RetrogeneDB ID: retro_itri_400

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393289.1:18289397..18289887(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL17
• Ensembl ID: ENSSTOG00000005193
• Aliases: None
• Description: ribosomal protein L17 [Source:HGNC Symbol;Acc:10307]

Sequence

>retro_itri_400
TGCAAGTTAAGAGGTTCCAGTCTTCATATTCACCTCAGGAGCTCAGTGAAACGGCCCAGCCCATCAAACGTAGGTCTACC
CAAAAAGCCACCAAGTATCTGAAAGGCGTCACCTTACAGAAGCCATGTGTGCCATTCCATTATCACAGTGGTGGATTGGG
AGGTGTGCCCAGGCCAAACCTTGAGGCTGTACAAAGGGCCAGTGGTCCCCCCAAGAAAAGGTCTGAATTTTTGCTACACA
TGTTTCATAAGGCAGAGGGTGCTGCTGAACTTGAAAGGTTTCGGCAGATTCTGTGGCTACTGAGCACCTCCAGATGAACG
AGGCACCCAAGATGCACATCACACTCTCAGAGCCCAGGCTCAGGTTAACTCAGACACAAGCTCCCCCTCCCACATCAAGA
TGATTCCCCACTAAAGAACAAGTTATTCTTAAACCAGCAGAGGAGGTTGCACATAAGAAAAAGATGTTCCAGAAGAAACC
AAAGGAAAAA

Alignment

ORF - retro_itri_400 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.33 %
• Parental protein coverage: 89.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  CKSRGSNLRVHFKNT-RETAQAIKGMHIRKATKYLKDVTLKKQCVPFRRYNGG-VGRCAQQAKQWGWTQG
          CK.RGS.L..H......ETAQ.IK.....KATKYLK.VTL.K.CVPF....GG..GRCA.QAK..G.T.G
Retrocopy CKLRGSSLHIHLRSS<SETAQPIKRRSTQKATKYLKGVTLQKPCVPFHYHSGG<IGRCA-QAKP*GCTKG

Parental  RW-PK-KSAEFLLHMLKNAESNAELK-GLDVDSLVIEHIQVNKAPKMR-RRTYRAHGRINPYMSSPCHIE
          .W.P..K..EFLLHM...AE..AEL......DS...EH.Q.N.APKM....T.RA....N...SSP.HI.
Retrocopy QWSPQ>KRSEFLLHMFHKAEGAAELE<KVSADSVATEHLQMNEAPKMH<HHTLRAQAQVNSDTSSPSHIK

Parental  MI-LTEKEQIVPKPEEEVAQKKKISQKKLKKQ
          MI..T....I..KP.EEVA.KKK..QKK.K..
Retrocopy MI>PTKEQVIL-KPAEEVAHKKKMFQKKPKEK

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_400 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_400 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 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,