RetrogeneDB ID: retro_itri_3

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393348.1:6555358..6555748(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000028320
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000020092
• Aliases: None
• Description: None

Sequence

>retro_itri_3
ATGTCGTTTCCAAAGTATAAGCAAGCCCTCAGAGTTGGGCCACTCTACCCCGACCCTCGACCCCGATATGACATATCTCC
GGAAACCCAGAAGGTGCAAGCCAAGAGGTTGGCCATAAGAGCCCGGCTTAAACTGGAGTATCTGCTTCAGTACAACGACC
CCAACCACCAAGGGCTCATTGAAGATCCTGCCTTAATTTGCTGGACCTACGAAAGATCAGCAAATATCTACCCAAATTTC
AGACCCACTCCCAAGAACTCACTCTTAGGAGCTCTGTTTGGAATTGGAGCCCTCTTCTTCTGGTATTATGTTTTCAAAAC
TGATAGGGATAGGAAGGAAAAACTTATCCAGGTAGGAAAATTGGACCTAAAATTTAATATCTCCTATTAG

Alignment

ORF - retro_itri_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.31 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSFPKYKPS-RLATLPPTLDPAEYDISPETRKAQAERLAIRARLKREYLLQYNDPNRRGLIEDPALIRWT
          MSFPKYK...R...L.P...P..YDISPET.K.QA.RLAIRARLK.EYLLQYNDPN..GLIEDPALI.WT
Retrocopy MSFPKYKQALRVGPLYPDPRP-RYDISPETQKVQAKRLAIRARLKLEYLLQYNDPNHQGLIEDPALICWT

Parental  YARSANIYPNFRPTPKNSLLGALFGIGPLFFWYYVFKTDRDRKEKLIQEGKLDRKFNISY
          Y.RSANIYPNFRPTPKNSLLGALFGIG.LFFWYYVFKTDRDRKEKLIQ.GKLD.KFNISY
Retrocopy YERSANIYPNFRPTPKNSLLGALFGIGALFFWYYVFKTDRDRKEKLIQVGKLDLKFNISY

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_3 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_3 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 26 parental genes, and 76 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000011462	1 retrocopy	retro_acar_74,
Ailuropoda melanoleuca	ENSAMEG00000004761	2 retrocopies	retro_amel_1289, retro_amel_1491,
Bos taurus	ENSBTAG00000015892	2 retrocopies	retro_btau_184, retro_btau_995,
Choloepus hoffmanni	ENSCHOG00000000006	2 retrocopies	retro_chof_188, retro_chof_777,
Callithrix jacchus	ENSCJAG00000008695	4 retrocopies	retro_cjac_1290, retro_cjac_2140, retro_cjac_302, retro_cjac_3251,
Danio rerio	ENSDARG00000019332	1 retrocopy	retro_drer_32,
Dasypus novemcinctus	ENSDNOG00000024123	4 retrocopies	retro_dnov_1290, retro_dnov_1833, retro_dnov_394, retro_dnov_486,
Homo sapiens	ENSG00000065518	6 retrocopies	retro_hsap_1378, retro_hsap_1729, retro_hsap_2238, retro_hsap_2656, retro_hsap_2926, retro_hsap_3103,
Gorilla gorilla	ENSGGOG00000013923	2 retrocopies	retro_ggor_1853, retro_ggor_2265,
Loxodonta africana	ENSLAFG00000021459	1 retrocopy	retro_lafr_1078,
Microcebus murinus	ENSMICG00000005226	4 retrocopies	retro_mmur_1409, retro_mmur_1415, retro_mmur_882, retro_mmur_915,
Myotis lucifugus	ENSMLUG00000027951	3 retrocopies	retro_mluc_1433, retro_mluc_2010, retro_mluc_489,
Macaca mulatta	ENSMMUG00000001592	4 retrocopies	retro_mmul_1217, retro_mmul_1514, retro_mmul_1979, retro_mmul_356,
Monodelphis domestica	ENSMODG00000018229	1 retrocopy	retro_mdom_1658,
Mustela putorius furo	ENSMPUG00000008272	1 retrocopy	retro_mputfur_81,
Mus musculus	ENSMUSG00000022820	4 retrocopies	retro_mmus_1075, retro_mmus_1077, retro_mmus_1405, retro_mmus_1820,
Nomascus leucogenys	ENSNLEG00000007706	4 retrocopies	retro_nleu_134, retro_nleu_2889, retro_nleu_2989, retro_nleu_762,
Otolemur garnettii	ENSOGAG00000005956	5 retrocopies	retro_ogar_1454, retro_ogar_1917, retro_ogar_1922, retro_ogar_2874, retro_ogar_3091,
Pongo abelii	ENSPPYG00000013503	3 retrocopies	retro_pabe_1526, retro_pabe_2500, retro_pabe_2565,
Pan troglodytes	ENSPTRG00000015270	6 retrocopies	retro_ptro_1226, retro_ptro_1582, retro_ptro_1791, retro_ptro_1980, retro_ptro_2099, retro_ptro_947,
Rattus norvegicus	ENSRNOG00000002721	3 retrocopies	retro_rnor_275, retro_rnor_291, retro_rnor_99,
Sorex araneus	ENSSARG00000012482	1 retrocopy	retro_sara_600,
Ictidomys tridecemlineatus	ENSSTOG00000020092	3 retrocopies	retro_itri_3 , retro_itri_666, retro_itri_786,
Tarsius syrichta	ENSTSYG00000006456	7 retrocopies	retro_tsyr_1062, retro_tsyr_109, retro_tsyr_1617, retro_tsyr_1635, retro_tsyr_410, retro_tsyr_627, retro_tsyr_736,
Tursiops truncatus	ENSTTRG00000016658	1 retrocopy	retro_ttru_625,
Vicugna pacos	ENSVPAG00000003774	1 retrocopy	retro_vpac_251,