RetrogeneDB ID: retro_xtro_55

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL181302.1:9366..10260(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FH
• Ensembl ID: ENSXETG00000032112
• Aliases: None
• Description: fumarate hydratase [Source:HGNC Symbol;Acc:3700]

Sequence

>retro_xtro_55
ATTGAGGTGCTGAAGAAGACCCTGGCGCAGAAGGCGCAGGACTTCGACGGTATCGTCAAGATCGGCCGCACCCACCTGCA
GGACGCGACGCCGCTCACGCTGGGCCAGGAGATCTCGGGCTGGGTCGCGCAGCTTGAGCACGGCGCGCGGCACGTGAAGG
ATGCGCTGCCCCACCTGTACGAACTGGCGCTGGGTGGCACCGCCGTGGGCACGGGTCTGAACGCGCCCAAGGGCTATGCC
GAAGGCGTGGCCAAGGAACTGGCGGCCATGACTGGCCTGCCCTTCGTCACCTCGCCCAACAAGTTCGAATCGCTGGCCAC
CCAGGATGCGCTGGTGCACGCCCATGGCGCGCTCAAGACCCTGGCGGCCAGCCTGAACAAGATCGCCAATGACGTGCGTT
GGCTCGCCAGCGGCCCGCGCAGCGGCATCGGCGAGCTCAGCATTCCCGAGAACGAGCCTGGCTCGTCCATCATGCCCGGC
AAGGTCAATCCCACGCAGAGCGAGGCCGTCACCATGCTGGCCGCACAGGTCATGGGCAACGACGTGGCGATCAACATCGG
CGGCATGTCGGGCAACTTCGAATTGAACGTGTTCCGCCCCGTGGTGGCGCACAACTTCCTGCAGAGCGTGCGCCTGCTGG
CCGACGGCATCGTGAGCTTCAACAACCACTGTGCCGTGGGCATCGAACCCAACCGCGAGCGCATCGACCATCTTGTCCAG
CAGTCGCTGATGCTGGTGACGGCGCTCAACCCGCACATTGGCTACGACAAGGCCGCCTACATCGCCAAGAAGGGCCACAA
GGAGGGCACCAGCCTGCGCGCGGCGGCCATCGCCTCGGGCCACGTCACGGCTGAGCAGTTCGACCAGTGGGTGGTGCCAG
AGAAGATGGTTGGT

Alignment

ORF - retro_xtro_55 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59. %
• Parental protein coverage: 58.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LQKLHDALEEKSKEFENIIKIGRTHTQDAVPLTLGQEFGGYVQQIKYSVSRIKAALPRVYELAAGGTAVG
          ...L...L..K...F..I.KIGRTH.QDA.PLTLGQE..G.V.Q........K.ALP..YELA.GGTAVG
Retrocopy IEVLKKTLAQKAQDFDGIVKIGRTHLQDATPLTLGQEISGWVAQLEHGARHVKDALPHLYELALGGTAVG

Parental  TGLNTRIGFAEKVAAKVAELTGLPFITAPNKFESLAAHDALVELSGALNTLACSLMKIANDIRFLGSGPR
          TGLN...G.AE.VA...A..TGLPF.T.PNKFESLA..DALV...GAL.TLA.SL.KIAND.R.L.SGPR
Retrocopy TGLNAPKGYAEGVAKELAAMTGLPFVTSPNKFESLATQDALVHAHGALKTLAASLNKIANDVRWLASGPR

Parental  SGLGELILPENEPGSSIMPAGKVNPTQCEAVTMVALRLMAHH-AYEIRTSGNAYPMLFLKNLQIKNVLQS
          SG.GEL..PENEPGSSIMP.GKVNPTQ.EAVTM.A...M....A..I..................N.LQS
Retrocopy SGIGELSIPENEPGSSIMP-GKVNPTQSEAVTMLAAQVMGNDVAINIGGMSGNFELNVFRPVVAHNFLQS

Parental  IRLLGDAAVSFTDNCIVGVQANTERINKLMSESLMLVTALNPHIAGYDKAAKIAKTAHKEGTTLKETAIK
          .RLL.D..VSF...C.VG...N.ERI..L...SLMLVTALNPHI.GYDKAA.IAK..HKEGT.L...AI.
Retrocopy VRLLADGIVSFNNHCAVGIEPNRERIDHLVQQSLMLVTALNPHI-GYDKAAYIAKKGHKEGTSLRAAAIA

Parental  LGFLTSDQFDQWVKPEDMLG
          .G..T..QFDQWV.PE.M.G
Retrocopy SGHVTAEQFDQWVVPEKMVG

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	25.76 RPM
SRP007412_heart	0.00 RPM	128.49 RPM
SRP007412_kidney	0.00 RPM	128.49 RPM
SRP007412_liver	0.00 RPM	57.47 RPM
SRP007412_skeletal_muscle	0.00 RPM	116.70 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_55 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_55 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017359	1 retrocopy	retro_cjac_2339,
Echinops telfairi	ENSETEG00000018721	2 retrocopies	retro_etel_1069, retro_etel_1457,
Microcebus murinus	ENSMICG00000003451	2 retrocopies	retro_mmur_1215, retro_mmur_720,
Mus musculus	ENSMUSG00000026526	1 retrocopy	retro_mmus_3600,
Oryctolagus cuniculus	ENSOCUG00000021494	1 retrocopy	retro_ocun_50,
Otolemur garnettii	ENSOGAG00000009936	1 retrocopy	retro_ogar_322,
Rattus norvegicus	ENSRNOG00000003653	1 retrocopy	retro_rnor_2979,
Xenopus tropicalis	ENSXETG00000032112	1 retrocopy	retro_xtro_55 ,