RetrogeneDB ID: retro_xtro_49

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL180709.1:8242..9172(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ndufv1
• Ensembl ID: ENSXETG00000003396
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) flavoprotein 1, 51kDa [Source:Jamboree;Acc:XB-GENE-495063]

Sequence

>retro_xtro_49
GATCAGGTGATCGCCACCGTCAAGGAGTCGGGCCTGCGCGGGCGCGGCGGTGCGGGCTTTCCCACGGGGCTGAAGTGGAG
CTTCATGCCGCGCCAGTTCCCGGGGCAGAAGCATCTGGTATGCAACTCCGACGAGGGTGAGCCGGGCACCTGCAAGGATC
GCGACATCCTGATGTACAACCCCCACATCGTGATTGAGGGGATGATCATCGGTGCCTACGCCATGGGCATTTCGCTGGGC
TACAACTACATTCACGGCGAGATTTTCCAGGCTTACGAACGCTTCGAGGCCGCACTGGAAGAAGCGCGCGCCGCAGGCTA
TCTGGGCGACCAGATCCTGGGCAGCCACTTCAGCTTTCAACTCCATGCCCACCATGGTTTCGGTGCCTACATCTGTGGCG
AGGAAACCGCTTTGCTGGAGTCGCTCGAAGGCAAGAAGGGCCAGCCGCGCTTCAAGCCGCCGTTCCCGGCCAGCTTCGGC
CTGTACGGCAAGCCCACGACGATCAACAACACGGAAACCTTTGCCGCCGTGCCGTGGATCATCCGCAACGGCGGGCCAGC
GTACCTGGAGTGCGGCAAGCCGAACAACGGCGGCACCAAGATTTTCTCGGTGTCGGGCGACGTGGAGCGCCCCGGCAATT
ACGAAATCCCGCTGGGCACGCCGTTCACCAAGCTGCTCGAACTCGCGGGGGGCGTGCGCAAGGGCCGCCAGCTCAAGGCC
GTGATTCCCGGTGGGTCGTCCTCGCCGGTGCTGCCCGCCCACATCATGATGGACTGCACGATGGATTACGACGCCATCTC
CAAGGCGGGCTCCATGCTCGGTTCGGGGGCGCTCATCGTGATGGACGATTCGCGCGACATGGTGGAGTCGCTGCTGCGCC
TGTCGTATTTCTACCAGCACGAATCTTGCGGCCAGTGCACACCGTGCCGC

Alignment

ORF - retro_xtro_49 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.32 %
• Parental protein coverage: 66.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DWILGEIKASGLRGRGGAGFPTGLKWSFMNKPSDGRPKYLVVNADEGEPGTCKDREIMRHDPHKLVEGCL
          D......K.SGLRGRGGAGFPTGLKWSFM.....G..K.LV.N.DEGEPGTCKDR.I....PH...EG..
Retrocopy DQVIATVKESGLRGRGGAGFPTGLKWSFMPRQFPGQ-KHLVCNSDEGEPGTCKDRDILMYNPHIVIEGMI

Parental  VAGRSMGARAAYIYIRGEFYNEASNLQVAVREAYSAGLIGRNACGSGYDFDVFVVRGAGAYICGEETALI
          .....MG....Y.YI.GE..........A..EA..AG..G....GS...F......G.GAYICGEETAL.
Retrocopy IGAYAMGISLGYNYIHGEIFQAYERFEAALEEARAAGYLGDQILGSHFSFQLHAHHGFGAYICGEETALL

Parental  ESIEGKQGKPRLKPPFPADVAGVFGCPTTVANVETVAVAPTICRRGGSWFASFGRERNAGTKLFNISGHV
          ES.EGK.G.PR.KPPFPA...G..G.PTT..N.ET.A..P.I.R.GG......G...N.GTK.F..SG.V
Retrocopy ESLEGKKGQPRFKPPFPASF-GLYGKPTTINNTETFAAVPWIIRNGGPAYLECGKPNNGGTKIFSVSGDV

Parental  NNPCTVEEEMSIPLKELIERHAGGVTGGWDNLLAVIPGGSSTPLIPQSVCETVLMDFDALVQAQTGLGTA
          ..P...E.....P...L.E..AGGV..G...L.AVIPGGSS.P..P........MD.DA...A...LG..
Retrocopy ERPGNYEIPLGTPFTKLLEL-AGGVRKG-RQLKAVIPGGSSSPVLPAHIMMDCTMDYDAISKAGSMLGSG

Parental  AIIVMNKSTDIVRAIARLIEFYKHESCGQCTPCR
          A.IVM..S.D.V....RL..FY.HESCGQCTPCR
Retrocopy ALIVMDDSRDMVESLLRLSYFYQHESCGQCTPCR

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	75.33 RPM
SRP007412_heart	0.00 RPM	344.72 RPM
SRP007412_kidney	0.00 RPM	344.72 RPM
SRP007412_liver	0.00 RPM	37.32 RPM
SRP007412_skeletal_muscle	0.00 RPM	274.26 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_49 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_49 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000005135	1 retrocopy	retro_meug_728,
Xenopus tropicalis	ENSXETG00000003396	1 retrocopy	retro_xtro_49 ,
Drosophila melanogaster	FBgn0031771	1 retrocopy	retro_dmel_59,