RetrogeneDB ID: retro_xtro_51

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL180723.1:3531..5103(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: mccc2
• Ensembl ID: ENSXETG00000018213
• Aliases: None
• Description: methylcrotonoyl-CoA carboxylase 2 (beta) [Source:Jamboree;Acc:XB-GENE-985830]

Sequence

>retro_xtro_51
TCCACCGACTTCCAGGGCAATGCGGCCGCCATGCGCGCTCTGGTGCAGGAGTTGCGGGCCCATCTCGCCAAGGTCGCCCA
GGGTGGCGGCGAGGCCGCGCGTGCCAAGCACGTGGCGCGCGGCAAGATGCTGCCGCGCGAGCGCGTGCAGATGCTGCTTG
ACCCCGGCACGCCCTTTCTGGAACTGGCCCCGCTGGCGGCGCTGGATATGTACGGTAACGAGGCGCCGGGCGCGGGCATC
ATCGTCGGCCTGGGCCGCGTGAATGGCGTGGATTGCATGGTGGTGTGCAACGACGCCACGGTGAAGGGCGGCACCTACTA
CCCCATGACGGTGAAGAAGCACCTGCGCGCCCAGGAAGTGGCGGCGCAGAACCACCTGCCCTGCATCTACCTGGTCGATT
CGGGCGGCGCCAACCTGCCCAATCAGGACGACGTGTTTCCTGACCGCGAGCACTTCGGCCGCATCTTCTACAACCAGGCC
CACATGAGCGCCCAGGGCATCGCGCAGATCGCCGTGGTCATGGGCAGTTGCACGGCTGGCGGCGCCTACGTGCCGGCGAT
GAGCGACGAATCCATCATCGTCAAGAACCAGGGCACTATCTTTCTGGGTGGCCCGCCGCTGGTGAAGGCCGCCACGGGCG
AGGTGGTGAGCGCCGAAGACCTGGGCGGCGGCGACGTGCACACGCGCCTCTCGGGCGTGGCCGACCATCTGGCGCAGAAC
GATATGCACGCGCTGGCGCTGGCGCGCGCGGCTGTGGCCAATTTGAATAGAAACAAGCCGCAAAACCCCGCCGATCAAGC
GCCAGCTGCTCCTCAATATGAAGCACAGGAACTGTATGGCGTGATCCCTACCGACACGCGCAAGCCCTTCGACGTGCGCG
AGATCATCGCGCGCATCGTCGATGGCAGCGCGTTCGACGAATTCAAGGCGCGCTTCGGCGCCACTCTGGTGTGCGGCTTT
GCGCGCATCGAGGGCATGCAGGTTGGCGTCATCGCCAACAACGGTATTTTGTTCAGCGAAAGCGCGCAAAAGGGCGCGCA
CTTCATCGCGTTGTGCTGCCAGCGCAAGGTTCCGCTGGTGTTTCTGCAGAACATCACCGGCTTCATGGTCGGGCGCAAGT
ACGAGAACGAGGGCATCGCACGCCACGGCGCCAAGCTGGTCACGGCCGTGGCCACGGCGCGTGTGCCCAAGTTCACCATC
ATCATTGGCGGCAGCTTTGGCGCTGGCAACTACGGCATGTGTGGCCGCGCCTACAGCCCGCGCTTCCTCTGGATGTGGCC
CAACGCGCGCATTTCCGTGATGGGCGGTGAGCAGGCCGCCAGCGTGCTGGCCACCGTCAAGCGCGACGGCATCGAGGCCC
AGGGCGGCAGCTGGAGCGCCGAGGAGGAGGAAGCCTTCAAGGCCCCCATCCGCCGCCAGTACGAGGAACAGGGCCACCCC
TACTACGCCACCGCGCGCCTGTGGGACGACGGCGTGATCGACCCCGCCGACACGCGCCGCGTGCTCGCGCTGGGCCTCTC
GGCCACGCGCAACGCGCCCATCGAGGACACCCGGTTTGGCGTGTTCCGCATG

Alignment

ORF - retro_xtro_51 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.97 %
• Parental protein coverage: 92.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SPAYQESYDRMKALVTELKERAQKIRLEGCGYPLNAYHTAVGRFLDREKVHLKINHISAFLEFSQFAGYQ
          S...Q.....M.ALV.EL.....K....G.G....A.H.A.G..L.RE.V.........FLE....A...
Retrocopy STDFQGNAAAMRALVQELRAHLAKVA-QGGGEAARAKHVARGKMLPRERVQMLLDPGTPFLELAPLAALD

Parental  LYGNEEVPAGGIISGIGRVSGVECLIVANDATVKGGSYYPITVKKHLRAQEIAMQNNLPCVYLVDSGGAN
          .YGNE..P..GII.G.GRV.GV.C..V.NDATVKGG.YYP.TVKKHLRAQE.A.QN.LPC.YLVDSGGAN
Retrocopy MYGNE-APGAGIIVGLGRVNGVDCMVVCNDATVKGGTYYPMTVKKHLRAQEVAAQNHLPCIYLVDSGGAN

Parental  LPRQAEVFPDRDHFGRIFYNQARMSSQGISQIAVVMGSCTAGGAYVPAMADESIIVRKQGTIFLGGPPLV
          LP.Q..VFPDR.HFGRIFYNQA.MS.QGI.QIAVVMGSCTAGGAYVPAM.DESIIV..QGTIFLGGPPLV
Retrocopy LPNQDDVFPDREHFGRIFYNQAHMSAQGIAQIAVVMGSCTAGGAYVPAMSDESIIVKNQGTIFLGGPPLV

Parental  KAATGEEVSAEDLGGADLHCRKSGVTDHYALDDNHALHLARKAVRSLNYNKNLDVTVEKPEDPVFPADEL
          KAATGE.VSAEDLGG.D.H.R.SGV.DH.A..D.HAL.LAR.AV..LN.NK........P..P...A.EL
Retrocopy KAATGEVVSAEDLGGGDVHTRLSGVADHLAQNDMHALALARAAVANLNRNKPQNPADQAPAAPQYEAQEL

Parental  YGIVGANLKKNVDVREVIARVVDGSKFDEFKALYGDTLITGFARIYGYPVGIIGNNGVLFSESAKKGTHF
          YG.......K..DVRE.IAR.VDGS.FDEFKA..G.TL..GFARI.G..VG.I.NNG.LFSESA.KG.HF
Retrocopy YGVIPTDTRKPFDVREIIARIVDGSAFDEFKARFGATLVCGFARIEGMQVGVIANNGILFSESAQKGAHF

Parental  IQLCCQRNIPLIFLQNITGFMVGRDYEAGGIAKDGAKMVTAVACANVPKITVIIGGSYGAGNYGMCGRAY
          I.LCCQR..PL.FLQNITGFMVGR.YE..GIA..GAK.VTAVA.A.VPK.T.IIGGS.GAGNYGMCGRAY
Retrocopy IALCCQRKVPLVFLQNITGFMVGRKYENEGIARHGAKLVTAVATARVPKFTIIIGGSFGAGNYGMCGRAY

Parental  SPRFLYMWPNARISVMGGEQAATVLATIAKDQKAREGKQFSEQEEAALKEPIIRRFEEEGNPYYSSARLW
          SPRFL.MWPNARISVMGGEQAA.VLAT...D.....G...S..EE.A.K.PI.R..EE.G.PYY..ARLW
Retrocopy SPRFLWMWPNARISVMGGEQAASVLATVKRDGIEAQGGSWSAEEEEAFKAPIRRQYEEQGHPYYATARLW

Parental  DDGIIDPADTRLVLGLSLSAALNAPTQKTQFGVFRM
          DDG.IDPADTR.VL.L.LSA..NAP...T.FGVFRM
Retrocopy DDGVIDPADTRRVLALGLSATRNAPIEDTRFGVFRM

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	16.75 RPM
SRP007412_heart	0.00 RPM	24.43 RPM
SRP007412_kidney	0.00 RPM	24.43 RPM
SRP007412_liver	0.00 RPM	7.79 RPM
SRP007412_skeletal_muscle	0.00 RPM	13.38 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_51 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_51 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Xenopus tropicalis	ENSXETG00000018213	1 retrocopy	retro_xtro_51 ,