RetrogeneDB ID: retro_itri_1675

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393629.1:812560..813516(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000006868
• Aliases: None
• Description: None

Sequence

>retro_itri_1675
CCCATCGAGCATGGCATCGTCACCAACTGGGATGACATGGAGAAGATCTGGCACCATACCTTCTACAATGAGCTGCGCGT
GGCCCCCGAGGAGCACCCGGTGCTGCTGACGGAGGCCCCCCTGAACCCCAAGGCCAACAGAGAGATGACTCAGATCATGT
TCGAGACCTTCAACACATCGGCCATGTATGTGGCCATCCAGGCTGTGCTGTCCCTGTACGCCTCTGGACGCACCACTGGT
ATTGTCATGGACTCTGGTGACGGGGTCACCCACACGGTACCCATCTATGAGGGCTACGCCCTTCCCCACGCCATCCTGCG
TCTGGACCTGGCTGGCTGGGACCTGACAGACTACCTCATGAAGATCCTGACAGAGCGCGGCTACAGCTTTACCACCATGG
CCGAGCGGGAGATCATGCGCGACATCAAGGAGAAGCTGTGCTACGTTGCCCCGGACCTCGAGCAGGAGATGGCCACTGCT
GCATCCTCCTCCTCCCTGGATTAGAGCTACGAGCTACCCGATGGGCAGGTGATCACCATCGGCAACGAGTGGTTCCGGTG
TCCAGAGTCACTCTTCCAGCCCTCTTTCCTGGATATGGAATCTTCCAGCATCCACGAGACCACCTTCAACTCCATCATGA
AGTGTGATGTCGACATCCGCAAAGACCTCTATGCCAACACGGTGCTGTCGGGCGGCACCACCATGTACCCAGGCATCGCT
GACAGGATGCAGAAAGAGATCACAGCCCTGGCCCCCAGCACCATGAAGATCAAGATCATCGCGCCCCCCTGAGCGCAAGT
ACTCTGTGTTGATCGGTGGCTCCATCCTGGCCTCACTGTCCACCTTCCAGCAGATGTGGATCAGCAAGCAGGAGTACGAC
GAGTCGGGCCCCTCCATTGTCCACCGCAAATGCTTCTAGATGGACTGAGCAGGTGCCAGGCACCTGCTGCATGAGC

Alignment

ORF - retro_itri_1675 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.33 %
• Parental protein coverage: 81.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAV
          PIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANRE.MTQIMFETFNT.AMYVAIQAV
Retrocopy PIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANRE-MTQIMFETFNTSAMYVAIQAV

Parental  LSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIV
          LSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAG.DLTDYLMKILTERGYSFTT.AEREI.
Retrocopy LSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGWDLTDYLMKILTERGYSFTTMAEREIM

Parental  RDIKEKLCYVALDLEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESSGIHETTF
          RDIKEKLCYVA.DLEQEMATAASSSSL..SYELPDGQVITIGNE.FRCPE.LFQPSFL.MESS.IHETTF
Retrocopy RDIKEKLCYVAPDLEQEMATAASSSSLD*SYELPDGQVITIGNEWFRCPESLFQPSFLDMESSSIHETTF

Parental  NSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPP-ERKYSVWIGGSILAS
          NSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPP.ERKYSV.IGGSILAS
Retrocopy NSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPP>ERKYSVLIGGSILAS

Parental  LSTFQQMWISKQEYDESG-PPLSTANASRWTEQVPGTCCMS
          LSTFQQMWISKQEYDESG.PPLSTANASRWTEQVPGTCCMS
Retrocopy LSTFQQMWISKQEYDESG>PPLSTANASRWTEQVPGTCCMS

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_1675 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1675 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 52 parental genes, and 265 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015238	3 retrocopies	retro_acar_176, retro_acar_199, retro_acar_7,
Ailuropoda melanoleuca	ENSAMEG00000006601	1 retrocopy	retro_amel_11,
Ailuropoda melanoleuca	ENSAMEG00000016015	1 retrocopy	retro_amel_929,
Anas platyrhynchos	ENSAPLG00000010147	1 retrocopy	retro_apla_2,
Bos taurus	ENSBTAG00000006189	2 retrocopies	retro_btau_286, retro_btau_903,
Canis familiaris	ENSCAFG00000016020	3 retrocopies	retro_cfam_120, retro_cfam_260, retro_cfam_934,
Callithrix jacchus	ENSCJAG00000000008	2 retrocopies	retro_cjac_243, retro_cjac_56,
Callithrix jacchus	ENSCJAG00000002885	3 retrocopies	retro_cjac_139, retro_cjac_336, retro_cjac_377,
Cavia porcellus	ENSCPOG00000012101	1 retrocopy	retro_cpor_361,
Cavia porcellus	ENSCPOG00000013467	1 retrocopy	retro_cpor_60,
Dipodomys ordii	ENSDORG00000010079	1 retrocopy	retro_dord_11,
Equus caballus	ENSECAG00000015935	2 retrocopies	retro_ecab_271, retro_ecab_994,
Equus caballus	ENSECAG00000018600	1 retrocopy	retro_ecab_98,
Felis catus	ENSFCAG00000006788	1 retrocopy	retro_fcat_1613,
Felis catus	ENSFCAG00000026434	2 retrocopies	retro_fcat_257, retro_fcat_377,
Homo sapiens	ENSG00000075624	6 retrocopies	retro_hsap_1563, retro_hsap_1894, retro_hsap_3386, retro_hsap_38, retro_hsap_4204, retro_hsap_518,
Homo sapiens	ENSG00000184009	10 retrocopies	retro_hsap_1548, retro_hsap_1607, retro_hsap_2405, retro_hsap_2591, retro_hsap_2605, retro_hsap_3466, retro_hsap_3631, retro_hsap_409, retro_hsap_4818, retro_hsap_4935,
Gallus gallus	ENSGALG00000009621	1 retrocopy	retro_ggal_4,
Gallus gallus	ENSGALG00000028749	1 retrocopy	retro_ggal_6,
Gorilla gorilla	ENSGGOG00000001133	18 retrocopies	retro_ggor_1177, retro_ggor_1188, retro_ggor_1211, retro_ggor_1266, retro_ggor_1297, retro_ggor_1332, retro_ggor_1387, retro_ggor_1622, retro_ggor_1825, retro_ggor_1890, retro_ggor_2292, retro_ggor_2774, retro_ggor_2817, retro_ggor_3002, retro_ggor_352, retro_ggor_405, retro_ggor_44, retro_ggor_477,
Gorilla gorilla	ENSGGOG00000014043	6 retrocopies	retro_ggor_1495, retro_ggor_2338, retro_ggor_2449, retro_ggor_273, retro_ggor_413, retro_ggor_520,
Loxodonta africana	ENSLAFG00000009167	1 retrocopy	retro_lafr_116,
Macropus eugenii	ENSMEUG00000016247	57 retrocopies	retro_meug_1006, retro_meug_1010, retro_meug_1018, retro_meug_1042, retro_meug_105, retro_meug_1085, retro_meug_1147, retro_meug_1186, retro_meug_1200, retro_meug_1230, retro_meug_1237, retro_meug_1380, retro_meug_1414, retro_meug_1437, retro_meug_1529, retro_meug_1534, retro_meug_1557, retro_meug_1588, retro_meug_1613, retro_meug_1624, retro_meug_1654, retro_meug_1656, retro_meug_1664, retro_meug_1669, retro_meug_1708, retro_meug_1716, retro_meug_1723, retro_meug_1753, retro_meug_1763, retro_meug_18, retro_meug_1935, retro_meug_1969, retro_meug_197, retro_meug_1982, retro_meug_1991, retro_meug_2100, retro_meug_2176, retro_meug_218, retro_meug_270, retro_meug_333, retro_meug_370, retro_meug_379, retro_meug_468, retro_meug_506, retro_meug_556, retro_meug_574, retro_meug_581, retro_meug_61, retro_meug_735, retro_meug_790, retro_meug_833, retro_meug_90, retro_meug_900, retro_meug_915, retro_meug_924, retro_meug_925, retro_meug_959,
Meleagris gallopavo	ENSMGAG00000003960	2 retrocopies	retro_mgal_5, retro_mgal_6,
Microcebus murinus	ENSMICG00000014863	3 retrocopies	retro_mmur_23, retro_mmur_352, retro_mmur_6,
Macaca mulatta	ENSMMUG00000011153	1 retrocopy	retro_mmul_135,
Monodelphis domestica	ENSMODG00000002647	3 retrocopies	retro_mdom_187, retro_mdom_59, retro_mdom_89,
Mustela putorius furo	ENSMPUG00000011610	1 retrocopy	retro_mputfur_279,
Mustela putorius furo	ENSMPUG00000016612	2 retrocopies	retro_mputfur_440, retro_mputfur_461,
Mus musculus	ENSMUSG00000029580	7 retrocopies	retro_mmus_1613, retro_mmus_1677, retro_mmus_283, retro_mmus_2880, retro_mmus_3411, retro_mmus_3532, retro_mmus_761,
Mus musculus	ENSMUSG00000062825	7 retrocopies	retro_mmus_1043, retro_mmus_1524, retro_mmus_2383, retro_mmus_3128, retro_mmus_3265, retro_mmus_3607, retro_mmus_3705,
Nomascus leucogenys	ENSNLEG00000013385	15 retrocopies	retro_nleu_1008, retro_nleu_1058, retro_nleu_1059, retro_nleu_1150, retro_nleu_1347, retro_nleu_1474, retro_nleu_1729, retro_nleu_2193, retro_nleu_2393, retro_nleu_2574, retro_nleu_2669, retro_nleu_3032, retro_nleu_344, retro_nleu_813, retro_nleu_974,
Nomascus leucogenys	ENSNLEG00000015506	3 retrocopies	retro_nleu_1525, retro_nleu_1536, retro_nleu_1930,
Ornithorhynchus anatinus	ENSOANG00000007716	2 retrocopies	retro_oana_4, retro_oana_8,
Oryctolagus cuniculus	ENSOCUG00000005867	1 retrocopy	retro_ocun_720,
Otolemur garnettii	ENSOGAG00000008040	3 retrocopies	retro_ogar_148, retro_ogar_1808, retro_ogar_2430,
Otolemur garnettii	ENSOGAG00000008348	1 retrocopy	retro_ogar_2637,
Petromyzon marinus	ENSPMAG00000004161	1 retrocopy	retro_pmar_4,
Pongo abelii	ENSPPYG00000008735	11 retrocopies	retro_pabe_1091, retro_pabe_1391, retro_pabe_1727, retro_pabe_2187, retro_pabe_2308, retro_pabe_2621, retro_pabe_2945, retro_pabe_3381, retro_pabe_3475, retro_pabe_3760, retro_pabe_600,
Pongo abelii	ENSPPYG00000017336	23 retrocopies	retro_pabe_1281, retro_pabe_1292, retro_pabe_1575, retro_pabe_1610, retro_pabe_1772, retro_pabe_1816, retro_pabe_1911, retro_pabe_2042, retro_pabe_2168, retro_pabe_2175, retro_pabe_2188, retro_pabe_227, retro_pabe_2754, retro_pabe_2811, retro_pabe_2824, retro_pabe_2862, retro_pabe_2978, retro_pabe_309, retro_pabe_3563, retro_pabe_3567, retro_pabe_3746, retro_pabe_745, retro_pabe_86,
Pelodiscus sinensis	ENSPSIG00000002102	2 retrocopies	retro_psin_25, retro_psin_4,
Pan troglodytes	ENSPTRG00000018890	27 retrocopies	retro_ptro_1042, retro_ptro_1051, retro_ptro_1076, retro_ptro_1143, retro_ptro_1272, retro_ptro_1515, retro_ptro_1756, retro_ptro_178, retro_ptro_2122, retro_ptro_2173, retro_ptro_2349, retro_ptro_2454, retro_ptro_263, retro_ptro_2805, retro_ptro_2854, retro_ptro_314, retro_ptro_3207, retro_ptro_3219, retro_ptro_3282, retro_ptro_3287, retro_ptro_3292, retro_ptro_3302, retro_ptro_3307, retro_ptro_387, retro_ptro_432, retro_ptro_53, retro_ptro_584,
Rattus norvegicus	ENSRNOG00000034254	10 retrocopies	retro_rnor_1324, retro_rnor_1386, retro_rnor_1799, retro_rnor_2371, retro_rnor_2714, retro_rnor_2856, retro_rnor_2978, retro_rnor_351, retro_rnor_459, retro_rnor_935,
Rattus norvegicus	ENSRNOG00000036701	1 retrocopy	retro_rnor_715,
Sorex araneus	ENSSARG00000012197	1 retrocopy	retro_sara_267,
Sarcophilus harrisii	ENSSHAG00000012694	4 retrocopies	retro_shar_120, retro_shar_370, retro_shar_62, retro_shar_93,
Sus scrofa	ENSSSCG00000007585	1 retrocopy	retro_sscr_548,
Sus scrofa	ENSSSCG00000028355	1 retrocopy	retro_sscr_389,
Ictidomys tridecemlineatus	ENSSTOG00000006868	2 retrocopies	retro_itri_1675 , retro_itri_531,
Ictidomys tridecemlineatus	ENSSTOG00000014797	3 retrocopies	retro_itri_149, retro_itri_1881, retro_itri_4,
Tupaia belangeri	ENSTBEG00000010781	1 retrocopy	retro_tbel_422,
Xenopus tropicalis	ENSXETG00000025116	1 retrocopy	retro_xtro_6,