RetrogeneDB ID: retro_itri_1161

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393390.1:3788032..3788475(+)
• Located in intron of: ENSSTOG00000014542

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS7
• Ensembl ID: ENSSTOG00000024830
• Aliases: None
• Description: ribosomal protein S7 [Source:HGNC Symbol;Acc:10440]

Sequence

>retro_itri_1161
AAGGAAAATGAAGTTGGTGATGGTCACAAATTGGTTATCATCTTTGTTCTCATTCCTTAACTGAAATCTTTCTAGAAAGT
CTAAATCTAACTAGTACATGAATTGGAGAAAAAACTCAGCAGGAAGCACATTATCTTTATTTCTCAAAGAAGAATTCTGC
CTAAGCTAACTCAAAAAAAGTCATGCAAAAAATAAGCACTATGTCCCAGCAACTGCATTCTGACTGCTATGATTGATATG
ATCTTTGAGGACTTAGTCTTTGCAAATGAAATTGTGGGCAAGAAAATCTGAGTAAGACTGGATGGTAGCCAGTTCATAAA
GGCGTATTTGGACAAAGCACAGCAGAACAATGTGGAGCATGAGGCTGAAACCATTTTTTCTGGTGTGTTATAAGAAGCTC
ACAGGGCAAAGATATTAATTTTGAATTCATACAGTTTCTGTTA

Alignment

ORF - retro_itri_1161 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.09 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KEIEVGGGRKAIIIFVPVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPR
          KE.EVG.G.K..IIFV..P.LKSF.K....LV.ELEKK.S.KH..FI.QRRILPK.T.K...K.....P.
Retrocopy KENEVGDGHKLVIIFVLIP*LKSF*KV*I*LVHELEKKLSRKHIIFISQRRILPKLTQKKSCKK*ALCPS

Parental  SRTLTAVHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVET-FSGV-YKKLT-GKDV
          ...LTA..D.I.EDLVF..EIVGK.I.V.LDGS..IK..LDKAQQNNVEH..ET.FSGV.YKKLT.GKD.
Retrocopy NCILTAMIDMIFEDLVFANEIVGKKI*VRLDGSQFIKAYLDKAQQNNVEHEAETIFSGV>YKKLT>GKDI

Parental  NFEFPEFQL
          NFEF..F.L
Retrocopy NFEFIQFLL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_1161 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1161 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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 19 parental genes, and 105 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016462	2 retrocopies	retro_cjac_16, retro_cjac_2287,
Dasypus novemcinctus	ENSDNOG00000013285	14 retrocopies	retro_dnov_1091, retro_dnov_1351, retro_dnov_1388, retro_dnov_1459, retro_dnov_1688, retro_dnov_1849, retro_dnov_1940, retro_dnov_1970, retro_dnov_238, retro_dnov_2409, retro_dnov_558, retro_dnov_582, retro_dnov_623, retro_dnov_791,
Equus caballus	ENSECAG00000020253	2 retrocopies	retro_ecab_276, retro_ecab_396,
Felis catus	ENSFCAG00000023243	2 retrocopies	retro_fcat_1534, retro_fcat_41,
Gorilla gorilla	ENSGGOG00000023095	13 retrocopies	retro_ggor_2028, retro_ggor_2090, retro_ggor_2161, retro_ggor_218, retro_ggor_2452, retro_ggor_2927, retro_ggor_294, retro_ggor_2965, retro_ggor_3047, retro_ggor_346, retro_ggor_400, retro_ggor_484, retro_ggor_597,
Loxodonta africana	ENSLAFG00000015087	11 retrocopies	retro_lafr_1223, retro_lafr_160, retro_lafr_217, retro_lafr_318, retro_lafr_319, retro_lafr_413, retro_lafr_514, retro_lafr_720, retro_lafr_786, retro_lafr_964, retro_lafr_970,
Myotis lucifugus	ENSMLUG00000006121	1 retrocopy	retro_mluc_1118,
Macaca mulatta	ENSMMUG00000011870	7 retrocopies	retro_mmul_1831, retro_mmul_1846, retro_mmul_1929, retro_mmul_23, retro_mmul_2403, retro_mmul_2540, retro_mmul_357,
Mus musculus	ENSMUSG00000061477	2 retrocopies	retro_mmus_271, retro_mmus_53,
Nomascus leucogenys	ENSNLEG00000015407	10 retrocopies	retro_nleu_1505, retro_nleu_1771, retro_nleu_1783, retro_nleu_2278, retro_nleu_2346, retro_nleu_2510, retro_nleu_2892, retro_nleu_3080, retro_nleu_817, retro_nleu_835,
Oryctolagus cuniculus	ENSOCUG00000008507	2 retrocopies	retro_ocun_203, retro_ocun_230,
Otolemur garnettii	ENSOGAG00000028165	1 retrocopy	retro_ogar_133,
Pongo abelii	ENSPPYG00000025872	12 retrocopies	retro_pabe_1033, retro_pabe_1555, retro_pabe_2506, retro_pabe_2982, retro_pabe_2983, retro_pabe_31, retro_pabe_313, retro_pabe_360, retro_pabe_3659, retro_pabe_3803, retro_pabe_499, retro_pabe_524,
Pan troglodytes	ENSPTRG00000011615	3 retrocopies	retro_ptro_202, retro_ptro_3132, retro_ptro_58,
Pteropus vampyrus	ENSPVAG00000002071	7 retrocopies	retro_pvam_1051, retro_pvam_1183, retro_pvam_1330, retro_pvam_1437, retro_pvam_207, retro_pvam_543, retro_pvam_887,
Rattus norvegicus	ENSRNOG00000008551	2 retrocopies	retro_rnor_39, retro_rnor_391,
Sus scrofa	ENSSSCG00000027353	5 retrocopies	retro_sscr_136, retro_sscr_137, retro_sscr_240, retro_sscr_364, retro_sscr_956,
Ictidomys tridecemlineatus	ENSSTOG00000024830	3 retrocopies	retro_itri_1147, retro_itri_1161 , retro_itri_1215,
Tursiops truncatus	ENSTTRG00000001616	6 retrocopies	retro_ttru_1422, retro_ttru_1659, retro_ttru_1706, retro_ttru_301, retro_ttru_323, retro_ttru_773,