RetrogeneDB ID: retro_xtro_35

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL174257.1:35867..36566(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: bdh2
• Ensembl ID: ENSXETG00000021320
• Aliases: None
• Description: 3-hydroxybutyrate dehydrogenase, type 2 [Source:Jamboree;Acc:XB-GENE-985755]

Sequence

>retro_xtro_35
CTCACCGGTAAACGCGTGCTGATCACCGCTGCCGCCCAGGGCATTGGCCGCGCCAGTGTCGAAGCCTATCTGGCGGCCGG
CGCCGAGGTGATTGCAGCCGACATCAATCAACAGGCGCTCGTTGACTTGTCGGGTGCGCAAACGGTCTTGCTGGACGTCA
CCGACGCCAGCGCCATCCAACGCCTTGCAGACGAAATCGGCCCGCTCGACGTGCTGTTCAACTGCGCAGGCGTGGTGCAC
GCCGGCAATATCCTCGAATGCCCGGAAAGCGACTGGACGTTTGCCCTGGACCTGAACGTCACCGCCATGTATCGCATGAT
CCGTGCATTTCTGCCGGGGATGCTGGCGGCGGGCGGCGGTTCGATCATCAATATGTCTTCGGTGGCCTCCAGCCTCAAGG
GCGTGCCCAACCGCTTTGCCTACTGCGCCAGCAAGGCCGCCGTCATCGGCCTGACCAAATCCGTCGCGGCCGATTTCGTC
ACCCAACGCATCCGCTGCAACGCCATTTGCCCCGGCACCGTAGAGTCGCCTTCGCTGCAGCAACGCATCATCGAACAAGC
CCGCCATGAAGGTCGCCAGCAGGATGAGGTGTACGCCGCCTTCACCGCCCGCCAGCCGATGGGCCGCTTGGGCACGCCCC
AGGAAATCGCCCAGTTGGCGCTGTACCTTGGCTCCGATGCCAGCGCCTTTACCACCGGC

Alignment

ORF - retro_xtro_35 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.9 %
• Parental protein coverage: 94.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VNGHDRVVTGVAQGIAFSGTLRAFVNEGAQVIATDINETKLKELEAYKGIQTRVLDVTKKDQIEKLCKEI
          ..G.....T..AQGI.......A....GA.VIA.DIN...L..L....G.QT..LDVT....I..L..EI
Retrocopy LTGKRVLITAAAQGIG-RASVEAYLAAGAEVIAADINQQALVDLS---GAQTVLLDVTDASAIQRLADEI

Parental  DRVDVLFNVAGFVHHGTILDCAEADWDFTMNVNVRSMYLMIKTFLPKMLAQKSGNIINMSSVASSIKGVV
          ...DVLFN.AG.VH.G.IL.C.E.DW.F....NV..MY.MI..FLP.MLA...G.IINMSSVASS.KGV.
Retrocopy GPLDVLFNCAGVVHAGNILECPESDWTFALDLNVTAMYRMIRAFLPGMLAAGGGSIINMSSVASSLKGVP

Parental  NRCVYSTSKAAVIGLTKSVASDFIEQGIRCNCICPGTVDTPSLRERI--QARPD---PEQAFKDFLARQR
          NR..Y..SKAAVIGLTKSVA.DF..Q.IRCN.ICPGTV..PSL..RI..QAR............F.ARQ.
Retrocopy NRFAYCASKAAVIGLTKSVAADFVTQRIRCNAICPGTVESPSLQQRIIEQARHEGRQQDEVYAAFTARQP

Parental  TGRMATAEEVAHLCVYLASDEQPYCNG
          .GR..T..E.A.L..YL.SD......G
Retrocopy MGRLGTPQEIAQLALYLGSDASAFTTG

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	25.89 RPM
SRP007412_heart	0.00 RPM	11.20 RPM
SRP007412_kidney	0.00 RPM	11.20 RPM
SRP007412_liver	0.00 RPM	20.28 RPM
SRP007412_skeletal_muscle	0.00 RPM	2.22 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_35 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_35 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000164039	1 retrocopy	retro_hsap_3499,
Gorilla gorilla	ENSGGOG00000006381	1 retrocopy	retro_ggor_199,
Pongo abelii	ENSPPYG00000025868	1 retrocopy	retro_pabe_2891,
Xenopus tropicalis	ENSXETG00000007721	1 retrocopy	retro_xtro_39,
Xenopus tropicalis	ENSXETG00000021320	2 retrocopies	retro_xtro_35 , retro_xtro_37,