RetrogeneDB ID: retro_xtro_61

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL181797.1:10319..11546(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: sdha
• Ensembl ID: ENSXETG00000023408
• Aliases: None
• Description: succinate dehydrogenase complex, subunit A, flavoprotein (Fp) [Source:Jamboree;Acc:XB-GENE-956942]

Sequence

>retro_xtro_61
ACCCAAGCCAACATCACCAAACGCAAGTTCGACGTGGTCATCGTGGGTGCCGGCGGCTCCGGCATGCGCGCCTCGCTGGA
GCTGTCGCGCGCCGGTCTGAACGTGGCCTGCCTGTCCAAGGTCTTCCCCACCCGCTCGCACACCGTGGCCGCGCAGGGCG
GCGTATCCGCCTCGCTGGGCAACATGAGCGAGGACAACTGGCACTACCACTTCTACGACACCATCAAGGGCTCCGACTGG
CTCGGCGATCAGGACGCCATCGAATTCATGTGCCGCGAGGCGCCGAACGTGGTGATCGAACTCGAACACTTCGGCATGCC
GTTCGACCGCAACCCCGACGGCTCCATCTACCAGCGCCCCTTCGGCGGCCACACCGCCAACTACGGCGAGAAGCCCGTGC
AACGCGCCTGCGCTGCCGCCGACCGCACCGGCCATGCCATGCTGCACACGCTGTACCAGCAGAACGTCAAGTCCAGAACC
AACTTCTTCGTCGAGTGGATGGCGCTGGACCTGATCCGCAACACCCAGGGCGACGTGGTCGGCGTCACCGCACTGGAACT
CGAAACCGGCGACCTGTACCAGCTGCACGCCAAGGCCGTGCTGCTGGCCACCGGCGGCGCGGGCCGCATCTTCGCGGCAT
CGACCAACGCCTTCATCAACACCGGCGACGGCCTGGGCATGGCGGCACGCGCCGGCATCCCGCTGCAAGACATGGAGTTC
TGGCAATTCCACCCCACCGGCGTGGCAGGTGCAGGCGTGCTGCTGACCGAAGGCTGCCGCGGCGAAGGCGCAATTTTGCT
GAACAGCAACGGCGAGCGCTTCATGGAGCGCTACGCGCCCACCTTGAAGGACCTGGCACCGCGCGACTTCGTCTCGCGCT
CGATGGATCAGGAGATCAAGGAAGGCCGGGGCTGCGGCCCGAACAAGGACTACATCCTGATGAAGCTCGACCACCTGGGC
GCCGACACCATCCGCAAGCGCCTGCCCTCGGTGGAAGAAATCGGCCACAACTTCGCCAACGTGGACATCACCAAGGAACC
AATCCCCGTAGTGCCCACCATCCACTACCAGATGGGCGGCATCCCGACCACCATCAACGGCCAGGTCGTGGTGCACGACG
GGGTGCAAAACCAGATCGTCAACGGCCTCTATGCCGTGGGCGAATGCTCCTGCGTGTCGGTACACGGCGCCAACCGGCTG
GGCACGAACTCGCTGCTCGACCTGCTG

Alignment

ORF - retro_xtro_61 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.23 %
• Parental protein coverage: 61.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TQYPVVDHDFDAVVVGAGGAGLRAAFGLSEAGFNTACITKLFPTRSHTVAAQGGINAALGNMEDDDWRWH
          TQ.......FD.V.VGAGG.G.RA...LS.AG.N.AC..K.FPTRSHTVAAQGG..A.LGNM..D.W..H
Retrocopy TQANITKRKFDVVIVGAGGSGMRASLELSRAGLNVACLSKVFPTRSHTVAAQGGVSASLGNMSEDNWHYH

Parental  FYDTVKGSDWLGDQDAIHYMTEQAPASVIELENYGMPFSRTEQGKIYQRAFGGQSLKFGKGGQAHRCCCV
          FYDT.KGSDWLGDQDAI..M...AP..VIELE..GMPF.R...G.IYQR.FGG.....G......R.C..
Retrocopy FYDTIKGSDWLGDQDAIEFMCREAPNVVIELEHFGMPFDRNPDGSIYQRPFGGHTANYGEK-PVQRACAA

Parental  ADRTGHSLLHTLYGRSLRYDTSYFVEYFALDLLMEN-GECRGVIALCMEDGSIHRFRAKNTVIATGGYGR
          ADRTGH..LHTLY.......T..FVE..ALDL.....G...GV.AL..E.G......AK....ATGG.GR
Retrocopy ADRTGHAMLHTLYQQNVKSRTNFFVEWMALDLIRNTQGDVVGVTALELETGDLYQLHAKAVLLATGGAGR

Parental  TFFSCTSAHTCTGDGTAMVTRAGLPCQDLEFVQFHPTGIYGAGCLITEGCRGEGGILINSEGERFMERYA
          .F...T.A...TGDG..M..RAG.P.QD.EF.QFHPTG..GAG.L.TEGCRGEG.IL.NS.GERFMERYA
Retrocopy IFAASTNAFINTGDGLGMAARAGIPLQDMEFWQFHPTGVAGAGVLLTEGCRGEGAILLNSNGERFMERYA

Parental  PVAKDLASRDVVSRSMTIEIREGRGCGKDKDHVYLQLHHLPPSQLASRLPGISETAMIFAGVDVTKEPIP
          P..KDLA.RD.VSRSM..EI.EGRGCG..KD.....L.HL.......RLP...E....FA.VD.TKEPIP
Retrocopy PTLKDLAPRDFVSRSMDQEIKEGRGCGPNKDYILMKLDHLGADTIRKRLPSVEEIGHNFANVDITKEPIP

Parental  VLPTVHYNMGGIPTNYKGQVKNNRNVRAQLLGVIFVIVGNTLCCAIHSIDRLEXSGLLNNL
          V.PT.HY.MGGIPT...GQV.....V..Q........VG...C...H...RL....LL..L
Retrocopy VVPTIHYQMGGIPTTINGQVVVHDGVQNQIVNGLYA-VGECSCVSVHGANRLGTNSLLDLL

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	53.38 RPM
SRP007412_heart	0.00 RPM	262.62 RPM
SRP007412_kidney	0.00 RPM	262.62 RPM
SRP007412_liver	0.00 RPM	24.27 RPM
SRP007412_skeletal_muscle	0.00 RPM	286.84 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_61 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_61 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Nomascus leucogenys	ENSNLEG00000001292	1 retrocopy	retro_nleu_2643,
Ornithorhynchus anatinus	ENSOANG00000010157	1 retrocopy	retro_oana_90,
Xenopus tropicalis	ENSXETG00000023408	1 retrocopy	retro_xtro_61 ,
Drosophila melanogaster	FBgn0261439	1 retrocopy	retro_dmel_7,