RetrogeneDB ID: retro_xtro_48

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL180709.1:6802..7204(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ndufs7
• Ensembl ID: ENSXETG00000003702
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) Fe-S protein 7, 20kDa (NADH-coenzyme Q reductase) [Source:Jamboree;Acc:XB-GENE-1008982]

Sequence

>retro_xtro_48
AAGGAAGGCTTCGTCACCACCAGCTATGACGCGGTGGTGAACTGGGCCAAAACCGGCTCCATCTGGCCCATGACCTTTGG
TCTGGCCTGCTGCGCGGTGGAGATGATGCATGCGGCCTCGGCGCGTTATGACCTGGCGCGCTTCGGCGCCGAGGTGTTCC
GCGCCAGTCCGCGCCAGTCCGACCTGATGATCGTGGCCGGCACGCTGTGCAACAAGATGGCGCCAGCCATGCGCAAGGTG
TACGACCAGATGTCCGAGCCGCGCTGGGTGCTGTCCATGGGCTCGTGCGCCAACGGCGGTGGCTACTACCACTACAGCTA
CTCGGTGGTGCGCGGCTGCGACCGCGTGGTGCCGGTAGATGTCTACGTGCCGGGCTGCCCGCCCACGGCAGAGGCGCTGA
TC

Alignment

ORF - retro_xtro_48 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.1 %
• Parental protein coverage: 61.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KGEFVITKLDELVNWARRSSLWPMTFGLACCAVEMMHMAAPRYDMDRFGV-VFRASPRQADVMIVAGTLT
          K..FV.T..D..VNWA...S.WPMTFGLACCAVEMMH.A..RYD..RFG..VFRASPRQ.D.MIVAGTL.
Retrocopy KEGFVTTSYDAVVNWAKTGSIWPMTFGLACCAVEMMHAASARYDLARFGAEVFRASPRQSDLMIVAGTLC

Parental  NKMAPALRKVYDQMPEPRYVVSMGSCANGGGYYHYSYSVVRGCDRIVPVDIYVPGCPPTAEALL
          NKMAPA.RKVYDQM.EPR.V.SMGSCANGGGYYHYSYSVVRGCDR.VPVD.YVPGCPPTAEAL.
Retrocopy NKMAPAMRKVYDQMSEPRWVLSMGSCANGGGYYHYSYSVVRGCDRVVPVDVYVPGCPPTAEALI

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	36.90 RPM
SRP007412_heart	0.00 RPM	134.63 RPM
SRP007412_kidney	0.00 RPM	134.63 RPM
SRP007412_liver	0.00 RPM	31.66 RPM
SRP007412_skeletal_muscle	0.00 RPM	111.76 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_48 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_48 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
Callithrix jacchus	ENSCJAG00000005587	1 retrocopy	retro_cjac_1242,
Macaca mulatta	ENSMMUG00000003045	1 retrocopy	retro_mmul_746,
Xenopus tropicalis	ENSXETG00000003702	1 retrocopy	retro_xtro_48 ,