RetrogeneDB ID: retro_xtro_1

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL172695.1:2686650..2687226(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSXETG00000030340
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: rac1
• Ensembl ID: ENSXETG00000027593
• Aliases: None
• Description: ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) [Source:Jamboree;Acc:XB-GENE-489008]

Sequence

>retro_xtro_1
AAGATGAATTCCATAAAGTGTGTACTGGTGGGCGATGCTGCTGTCGGTAAGACAGCCCTTCTTGTACGCTTCACATCAGA
GGCATTCCCTGATTCATACAGACCCACAGTCTATGAGAACACAGGAGTGGATGTCTATATGGATGGTGTACAGATCAGCC
TTGGACTATGGGACACGGCAGGGAACGACGCGTTCAGAAGCATTCGTCCTCTTTCCCTTCAGAATGCAGACATTGTGTTA
CTGTGTTTTTCAGTGGCCAACCACACCTCATTTTTAAATGTAAGGAATAAGTGGATTGGTGAAGTGAGACAGCACTTGCC
TCGTATTCCTGTGCTTGTGGTGGCAACTCAGACTGACCAGAGGGAACTGGACCACATGCGACTTCCTTGCATTAACTCAA
TAGATGGCAAGCAACTAGCCCAGGATGTCCGAGCCAAAGGCTACTTGGAGTGTTCGGCTCTCAGTAACAGAGGAGTCCAG
CAGGTATTTGAGTGCGCAGTTAGGACAGCGATTAACCAGGCGAAGAAGAGGGCCAGGCGGCACCGTTTCCTGTCCCAAGA
ATGCAAAATCTTTTGA

Alignment

ORF - retro_xtro_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.41 %
• Parental protein coverage: 63.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPL
          M..IKCV.VGD.AVGKT.LL...T..AFP..Y.PTV..N....V..DG....LGLWDTAG.......RPL
Retrocopy MNSIKCVLVGDAAVGKTALLVRFTSEAFPDSYRPTVYENTGVDVYMDGVQISLGLWDTAGNDAFRSIRPL

Parental  SYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRD
          S....D..L.CFS.....SF.NVR.KW..EVR.H.P..P...V.T..D.R.
Retrocopy SLQNADIVLLCFSVANHTSFLNVRNKWIGEVRQHLPRIPVLVVATQTDQRE

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	490.11 RPM
SRP007412_heart	0.19 RPM	145.33 RPM
SRP007412_kidney	0.19 RPM	145.33 RPM
SRP007412_liver	0.96 RPM	72.67 RPM
SRP007412_skeletal_muscle	0.06 RPM	63.99 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_1 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_1 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 16 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009233	2 retrocopies	retro_btau_1601, retro_btau_332,
Canis familiaris	ENSCAFG00000015716	1 retrocopy	retro_cfam_496,
Felis catus	ENSFCAG00000011361	2 retrocopies	retro_fcat_1632, retro_fcat_717,
Homo sapiens	ENSG00000136238	6 retrocopies	retro_hsap_1256, retro_hsap_1925, retro_hsap_28, retro_hsap_3036, retro_hsap_3072, retro_hsap_4910,
Gorilla gorilla	ENSGGOG00000026733	2 retrocopies	retro_ggor_2110, retro_ggor_217,
Loxodonta africana	ENSLAFG00000012844	1 retrocopy	retro_lafr_818,
Myotis lucifugus	ENSMLUG00000009701	1 retrocopy	retro_mluc_1059,
Macaca mulatta	ENSMMUG00000021075	4 retrocopies	retro_mmul_1310, retro_mmul_1964, retro_mmul_2642, retro_mmul_721,
Mus musculus	ENSMUSG00000001847	2 retrocopies	retro_mmus_1372, retro_mmus_234,
Oryctolagus cuniculus	ENSOCUG00000009956	1 retrocopy	retro_ocun_305,
Pan troglodytes	ENSPTRG00000018910	4 retrocopies	retro_ptro_1288, retro_ptro_3044, retro_ptro_3274, retro_ptro_36,
Rattus norvegicus	ENSRNOG00000001068	1 retrocopy	retro_rnor_230,
Ictidomys tridecemlineatus	ENSSTOG00000006784	1 retrocopy	retro_itri_1503,
Tupaia belangeri	ENSTBEG00000007272	4 retrocopies	retro_tbel_1796, retro_tbel_2564, retro_tbel_4296, retro_tbel_9,
Tarsius syrichta	ENSTSYG00000001618	2 retrocopies	retro_tsyr_2027, retro_tsyr_2068,
Xenopus tropicalis	ENSXETG00000027593	1 retrocopy	retro_xtro_1 ,