RetrogeneDB ID: retro_xtro_53

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL180814.1:16776..17340(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: clpp
• Ensembl ID: ENSXETG00000005576
• Aliases: None
• Description: ClpP caseinolytic peptidase, ATP-dependent, proteolytic subunit homolog [Source:Jamboree;Acc:XB-GENE-969408]

Sequence

>retro_xtro_53
CTGATCCCCATGGTCATCGAGCAGTCGGGTCGTGGCGAACGGTCGTACGACATCTACTCACGCCTGCTCAAGGAGCGGGT
GGTTTTTTTGGTCGGGCCGGTCAACGACCAGTCTGCCAATCTGGTGGTGGCGCAGCTGCTGTTTCTGGAGAGCGAGAATC
CCGACAAGGACATTTCGTTCTACATCAACTCCCCGGGGGGGGCGGTCAGCGCCGGTCTGGCGATTTTCGACACCATGAAT
TTCATCAAGCCGGATGTTTCAACGCTGTGCACCGGCATGGCGGCCAGTATGGGCGCGTTTCTGCTGGCGGCGGGGGCCAA
GGGCAAGCGTTTCGCGTTGCCCAATTCCAAGGTGATGATCCACCAGCCGCTCGGCGGCATGCAGGGCCAGGCGACCGAGA
TCGAGATCCATGCGCGTGAAATCCTCAAGACCCGCGAGCAACTCAACCAGATTCTGGCGGAGCGCACCGGCCAGCCCCTG
GCAAAGATTCAGCAGGACACGGAGCGCGACTACTACCTGAGCGCCGCCGAAGCCCAGTCTTATGGTCTGGTGGATCAGGT
CATC

Alignment

ORF - retro_xtro_53 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.91 %
• Parental protein coverage: 70.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LVPIVVEQTGRGERAYDIYSRLLRERIICVMGPIDDSLSSLVVAQLLFLQSESNKKPIHMYINSPGGSVT
          L.P.V.EQ.GRGER.YDIYSRLL.ER.....GP..D....LVVAQLLFL.SE...K.I..YINS....V.
Retrocopy LIPMVIEQSGRGERSYDIYSRLLKERVVFLVGPVNDQSANLVVAQLLFLESENPDKDISFYINSXXXXVS

Parental  AGLAIYDTMQYILNPICTWCVGQAASMGSLLLAAGSSGMRHSLPNSRIMIHQPSGGARGQATDIAIQAEE
          AGLAI.DTM..I.....T.C.G.AASMG..LLAAG..G.R..LPNS..MIHQP.GG..GQAT.I.I.A.E
Retrocopy AGLAIFDTMNFIKPDVSTLCTGMAASMGAFLLAAGAKGKRFALPNSKVMIHQPLGGMQGQATEIEIHARE

Parental  ILKLKKQINEIYAKHTRQPLSVIESVMERDRYMSPTEAQEFGILDKVL
          ILK...Q.N.I.A..T.QPL..I....ERD.Y.S..EAQ..G..D.V.
Retrocopy ILKTREQLNQILAERTGQPLAKIQQDTERDYYLSAAEAQSYGLVDQVI

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	14.75 RPM
SRP007412_heart	0.00 RPM	15.76 RPM
SRP007412_kidney	0.00 RPM	15.76 RPM
SRP007412_liver	0.00 RPM	16.52 RPM
SRP007412_skeletal_muscle	0.00 RPM	15.41 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_53 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_53 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016699	1 retrocopy	retro_cjac_2380,
Microcebus murinus	ENSMICG00000006284	1 retrocopy	retro_mmur_1142,
Myotis lucifugus	ENSMLUG00000007981	1 retrocopy	retro_mluc_2501,
Xenopus tropicalis	ENSXETG00000005576	1 retrocopy	retro_xtro_53 ,