RetrogeneDB ID: retro_xtro_3

Retrocopy location

• Organism: Xenopus (Xenopus tropicalis)
• Coordinates: GL172892.1:885660..886077(+)
• Located in intron of: ENSXETG00000000810

Retrocopy information

• Ensembl ID: ENSXETG00000000809
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: rpl14
• Ensembl ID: ENSXETG00000022018
• Aliases: None
• Description: ribosomal protein L14 [Source:Jamboree;Acc:XB-GENE-5819035]

Sequence

>retro_xtro_3
ATGGTATTCAAGCGTTACATCCAGATTGGCCGCGTAGCCTATGTCTCCTTTGGACCACACGCTGGCAAACTAGTGGCAAT
TGTTGATGTCATTGACCAAAACAGGGCCCTTGTAGATGGTCCTTGTACTGGAGTAAGACGTCAGGCTATGCCTTTTAAGT
GTATGCAGCTGACAGATTTTGTAATAAAGGTCCCACACAGTGCCCGTCAAAAGTATGTTCGACGTGCCTGGGAGAAAGCA
AATGTTAATGAGAAATGGAGTGCATCCAACTGGGCAAAGAAAATTGATGCAAGACAAAGGAAAGCAAAGATGACAGACTT
TGACTGCTACAAAGTTATGAAGGCAAAGAAGATGAGAAACAAGATCATCAGACATGAAATTAAAAAACTCCAAAAAAAGG
CTGTCAAGAAAGCATAA

Alignment

ORF - retro_xtro_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.35 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VFKRYVQIGRVAYVSFGPHAGKLVAIVDVIDQNRALVDGPCTGVRRQAMPFKCMQLTDFVIKVPHSARQK
          VFKRY.QIGRVAYVSFGPHAGKLVAIVDVIDQNRALVDGPCTGVRRQAMPFKCMQLTDFVIKVPHSARQK
Retrocopy VFKRYIQIGRVAYVSFGPHAGKLVAIVDVIDQNRALVDGPCTGVRRQAMPFKCMQLTDFVIKVPHSARQK

Parental  YVRRAWEKANVNEKWTASNWAKKIDARQRKAKMTDFDRYKVMKAKKMRNKIIRHEMKKLQKEAVKKA
          YVRRAWEKANVNEKW.ASNWAKKIDARQRKAKMTDFD.YKVMKAKKMRNKIIRHE.KKLQK.AVKKA
Retrocopy YVRRAWEKANVNEKWSASNWAKKIDARQRKAKMTDFDCYKVMKAKKMRNKIIRHEIKKLQKKAVKKA

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	3.95 RPM	177.17 RPM
SRP007412_heart	20.19 RPM	413.14 RPM
SRP007412_kidney	20.19 RPM	413.14 RPM
SRP007412_liver	33.65 RPM	1012.64 RPM
SRP007412_skeletal_muscle	7.52 RPM	191.78 RPM

ChIP-Seq

Xenopus tropicalis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xtro_3 retrocopy.

TSS

Xenopus tropicalis was not studied using FANTOM5 data.

Lab

retro_xtro_3 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 27 parental genes, and 88 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001709	4 retrocopies	retro_amel_1876, retro_amel_1933, retro_amel_296, retro_amel_660,
Canis familiaris	ENSCAFG00000005138	1 retrocopy	retro_cfam_31,
Callithrix jacchus	ENSCJAG00000017884	9 retrocopies	retro_cjac_1249, retro_cjac_1393, retro_cjac_1835, retro_cjac_2138, retro_cjac_2139, retro_cjac_2332, retro_cjac_2797, retro_cjac_3240, retro_cjac_630,
Cavia porcellus	ENSCPOG00000000711	1 retrocopy	retro_cpor_529,
Equus caballus	ENSECAG00000026813	2 retrocopies	retro_ecab_377, retro_ecab_743,
Echinops telfairi	ENSETEG00000012894	6 retrocopies	retro_etel_2117, retro_etel_2155, retro_etel_251, retro_etel_315, retro_etel_356, retro_etel_387,
Felis catus	ENSFCAG00000015655	4 retrocopies	retro_fcat_1000, retro_fcat_1457, retro_fcat_587, retro_fcat_671,
Homo sapiens	ENSG00000188846	6 retrocopies	retro_hsap_1015, retro_hsap_1047, retro_hsap_2796, retro_hsap_3104, retro_hsap_3352, retro_hsap_4777,
Gorilla gorilla	ENSGGOG00000025958	3 retrocopies	retro_ggor_122, retro_ggor_1945, retro_ggor_2272,
Latimeria chalumnae	ENSLACG00000015639	1 retrocopy	retro_lcha_29,
Microcebus murinus	ENSMICG00000009217	4 retrocopies	retro_mmur_1218, retro_mmur_1352, retro_mmur_279, retro_mmur_3,
Myotis lucifugus	ENSMLUG00000014429	4 retrocopies	retro_mluc_1294, retro_mluc_2263, retro_mluc_420, retro_mluc_563,
Monodelphis domestica	ENSMODG00000015262	2 retrocopies	retro_mdom_1499, retro_mdom_1939,
Mustela putorius furo	ENSMPUG00000017961	1 retrocopy	retro_mputfur_90,
Mus musculus	ENSMUSG00000025794	3 retrocopies	retro_mmus_2904, retro_mmus_2929, retro_mmus_3011,
Nomascus leucogenys	ENSNLEG00000005682	2 retrocopies	retro_nleu_763, retro_nleu_918,
Oryctolagus cuniculus	ENSOCUG00000010309	3 retrocopies	retro_ocun_410, retro_ocun_464, retro_ocun_656,
Pan troglodytes	ENSPTRG00000011963	4 retrocopies	retro_ptro_1893, retro_ptro_2100, retro_ptro_2135, retro_ptro_713,
Pteropus vampyrus	ENSPVAG00000013914	7 retrocopies	retro_pvam_1108, retro_pvam_1413, retro_pvam_246, retro_pvam_446, retro_pvam_683, retro_pvam_903, retro_pvam_904,
Rattus norvegicus	ENSRNOG00000019007	4 retrocopies	retro_rnor_2268, retro_rnor_2620, retro_rnor_415, retro_rnor_591,
Sorex araneus	ENSSARG00000003974	2 retrocopies	retro_sara_349, retro_sara_504,
Sarcophilus harrisii	ENSSHAG00000001591	5 retrocopies	retro_shar_397, retro_shar_539, retro_shar_696, retro_shar_737, retro_shar_788,
Sus scrofa	ENSSSCG00000011272	2 retrocopies	retro_sscr_521, retro_sscr_63,
Ictidomys tridecemlineatus	ENSSTOG00000021460	1 retrocopy	retro_itri_946,
Tarsius syrichta	ENSTSYG00000002161	5 retrocopies	retro_tsyr_1036, retro_tsyr_1404, retro_tsyr_176, retro_tsyr_361, retro_tsyr_956,
Tursiops truncatus	ENSTTRG00000006708	1 retrocopy	retro_ttru_113,
Xenopus tropicalis	ENSXETG00000022018	1 retrocopy	retro_xtro_3 ,