAGGCATCGAGAACCTGAGCGACGCCGAAGCCGCCGCCGTAATCGCCACTGATCGCGAGAGCAGCCAGCGCGACCTGCTC
GAAGCCATCGACCGTGGTGACTTCCCGAAGTGGAAGCTGTGCGTGCAAATCATGACCGAGGCGCAGGCGCAGACCTACCG
CTTCCACCCATTCGATCTGACCAAGGTATGGAGCAAGAAGGACTTCCCGCTCATCGAAGTCGGCGTGATGGAGCTGAACC
GCAACCCCGACAACTACTACGCCGAGGTAGAGCAGGCCTCATTCGCGCCGAGCAATCTGGTGCCCGGCATCGGCCCCTCG
CCCGACCGCATGCTGCAATCGCGCCTGTTCTCGTACTCTGACGCTGCACGCTACCGCCTGGGCGTGAACCACCACCAGAT
TCCGGTCAACGCGCCGCGCTGCCCCGTGGCCCACTACCACCGCGACGGTGCCATGCGCGTGGACGGCAACTTCGGTCGCA
CCATCGCCTACGAGCCCAACACCCAAGGCGCGTGGCAAGAGCAGCCCGCCTACGCCGAG

Alignment

ORF - retro_xtro_41 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.57 %
• Parental protein coverage: 74.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LTTGGGNPISDKLNLLTVGPRGPLLVQDVVFTDEMAHFDRERIPERVVHAKGAGAFGYFEITHDITKYSK
          LTT..G.P.......LT.GPRGP.L.QD.......AHF.RE.IPER..HAKG.GA.G.F..T.DIT.Y..
Retrocopy LTTAAGAPVANNQDALTAGPRGPMLLQDLWHLEKLAHFHREVIPERRMHAKGSGAYGSFTVTGDITRYTR

Parental  AKVFEHIGKRTPIAIRFSTVAGESGSADTVRDPRGFAVKMYTEDGNWDLTGNNTPVFFIRDAMLFPSFIH
          AKVF..IG..TP...RFSTVAGE.G.AD..RD.RGFAVKMYTE.GNWDL.GNNTPVFF.RD...FP....
Retrocopy AKVFSGIGRQTPLFVRFSTVAGERGAADAERDIRGFAVKMYTEEGNWDLVGNNTPVFFFRDPLKFPDLNK

Parental  SQKRNPQTHLKDPDMVWDFWALRPESLHQVSFLFSDRGIPDGHRHMNGYGSHTFKLVNAKDEAVYCKFHY
          ..KR.P.T.L..P...WDFW...PE.LHQ.....SDRGIP...RHM.G.GSHT..L.N...E..Y.KFH.
Retrocopy AVKRDPYTNLRSPESNWDFWTSLPEALHQITIVMSDRGIPKSYRHMHGFGSHTYSLINQAGERHYVKFHW

Parental  KTDQGIRNLTVEEANRLSASDPDYGIHDLYESIAAGNYPSWSFYIQVMTFQQAEKFKFNPFDLTKIWPHG
          ...QGI.NL...EA....A.D......DL.E.I..G..P.W....Q.MT..QA....F.PFDLTK.W...
Retrocopy VSQQGIENLSDAEAAAVIATDRESSQRDLLEAIDRGDFPKWKLCVQIMTEAQAQTYRFHPFDLTKVWSKK

Parental  DYPLIPVGKLVLNRNPTNYFAEVEQLAFDPSNMPPGIEPSPDKMLQGRLFSYPDTHRHRLGPNYLQLPVN
          D.PLI.VG...LNRNP.NY.AEVEQ..F.PSN..PGI.PSPD.MLQ.RLFSY.D..R.RLG.N..Q.PVN
Retrocopy DFPLIEVGVMELNRNPDNYYAEVEQASFAPSNLVPGIGPSPDRMLQSRLFSYSDAARYRLGVNHHQIPVN

Parental  CPYRTRVANYQRDGPMCFTDNQGGAPNYYPNSFCAPENQPQVRE
          .P.R..VA.Y.RDG.M....N.G....Y.PN...A...QP...E
Retrocopy AP-RCPVAHYHRDGAMRVDGNFGRTIAYEPNTQGAWQEQPAYAE

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	77.75 RPM
SRP007412_heart	0.00 RPM	145.46 RPM
SRP007412_kidney	0.00 RPM	145.46 RPM
SRP007412_liver	0.00 RPM	2206.75 RPM
SRP007412_skeletal_muscle	0.00 RPM	64.24 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_41 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_41 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
Microcebus murinus	ENSMICG00000003672	1 retrocopy	retro_mmur_930,
Xenopus tropicalis	ENSXETG00000003981	1 retrocopy	retro_xtro_41 ,