RetrogeneDB - Retrocopy retro_itri

						
>retro_itri_601
ATGGTTTACTACTCTCTTGATCCAGAAAGCCTCACAAAATCATGCACATCAGGAGATTCAAATATTTATATTCAGTTTAA

AAACACCCATGAAGCTGCCCAGACCATCGAGTGTATGCATATTCAAAAAGCCACCAAGTATCCAAAAGATGTCACTTCAT

AGAAGCAACATTTGCCAGTCCTTGGTTATAATGGTGGAGCTGACAGGTGTGCCCAGGCCAAACAGTGGGGCTGGGTGCAG

ATCAGTGGCCCAAAAACAGTGCTAATTTTTTTGCTGCATATATTTAAAAATGCAAAGTCATGCTTAACTTTGGGGTTTAG

ATGCAGACCTCTGGTCACTGAACACATCCAGGTGAACAAAGCACCCGAGATGCACTGCCACACTTACAGAACCCACGGTT

GGATCAATCCATACCCGAGCTCCTTCCCCTGTCACATGAGATGATCTTATTGGAAAGGAAAAAAATTCTTCCTAAACCAG

ATGAGGTGATTGTACGATAGGAAAAGATATCCCAGAATAAACCGAAGAAACAAAACTTATGGCACAGGAA

ORF - retro_itri_601 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	61.58 %
Parental protein coverage:	100. %
Number of stop codons detected:	2
Number of frameshifts detected	4

Retrocopy - Parental Gene Alignment:

									ParentalMVRYSLDPENPTKSCKSRGSNLRVHFKNTRETAQAIKGMHIRKATKYLKDVTLKKQCVPFRRYNGGVGRC
		MV.YSLDPE..TKSC.S..SN....FKNT.E.AQ.I..MHI.KATKY.KDVT..KQ..P...YNGG..RC
RetrocopyMVYYSLDPESLTKSCTSGDSNIYIQFKNTHEAAQTIECMHIQKATKYPKDVTS*KQHLPVLGYNGGADRC
ParentalAQQAKQWGWTQ-GRWPKKSAE-FLLHMLKNAESNAELKGLDVDSLVIEHIQVNKAPKMRRRTYRAHGRIN
		A.QAKQWGW.Q...WPK.SA..FLLH..KNA.S...L.G.....LV.EHIQVNKAP.M...TYR.HG.IN
RetrocopyA-QAKQWGWVQ<DQWPKNSAN>FLLHIFKNAKSCLTL-GFRCRPLVTEHIQVNKAPEMHCHTYRTHGWIN
ParentalPYMSS-PCHI-EMILTEKEQIVPKPEEEVAQKKKISQKKLKKQ-KLMARE
		PY.SS.PCH..EMIL.E...I.PKP.E......KISQ.K.KKQ.KLMA.E
RetrocopyPYPSSFPCHM<EMILLERKKILPKPDEVIVR*EKISQNKPKKQ<KLMAQE

							

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

						

RNA-Seq - click to see more details

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

ChIP-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_itri_601 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_601 was not experimentally validated.

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.

Parental genes homology:

Parental genes homology involve 13 parental genes, and 217 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000022902	5 retrocopies	retro_btau_164, retro_btau_221, retro_btau_4, retro_btau_50, retro_btau_75,
Echinops telfairi	ENSETEG00000011322	10 retrocopies	retro_etel_1787, retro_etel_1810, retro_etel_1900, retro_etel_1936, retro_etel_1954, retro_etel_207, retro_etel_396, retro_etel_470, retro_etel_565, retro_etel_831,
Homo sapiens	ENSG00000215472	1 retrocopy	retro_hsap_2367,
Latimeria chalumnae	ENSLACG00000008835	1 retrocopy	retro_lcha_38,
Macropus eugenii	ENSMEUG00000016709	26 retrocopies	retro_meug_1111, retro_meug_127, retro_meug_1285, retro_meug_1485, retro_meug_1821, retro_meug_188, retro_meug_1886, retro_meug_191, retro_meug_204, retro_meug_2159, retro_meug_2167, retro_meug_2183, retro_meug_257, retro_meug_326, retro_meug_355, retro_meug_373, retro_meug_410, retro_meug_413, retro_meug_509, retro_meug_58, retro_meug_703, retro_meug_738, retro_meug_740, retro_meug_779, retro_meug_81, retro_meug_934,
Myotis lucifugus	ENSMLUG00000025554	22 retrocopies	retro_mluc_1141, retro_mluc_1224, retro_mluc_1300, retro_mluc_1375, retro_mluc_1468, retro_mluc_1500, retro_mluc_1547, retro_mluc_1579, retro_mluc_1739, retro_mluc_1755, retro_mluc_1822, retro_mluc_1870, retro_mluc_1959, retro_mluc_2018, retro_mluc_2027, retro_mluc_2036, retro_mluc_2059, retro_mluc_2165, retro_mluc_2198, retro_mluc_719, retro_mluc_835, retro_mluc_929,
Myotis lucifugus	ENSMLUG00000029264	36 retrocopies	retro_mluc_1043, retro_mluc_1060, retro_mluc_1061, retro_mluc_1081, retro_mluc_1094, retro_mluc_1163, retro_mluc_1193, retro_mluc_1206, retro_mluc_123, retro_mluc_1230, retro_mluc_1241, retro_mluc_1416, retro_mluc_157, retro_mluc_1581, retro_mluc_1652, retro_mluc_1677, retro_mluc_1693, retro_mluc_170, retro_mluc_1711, retro_mluc_1848, retro_mluc_1890, retro_mluc_2003, retro_mluc_2064, retro_mluc_2095, retro_mluc_2125, retro_mluc_2387, retro_mluc_2636, retro_mluc_2637, retro_mluc_661, retro_mluc_734, retro_mluc_763, retro_mluc_779, retro_mluc_785, retro_mluc_807, retro_mluc_938, retro_mluc_977,
Macaca mulatta	ENSMMUG00000018837	26 retrocopies	retro_mmul_1015, retro_mmul_1046, retro_mmul_1205, retro_mmul_1216, retro_mmul_1225, retro_mmul_1441, retro_mmul_163, retro_mmul_172, retro_mmul_1784, retro_mmul_1858, retro_mmul_1952, retro_mmul_2006, retro_mmul_2008, retro_mmul_2257, retro_mmul_2268, retro_mmul_2284, retro_mmul_2304, retro_mmul_2512, retro_mmul_46, retro_mmul_474, retro_mmul_589, retro_mmul_652, retro_mmul_669, retro_mmul_825, retro_mmul_956, retro_mmul_971,
Monodelphis domestica	ENSMODG00000003534	11 retrocopies	retro_mdom_1153, retro_mdom_1194, retro_mdom_1437, retro_mdom_1734, retro_mdom_1783, retro_mdom_1980, retro_mdom_321, retro_mdom_337, retro_mdom_491, retro_mdom_541, retro_mdom_91,
Oryctolagus cuniculus	ENSOCUG00000012485	2 retrocopies	retro_ocun_1433, retro_ocun_231,
Pongo abelii	ENSPPYG00000009151	43 retrocopies	retro_pabe_1177, retro_pabe_1178, retro_pabe_1179, retro_pabe_1197, retro_pabe_1373, retro_pabe_1408, retro_pabe_1448, retro_pabe_1464, retro_pabe_1531, retro_pabe_1565, retro_pabe_1574, retro_pabe_1725, retro_pabe_1807, retro_pabe_1832, retro_pabe_1902, retro_pabe_2052, retro_pabe_2053, retro_pabe_2088, retro_pabe_2102, retro_pabe_2164, retro_pabe_2231, retro_pabe_2317, retro_pabe_2520, retro_pabe_2635, retro_pabe_2638, retro_pabe_2871, retro_pabe_2917, retro_pabe_2921, retro_pabe_2971, retro_pabe_3020, retro_pabe_3029, retro_pabe_3103, retro_pabe_3187, retro_pabe_3248, retro_pabe_3253, retro_pabe_3262, retro_pabe_3277, retro_pabe_347, retro_pabe_3493, retro_pabe_539, retro_pabe_567, retro_pabe_617, retro_pabe_882,
Ictidomys tridecemlineatus	ENSSTOG00000005193	33 retrocopies	retro_itri_1006, retro_itri_1015, retro_itri_1066, retro_itri_1070, retro_itri_1148, retro_itri_1212, retro_itri_1238, retro_itri_1312, retro_itri_1351, retro_itri_1360, retro_itri_1385, retro_itri_1424, retro_itri_1451, retro_itri_1476, retro_itri_1479, retro_itri_1625, retro_itri_1648, retro_itri_1712, retro_itri_181, retro_itri_213, retro_itri_300, retro_itri_320, retro_itri_400, retro_itri_425, retro_itri_513, retro_itri_575, retro_itri_601 , retro_itri_621, retro_itri_625, retro_itri_708, retro_itri_816, retro_itri_834, retro_itri_949,
Vicugna pacos	ENSVPAG00000009568	1 retrocopy	retro_vpac_10,

	RetrogeneDB ID:	retro_itri_601
Retrocopy location	Organism:	*Squirrel (Ictidomys tridecemlineatus)*
	Coordinates:	JH393305.1:12742414..12742964(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	RPL17
	Ensembl ID:	ENSSTOG00000005193
	Aliases:	None
	Description:	ribosomal protein L17 [Source:HGNC Symbol;Acc:10307]

Parental	MVRYSLDPENPTKSCKSRGSNLRVHFKNTRETAQAIKGMHIRKATKYLKDVTLKKQCVPFRRYNGGVGRC
	MV.YSLDPE..TKSC.S..SN....FKNT.E.AQ.I..MHI.KATKY.KDVT..KQ..P...YNGG..RC
Retrocopy	MVYYSLDPESLTKSCTSGDSNIYIQFKNTHEAAQTIECMHIQKATKYPKDVTS*KQHLPVLGYNGGADRC

Parental	AQQAKQWGWTQ-GRWPKKSAE-FLLHMLKNAESNAELKGLDVDSLVIEHIQVNKAPKMRRRTYRAHGRIN
	A.QAKQWGW.Q...WPK.SA..FLLH..KNA.S...L.G.....LV.EHIQVNKAP.M...TYR.HG.IN
Retrocopy	A-QAKQWGWVQ<DQWPKNSAN>FLLHIFKNAKSCLTL-GFRCRPLVTEHIQVNKAPEMHCHTYRTHGWIN

Parental	PYMSS-PCHI-EMILTEKEQIVPKPEEEVAQKKKISQKKLKKQ-KLMARE
	PY.SS.PCH..EMIL.E...I.PKP.E......KISQ.K.KKQ.KLMA.E
Retrocopy	PYPSSFPCHM<EMILLERKKILPKPDEVIVR*EKISQNKPKKQ<KLMAQE

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

RetrogeneDB ID:

retro_itri_601