RetrogeneDB ID: retro_itri_1222

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393406.1:1347826..1348210(+)
• Located in intron of: ENSSTOG00000008249

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000013481
• Aliases: None
• Description: None

Sequence

>retro_itri_1222
ATGGCGCTGAAACGGATTAATAAGGAACTTAGTGATTTGGCCCGTGACCCTCCAGCACAATGTTCTGCAGGTCCAGTTGG
GGATGATATGTTTCATTGGCAAGCCACAATTATGGGACCTAATGATAGCCCATATCATGGTGATGTATTCTTTTTGACAA
TTCATTTTCCTACAGACTTCAAACCACCTAAGGTTGCATTTACAACAAGAATTTATCATCCAAATATTAACACTAATGGC
AGCATTTGTCTTGATATTCTAAGATCACAATAGTCTCCTGCTTTAACTTTTCCTAAAGTTCTTTTATCCATTTTTCCACT
GCTATGTGATCCAAACCCAGATGACCCTTTAGTGCCAGAGATTGCACGGATCTATAAAACAGAG

Alignment

ORF - retro_itri_1222 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.79 %
• Parental protein coverage: 88.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MILKSFNSKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAF
          M.LK..N.KEL.DLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPY.G.VFFLTIHFPTD..FKPPKVAF
Retrocopy MALKRIN-KELSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYHGDVFFLTIHFPTD--FKPPKVAF

Parental  TTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTD
          TTRIYHPNIN.NGSICLDILRSQ.SPALT..KVLLSI..LLCDPNPDDPLVPEIARIYKT.
Retrocopy TTRIYHPNINTNGSICLDILRSQ*SPALTFPKVLLSIFPLLCDPNPDDPLVPEIARIYKTE

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_1222 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1222 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 30 parental genes, and 101 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004161	6 retrocopies	retro_btau_1421, retro_btau_1602, retro_btau_1739, retro_btau_1775, retro_btau_1851, retro_btau_1852,
Canis familiaris	ENSCAFG00000031041	5 retrocopies	retro_cfam_1191, retro_cfam_1439, retro_cfam_1602, retro_cfam_2034, retro_cfam_785,
Ciona intestinalis	ENSCING00000018711	2 retrocopies	retro_cint_19, retro_cint_29,
Callithrix jacchus	ENSCJAG00000015492	3 retrocopies	retro_cjac_512, retro_cjac_657, retro_cjac_791,
Ciona savignyi	ENSCSAVG00000006136	1 retrocopy	retro_csav_18,
Equus caballus	ENSECAG00000020678	1 retrocopy	retro_ecab_859,
Erinaceus europaeus	ENSEEUG00000014658	3 retrocopies	retro_eeur_263, retro_eeur_566, retro_eeur_591,
Echinops telfairi	ENSETEG00000001291	3 retrocopies	retro_etel_1218, retro_etel_1998, retro_etel_36,
Felis catus	ENSFCAG00000024918	2 retrocopies	retro_fcat_1106, retro_fcat_785,
Gorilla gorilla	ENSGGOG00000001368	2 retrocopies	retro_ggor_1156, retro_ggor_2321,
Gorilla gorilla	ENSGGOG00000010832	1 retrocopy	retro_ggor_953,
Loxodonta africana	ENSLAFG00000006878	2 retrocopies	retro_lafr_288, retro_lafr_290,
Macaca mulatta	ENSMMUG00000020666	3 retrocopies	retro_mmul_1298, retro_mmul_2143, retro_mmul_2246,
Monodelphis domestica	ENSMODG00000011783	2 retrocopies	retro_mdom_17, retro_mdom_884,
Mus musculus	ENSMUSG00000078578	11 retrocopies	retro_mmus_1818, retro_mmus_1895, retro_mmus_1913, retro_mmus_2293, retro_mmus_2635, retro_mmus_2643, retro_mmus_3119, retro_mmus_3636, retro_mmus_850, retro_mmus_875, retro_mmus_923,
Mus musculus	ENSMUSG00000091896	3 retrocopies	retro_mmus_2267, retro_mmus_27, retro_mmus_629,
Ornithorhynchus anatinus	ENSOANG00000005415	1 retrocopy	retro_oana_51,
Ochotona princeps	ENSOPRG00000011695	9 retrocopies	retro_opri_1042, retro_opri_1189, retro_opri_206, retro_opri_310, retro_opri_447, retro_opri_457, retro_opri_627, retro_opri_77, retro_opri_838,
Pongo abelii	ENSPPYG00000014967	1 retrocopy	retro_pabe_91,
Pongo abelii	ENSPPYG00000015844	6 retrocopies	retro_pabe_1016, retro_pabe_1164, retro_pabe_1257, retro_pabe_2330, retro_pabe_30, retro_pabe_3670,
Pan troglodytes	ENSPTRG00000017303	3 retrocopies	retro_ptro_26, retro_ptro_3141, retro_ptro_341,
Pteropus vampyrus	ENSPVAG00000015438	1 retrocopy	retro_pvam_234,
Rattus norvegicus	ENSRNOG00000013741	9 retrocopies	retro_rnor_2777, retro_rnor_342, retro_rnor_345, retro_rnor_539, retro_rnor_650, retro_rnor_724, retro_rnor_725, retro_rnor_772, retro_rnor_784,
Sus scrofa	ENSSSCG00000024306	1 retrocopy	retro_sscr_783,
Sus scrofa	ENSSSCG00000029822	4 retrocopies	retro_sscr_1016, retro_sscr_672, retro_sscr_673, retro_sscr_918,
Ictidomys tridecemlineatus	ENSSTOG00000013481	6 retrocopies	retro_itri_1222 , retro_itri_1474, retro_itri_1628, retro_itri_463, retro_itri_672, retro_itri_998,
Ictidomys tridecemlineatus	ENSSTOG00000016293	2 retrocopies	retro_itri_1528, retro_itri_655,
Ictidomys tridecemlineatus	ENSSTOG00000025799	2 retrocopies	retro_itri_1371, retro_itri_645,
Tupaia belangeri	ENSTBEG00000000270	5 retrocopies	retro_tbel_1336, retro_tbel_145, retro_tbel_1837, retro_tbel_262, retro_tbel_3134,
Tarsius syrichta	ENSTSYG00000005459	1 retrocopy	retro_tsyr_1421,