RetrogeneDB ID: retro_itri_339

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393284.1:26382294..26382802(-)
• Located in intron of: ENSSTOG00000006525

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL9
• Ensembl ID: ENSSTOG00000002077
• Aliases: None
• Description: ribosomal protein L9 [Source:HGNC Symbol;Acc:10369]

Sequence

>retro_itri_339
ATGAAGACCATTCTCAGCAATCAGACTGTTGAAATTCCAGAAATTGACAGTATCACTCTGAAGGAACACACAGTTATCTT
TGAAGGCCTTAGAACTCTATAGAGAGACTTCAGTCACATCAGTGTGGAAGTCAGTCTCCTTGGGAAGAAAAAGGACAGGC
TCTGGTTGATAAATGGTAGGGGAAGAAAAAGGAACTGGTTACTCTTCACACTGTCTGTAATCATGTATACAACATAATCA
AGGGTTTTGTGCTGGGTTTCTGTTACAAGAAGTCCGTGTACATTCACTTTCCCATCAAGGTTGTATTCAGAAGAATGAGT
CTCTCTGGTTCAAGTCCAAAATTTCTTGGGTGAAAAATACATTCAGGGTTTAGATGATACCAGATGTTATTTGTTCAATA
TTTCAAGTCCAGAAGCATGATTTAATCCTTGGAGGACACAACATTGAACTTGTTTCAAACATAGCTGCTTTTATTTAGTA
AGGTAAAACAGTTAAAAAAACAAGGATA

Alignment

ORF - retro_itri_339 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.23 %
• Parental protein coverage: 89.58 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MKTILSNQTVDIPENVDITLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRL-RVDKWWGNRKELAT
          MKTILSNQTV.IPE...ITLK..TVI..G.R.TL.RDF.HI.VE.SLLGKKK.RL..VDKW.G..KEL.T
Retrocopy MKTILSNQTVEIPEIDSITLKEHTVIFEGLR-TL*RDFSHISVEVSLLGKKKDRL<LVDKW*GKKKELVT

Parental  VRTICSHVQNMIKGVTLGFRYKMRSVYAHFPINVVI-QENGSLVEIRN-FLG-EKYIRRVRMRTGVACSV
          ..T.C.HV.N.IKG..LGF.YK..SVY.HFPI.VV...E..SLV...N.FLG..K...RV.M...V.CS.
Retrocopy LHTVCNHVYNIIKGFVLGFCYK-KSVYIHFPIKVVF>EE*VSLVQVQN<FLG<VKNTFRV*MIPDVICSI

Parental  SQAQKDELILEGNDIELVSNSAALIQQATTVKNKDI
          .Q.QK..LIL.G..IELVSN.AA.I....TVK...I
Retrocopy FQVQKHDLILGGHNIELVSNIAAFI**GKTVKKTRI

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_339 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_339 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 15 parental genes, and 176 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000007317	1 retrocopy	retro_acar_163,
Cavia porcellus	ENSCPOG00000004543	15 retrocopies	retro_cpor_1037, retro_cpor_1160, retro_cpor_1264, retro_cpor_1400, retro_cpor_1483, retro_cpor_182, retro_cpor_346, retro_cpor_354, retro_cpor_395, retro_cpor_472, retro_cpor_530, retro_cpor_565, retro_cpor_628, retro_cpor_665, retro_cpor_684,
Danio rerio	ENSDARG00000037350	1 retrocopy	retro_drer_18,
Dasypus novemcinctus	ENSDNOG00000007411	18 retrocopies	retro_dnov_1298, retro_dnov_1560, retro_dnov_1684, retro_dnov_1845, retro_dnov_1877, retro_dnov_1936, retro_dnov_2148, retro_dnov_2277, retro_dnov_2624, retro_dnov_2659, retro_dnov_282, retro_dnov_407, retro_dnov_437, retro_dnov_450, retro_dnov_615, retro_dnov_787, retro_dnov_82, retro_dnov_975,
Dipodomys ordii	ENSDORG00000001088	6 retrocopies	retro_dord_276, retro_dord_42, retro_dord_435, retro_dord_604, retro_dord_637, retro_dord_718,
Erinaceus europaeus	ENSEEUG00000004394	39 retrocopies	retro_eeur_11, retro_eeur_136, retro_eeur_153, retro_eeur_162, retro_eeur_184, retro_eeur_191, retro_eeur_229, retro_eeur_246, retro_eeur_27, retro_eeur_279, retro_eeur_280, retro_eeur_282, retro_eeur_296, retro_eeur_307, retro_eeur_352, retro_eeur_383, retro_eeur_399, retro_eeur_410, retro_eeur_429, retro_eeur_433, retro_eeur_449, retro_eeur_453, retro_eeur_461, retro_eeur_471, retro_eeur_486, retro_eeur_493, retro_eeur_51, retro_eeur_540, retro_eeur_572, retro_eeur_590, retro_eeur_599, retro_eeur_600, retro_eeur_619, retro_eeur_624, retro_eeur_65, retro_eeur_670, retro_eeur_678, retro_eeur_68, retro_eeur_98,
Gadus morhua	ENSGMOG00000001002	1 retrocopy	retro_gmor_28,
Macropus eugenii	ENSMEUG00000016722	8 retrocopies	retro_meug_1087, retro_meug_1411, retro_meug_1961, retro_meug_22, retro_meug_440, retro_meug_490, retro_meug_650, retro_meug_763,
Myotis lucifugus	ENSMLUG00000004597	34 retrocopies	retro_mluc_1028, retro_mluc_1029, retro_mluc_1261, retro_mluc_1269, retro_mluc_127, retro_mluc_1320, retro_mluc_1368, retro_mluc_1380, retro_mluc_1572, retro_mluc_1655, retro_mluc_1704, retro_mluc_1757, retro_mluc_1813, retro_mluc_1858, retro_mluc_1880, retro_mluc_1983, retro_mluc_2041, retro_mluc_2067, retro_mluc_2112, retro_mluc_2119, retro_mluc_220, retro_mluc_2229, retro_mluc_223, retro_mluc_2230, retro_mluc_2370, retro_mluc_2428, retro_mluc_2495, retro_mluc_2611, retro_mluc_293, retro_mluc_461, retro_mluc_533, retro_mluc_648, retro_mluc_75, retro_mluc_895,
Monodelphis domestica	ENSMODG00000020553	7 retrocopies	retro_mdom_1026, retro_mdom_1078, retro_mdom_1261, retro_mdom_1352, retro_mdom_1414, retro_mdom_401, retro_mdom_637,
Mus musculus	ENSMUSG00000047215	2 retrocopies	retro_mmus_262, retro_mmus_81,
Otolemur garnettii	ENSOGAG00000004935	20 retrocopies	retro_ogar_117, retro_ogar_1223, retro_ogar_1471, retro_ogar_1614, retro_ogar_1694, retro_ogar_1807, retro_ogar_1884, retro_ogar_1906, retro_ogar_1933, retro_ogar_2162, retro_ogar_2173, retro_ogar_2806, retro_ogar_3036, retro_ogar_3115, retro_ogar_3276, retro_ogar_329, retro_ogar_429, retro_ogar_864, retro_ogar_886, retro_ogar_963,
Rattus norvegicus	ENSRNOG00000026716	3 retrocopies	retro_rnor_237, retro_rnor_310, retro_rnor_332,
Sarcophilus harrisii	ENSSHAG00000004918	8 retrocopies	retro_shar_191, retro_shar_192, retro_shar_236, retro_shar_340, retro_shar_359, retro_shar_406, retro_shar_600, retro_shar_607,
Ictidomys tridecemlineatus	ENSSTOG00000002077	13 retrocopies	retro_itri_1106, retro_itri_1182, retro_itri_1328, retro_itri_305, retro_itri_313, retro_itri_339 , retro_itri_392, retro_itri_588, retro_itri_663, retro_itri_838, retro_itri_908, retro_itri_914, retro_itri_956,