RetrogeneDB ID: retro_xtro_50

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL180709.1:12225..12705(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ndufs8
• Ensembl ID: ENSXETG00000020882
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) Fe-S protein 8, 23kDa (NADH-coenzyme Q reductase) [Source:Jamboree;Acc:XB-GENE-945877]

Sequence

>retro_xtro_50
TCGATCAAGGACTTTCTCAAGAGCTTCATCCTGTGGGAACTCGCCAAGGGCATGGTTCTGACGGGGCGCTATGCCTTCGC
GCGCAAAGTCACCGTGTACTACCCGGAGGAAAAGACGCCGCTGTCGCCGCGTTTTCGCGGGCTGCACGCGCTGCGCCGCT
ATGACAACGGCGAGGAGCGCTGCATTGCCTGCAAGCTGTGCGAGGCCGTATGCCCGGCCATGGCCATCACCATCGAGTCC
GACGTGCGCGCCGATGGCTCACGCCGCACCACGCGCTACGACATCGACCTGACCAAGTGCATCTTCTGCGGTTTCTGCGA
GGAAAGCTGTCCGGTGGATTCGATCGTGGAAACGCAGATCTTCGAATACCACGGCGAAAAGCGCGGTGATCTGTACTTCA
CCAAGGACATGCTTCTGGCCGTTGGCGATCGCTACGAACCCCAGATCGCCGCAGCCAAGGCTGCGGACGCCAAATACCGT

Alignment

ORF - retro_xtro_50 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.63 %
• Parental protein coverage: 77.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SVTDRAAQTLLWTELFRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEA
          S..D......LW.EL..G...T..Y.F....T..YP.EK.PLSPRFRG.HALRRY..GEERCIACKLCEA
Retrocopy SIKDFLKSFILW-ELAKGMVLTGRYAFARKVTVYYPEEKTPLSPRFRGLHALRRYDNGEERCIACKLCEA

Parental  VCPAQAITIEAEPRTDGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTETHEELLYNKEKLL
          VCPA.AITIE...R.DGSRRTTRYDID.TKCI.CGFC.E.CPVD.IVE...FE...E....L...K..LL
Retrocopy VCPAMAITIESDVRADGSRRTTRYDIDLTKCIFCGFCEESCPVDSIVETQIFEYHGEKRGDLYFTKDMLL

Parental  NNGDKWEVEIGANIQADFLYR
          ..GD..E..I.A...AD..YR
Retrocopy AVGDRYEPQIAAAKAADAKYR

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	39.19 RPM
SRP007412_heart	0.00 RPM	168.69 RPM
SRP007412_kidney	0.00 RPM	168.69 RPM
SRP007412_liver	0.00 RPM	20.45 RPM
SRP007412_skeletal_muscle	0.00 RPM	85.93 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_50 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_50 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 3 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011083	2 retrocopies	retro_cfam_1258, retro_cfam_129,
Callithrix jacchus	ENSCJAG00000015686	4 retrocopies	retro_cjac_1088, retro_cjac_1652, retro_cjac_2237, retro_cjac_3810,
Xenopus tropicalis	ENSXETG00000020882	1 retrocopy	retro_xtro_50 ,