RetrogeneDB ID: retro_xtro_43

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL175396.1:12325..13213(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ivd
• Ensembl ID: ENSXETG00000016078
• Aliases: None
• Description: isovaleryl-CoA dehydrogenase [Source:Jamboree;Acc:XB-GENE-1008677]

Sequence

>retro_xtro_43
CTGCGCGACGCCGTGCGCGACTTTGCCCAGAGCGAGATTGCGCCGCGCGCGGCCGAGATTGACCGCGCCGACCAGTTCCC
GATGGATTTGTGGCGCAAGCTCGGCGATCTGGGCGTGCTGGGCATTACCGTGCCCGAGCAGTACGGCGGTGCTGACATGG
GTTATCTGGCACATATGGTGGCCATGGAGGAGATTTCGCGCGCCAGCGCCTCGGTCGGCCTGTCTTACGGTGCGCACAGC
AATCTGTGCGTGAACCAGATCCAGCGCAATGGTGACGCGGCGCAGAAGGCCAGGTATCTGCCCAGGCTCATCAGCGGCGA
GCATGTCGGCGCGCTGGCCATGAGTGAGCCTGGCGCGGGTTCCGATGTGATGGGCATGCAGCTCAAGGCCGAGGCCCAGG
GTGGCTACTACCTGCTCAATGGCAGCAAGATGTGGATCACCAACGGGCCCGATGCCGACACGCTGGTGGTCTATGCCAAG
ACCGAGCCGGAGTTGGGCGCGCGCGGCGTTACGGCCTTTCTGATCGAGAAGGGCATGAAGGGCTTCTCGGTCGCGCAGAA
GCTCGACAAGCTCGGCATGCGCGGCAGCCACACGGGCGAACTGGTGTTCGAGAACGTCGAGGTGCCCGAGTCCCACGTGC
TCGGCGGCGTGAACCAGGGTGCCAAGGTGCTGATGAGTGGCCTGGACTATGAACGTGCCGTGCTCACCGGCGGGCCGCTC
GGCATCATGCAGTCGGTGATGGACAATGTGCTGCCCTACATCCATGCGCGCAAGCAGTTTGGGCAGAGCATTGGCGAATT
CCAGCTGATCCAGGGCAAGGTGGCCGATATGTACACCGTGCTGCAGGCGGGGCGCTCCTTCGCCTATACCGTGGCGAAAA
ATCTGGAT

Alignment

ORF - retro_xtro_43 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.33 %
• Parental protein coverage: 69.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LRQTLHRFCQDHLNPVANEIDQKNNFAEMRSFWKKLGELGVLGITAPVEYGGSAMGYLEHVLVVEEISRA
          LR.....F.Q....P.A.EID....F......W.KLG.LGVLGIT.P..YGG..MGYL.H....EEISRA
Retrocopy LRDAVRDFAQSEIAPRAAEIDRADQFP--MDLWRKLGDLGVLGITVPEQYGGADMGYLAHMVAMEEISRA

Parental  SAAVGLSYGAHSNLCINQIVRNGNEAQKEKYLPKLISGEYIGALAMSEPNSGSDVVSMRLKAEKKGDYYV
          SA.VGLSYGAHSNLC.NQI.RNG..AQK..YLP.LISGE..GALAMSEP..GSDV..M.LKAE..G.YY.
Retrocopy SASVGLSYGAHSNLCVNQIQRNGDAAQKARYLPRLISGEHVGALAMSEPGAGSDVMGMQLKAEAQGGYYL

Parental  LNGNKFWITNGPDADVLVVYAKTDPSAQPASHGITAFLVEKGMPGFSTAQKLDKLGMRGSNTCELVFEDC
          LNG.K.WITNGPDAD.LVVYAKT.P.......G.TAFL.EKGM.GFS.AQKLDKLGMRGS.T.ELVFE..
Retrocopy LNGSKMWITNGPDADTLVVYAKTEP--ELGARGVTAFLIEKGMKGFSVAQKLDKLGMRGSHTGELVFENV

Parental  KIPEQNVLGHLGKGVYVLMSGLDLERLVLSGGPLGIMQAVLDHAIPYLHTREAFGQKIGHFQLMQGKMAD
          ..PE..VLG....G..VLMSGLD.ER.VL.GGPLGIMQ.V.D...PY.H.R..FGQ.IG.FQL.QGK.AD
Retrocopy EVPESHVLGGVNQGAKVLMSGLDYERAVLTGGPLGIMQSVMDNVLPYIHARKQFGQSIGEFQLIQGKVAD

Parental  MYTRLAACRQYVYNVAKACD
          MYT.L.A.R...Y.VAK..D
Retrocopy MYTVLQAGRSFAYTVAKNLD

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	59.54 RPM
SRP007412_heart	0.00 RPM	139.25 RPM
SRP007412_kidney	0.00 RPM	139.25 RPM
SRP007412_liver	0.00 RPM	46.77 RPM
SRP007412_skeletal_muscle	0.00 RPM	58.50 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_43 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_43 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.

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000014462	1 retrocopy	retro_mmul_659,
Xenopus tropicalis	ENSXETG00000001085	1 retrocopy	retro_xtro_10,
Xenopus tropicalis	ENSXETG00000007932	1 retrocopy	retro_xtro_42,
Xenopus tropicalis	ENSXETG00000016078	1 retrocopy	retro_xtro_43 ,