RetrogeneDB ID: retro_csav_25

Retrocopy location

• Organism: Pacific transparent sea squirt (Ciona savignyi)
• Coordinates: reftig_431:115299..115575(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSA.1484
• Ensembl ID: ENSCSAVG00000009653
• Aliases: None
• Description: None

Sequence

>retro_csav_25
ATGAATAAAGACAAATTAACCAAGTTGCAAAATGAAGTAACGATGAGAGGAAAGGGATCACCTCGAAGAAAGCGTAAATT
TGTTCGTCGAAGAGCCACGATCGATGAAAAGAAATTGCAAAGTTTGTTGGAAAAAATAGCTGTGAAAACTATCCCCGGGT
TCGATGAAGTGGATATGATTAAGGACGACGGCAACGTAATTCACTTTAACAAACCGAACGTTCAGATTTCTTTGTCAGCG
AATACAACCGTGGTGACCGGTCACGCTGAGAACCAA

Alignment

ORF - retro_csav_25 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.65 %
• Parental protein coverage: 85.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNKDKLNKLQDQVRIGGKGSARRKRKVVHRTATTDDKKLQSSLKKLAVNNIPGIEEVNMIKDDGNVIHFN
          MNKDKL.KLQ..V...GKGS.RRKRK.V.R.AT.D.KKLQS.L.K.AV..IPG..EV.MIKDDGNVIHFN
Retrocopy MNKDKLTKLQNEVTMRGKGSPRRKRKFVRRRATIDEKKLQSLLEKIAVKTIPGFDEVDMIKDDGNVIHFN

Parental  NPKVQASPSANTFAVTGHAENK
          .P.VQ.S.SANT..VTGHAEN.
Retrocopy KPNVQISLSANTTVVTGHAENQ

Legend:

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

Expression

RNA-Seq

Ciona savignyi was not studied using RNA-Seq expression data.

ChIP-Seq

Ciona savignyi was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_csav_25 retrocopy.

TSS

Ciona savignyi was not studied using FANTOM5 data.

Lab

retro_csav_25 was not experimentally validated.

Homology

Retrocopy orthology:

Ciona savignyi 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 59 parental genes, and 340 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011563	14 retrocopies	retro_amel_1257, retro_amel_1279, retro_amel_1324, retro_amel_1334, retro_amel_1433, retro_amel_166, retro_amel_1769, retro_amel_182, retro_amel_1841, retro_amel_480, retro_amel_513, retro_amel_784, retro_amel_908, retro_amel_986,
Bos taurus	ENSBTAG00000010012	5 retrocopies	retro_btau_1161, retro_btau_1344, retro_btau_1361, retro_btau_459, retro_btau_551,
Bos taurus	ENSBTAG00000011025	1 retrocopy	retro_btau_1030,
Canis familiaris	ENSCAFG00000003782	2 retrocopies	retro_cfam_2135, retro_cfam_938,
Canis familiaris	ENSCAFG00000008212	3 retrocopies	retro_cfam_1660, retro_cfam_1741, retro_cfam_531,
Choloepus hoffmanni	ENSCHOG00000001861	13 retrocopies	retro_chof_1027, retro_chof_1166, retro_chof_117, retro_chof_1397, retro_chof_1406, retro_chof_1884, retro_chof_1960, retro_chof_2194, retro_chof_2682, retro_chof_2703, retro_chof_344, retro_chof_364, retro_chof_700,
Callithrix jacchus	ENSCJAG00000016600	4 retrocopies	retro_cjac_1454, retro_cjac_1673, retro_cjac_2640, retro_cjac_281,
Callithrix jacchus	ENSCJAG00000021582	4 retrocopies	retro_cjac_2000, retro_cjac_2929, retro_cjac_4160, retro_cjac_451,
Cavia porcellus	ENSCPOG00000004006	1 retrocopy	retro_cpor_908,
Cavia porcellus	ENSCPOG00000012832	1 retrocopy	retro_cpor_81,
Ciona savignyi	ENSCSAVG00000009653	1 retrocopy	retro_csav_25 ,
Dasypus novemcinctus	ENSDNOG00000003181	4 retrocopies	retro_dnov_1690, retro_dnov_1928, retro_dnov_2672, retro_dnov_921,
Dasypus novemcinctus	ENSDNOG00000018682	4 retrocopies	retro_dnov_1958, retro_dnov_2107, retro_dnov_497, retro_dnov_817,
Dipodomys ordii	ENSDORG00000014031	5 retrocopies	retro_dord_287, retro_dord_341, retro_dord_422, retro_dord_54, retro_dord_66,
Equus caballus	ENSECAG00000021629	1 retrocopy	retro_ecab_200,
Erinaceus europaeus	ENSEEUG00000004502	3 retrocopies	retro_eeur_215, retro_eeur_447, retro_eeur_456,
Echinops telfairi	ENSETEG00000011923	11 retrocopies	retro_etel_1017, retro_etel_1167, retro_etel_1207, retro_etel_1409, retro_etel_1990, retro_etel_2113, retro_etel_2203, retro_etel_291, retro_etel_663, retro_etel_804, retro_etel_953,
Echinops telfairi	ENSETEG00000017341	5 retrocopies	retro_etel_1216, retro_etel_1394, retro_etel_1997, retro_etel_405, retro_etel_960,
Felis catus	ENSFCAG00000023973	10 retrocopies	retro_fcat_1044, retro_fcat_1378, retro_fcat_1438, retro_fcat_187, retro_fcat_188, retro_fcat_225, retro_fcat_28, retro_fcat_419, retro_fcat_593, retro_fcat_919,
Homo sapiens	ENSG00000134717	3 retrocopies	retro_hsap_2173, retro_hsap_2514, retro_hsap_3669,
Homo sapiens	ENSG00000145741	11 retrocopies	retro_hsap_1215, retro_hsap_1396, retro_hsap_2259, retro_hsap_2525, retro_hsap_2819, retro_hsap_2964, retro_hsap_3533, retro_hsap_3551, retro_hsap_3972, retro_hsap_4270, retro_hsap_625,
Gorilla gorilla	ENSGGOG00000000166	10 retrocopies	retro_ggor_1082, retro_ggor_1682, retro_ggor_1961, retro_ggor_2054, retro_ggor_2399, retro_ggor_2647, retro_ggor_2667, retro_ggor_548, retro_ggor_81, retro_ggor_946,
Loxodonta africana	ENSLAFG00000016124	3 retrocopies	retro_lafr_206, retro_lafr_769, retro_lafr_947,
Macropus eugenii	ENSMEUG00000006135	10 retrocopies	retro_meug_1114, retro_meug_1164, retro_meug_1333, retro_meug_1395, retro_meug_1512, retro_meug_1663, retro_meug_2008, retro_meug_298, retro_meug_903, retro_meug_966,
Microcebus murinus	ENSMICG00000002807	1 retrocopy	retro_mmur_804,
Microcebus murinus	ENSMICG00000017182	3 retrocopies	retro_mmur_1219, retro_mmur_1301, retro_mmur_651,
Myotis lucifugus	ENSMLUG00000012912	11 retrocopies	retro_mluc_1024, retro_mluc_1349, retro_mluc_1459, retro_mluc_1748, retro_mluc_1820, retro_mluc_1823, retro_mluc_2560, retro_mluc_2602, retro_mluc_482, retro_mluc_682, retro_mluc_694,
Myotis lucifugus	ENSMLUG00000016884	1 retrocopy	retro_mluc_912,
Macaca mulatta	ENSMMUG00000003636	1 retrocopy	retro_mmul_59,
Macaca mulatta	ENSMMUG00000022291	2 retrocopies	retro_mmul_105, retro_mmul_2424,
Monodelphis domestica	ENSMODG00000000770	2 retrocopies	retro_mdom_33, retro_mdom_992,
Monodelphis domestica	ENSMODG00000001762	3 retrocopies	retro_mdom_189, retro_mdom_454, retro_mdom_931,
Mustela putorius furo	ENSMPUG00000005864	28 retrocopies	retro_mputfur_1125, retro_mputfur_1149, retro_mputfur_1267, retro_mputfur_1289, retro_mputfur_1319, retro_mputfur_1321, retro_mputfur_1386, retro_mputfur_1414, retro_mputfur_1472, retro_mputfur_1525, retro_mputfur_1548, retro_mputfur_1576, retro_mputfur_1599, retro_mputfur_246, retro_mputfur_324, retro_mputfur_392, retro_mputfur_403, retro_mputfur_431, retro_mputfur_618, retro_mputfur_661, retro_mputfur_724, retro_mputfur_728, retro_mputfur_753, retro_mputfur_760, retro_mputfur_795, retro_mputfur_901, retro_mputfur_926, retro_mputfur_972,
Mustela putorius furo	ENSMPUG00000006966	2 retrocopies	retro_mputfur_1444, retro_mputfur_924,
Mus musculus	ENSMUSG00000021660	11 retrocopies	retro_mmus_1904, retro_mmus_2445, retro_mmus_2769, retro_mmus_3054, retro_mmus_3272, retro_mmus_3344, retro_mmus_3525, retro_mmus_443, retro_mmus_451, retro_mmus_470, retro_mmus_707,
Mus musculus	ENSMUSG00000028568	2 retrocopies	retro_mmus_1134, retro_mmus_2743,
Nomascus leucogenys	ENSNLEG00000004718	9 retrocopies	retro_nleu_1081, retro_nleu_1199, retro_nleu_1284, retro_nleu_1446, retro_nleu_1797, retro_nleu_2526, retro_nleu_451, retro_nleu_496, retro_nleu_734,
Nomascus leucogenys	ENSNLEG00000016041	2 retrocopies	retro_nleu_1439, retro_nleu_521,
Oryctolagus cuniculus	ENSOCUG00000001517	3 retrocopies	retro_ocun_1001, retro_ocun_1412, retro_ocun_1912,
Oryctolagus cuniculus	ENSOCUG00000024914	6 retrocopies	retro_ocun_1186, retro_ocun_1299, retro_ocun_1364, retro_ocun_446, retro_ocun_857, retro_ocun_916,
Otolemur garnettii	ENSOGAG00000013918	1 retrocopy	retro_ogar_46,
Otolemur garnettii	ENSOGAG00000030256	2 retrocopies	retro_ogar_2759, retro_ogar_570,
Ochotona princeps	ENSOPRG00000013335	2 retrocopies	retro_opri_719, retro_opri_974,
Procavia capensis	ENSPCAG00000006428	3 retrocopies	retro_pcap_129, retro_pcap_307, retro_pcap_373,
Pongo abelii	ENSPPYG00000001353	2 retrocopies	retro_pabe_1850, retro_pabe_3010,
Pongo abelii	ENSPPYG00000029576	14 retrocopies	retro_pabe_1154, retro_pabe_1477, retro_pabe_180, retro_pabe_1885, retro_pabe_1956, retro_pabe_2207, retro_pabe_2458, retro_pabe_2918, retro_pabe_2919, retro_pabe_2932, retro_pabe_3329, retro_pabe_3484, retro_pabe_558, retro_pabe_649,
Pan troglodytes	ENSPTRG00000000735	3 retrocopies	retro_ptro_1459, retro_ptro_1658, retro_ptro_2489,
Pan troglodytes	ENSPTRG00000016979	12 retrocopies	retro_ptro_1470, retro_ptro_1599, retro_ptro_1675, retro_ptro_1912, retro_ptro_2006, retro_ptro_2413, retro_ptro_2494, retro_ptro_2697, retro_ptro_2896, retro_ptro_455, retro_ptro_832, retro_ptro_959,
Pteropus vampyrus	ENSPVAG00000007160	11 retrocopies	retro_pvam_1011, retro_pvam_241, retro_pvam_301, retro_pvam_440, retro_pvam_456, retro_pvam_515, retro_pvam_602, retro_pvam_647, retro_pvam_70, retro_pvam_882, retro_pvam_919,
Rattus norvegicus	ENSRNOG00000008512	8 retrocopies	retro_rnor_1113, retro_rnor_1666, retro_rnor_1870, retro_rnor_1871, retro_rnor_1872, retro_rnor_537, retro_rnor_760, retro_rnor_998,
Rattus norvegicus	ENSRNOG00000016912	9 retrocopies	retro_rnor_187, retro_rnor_194, retro_rnor_2121, retro_rnor_2520, retro_rnor_2990, retro_rnor_2991, retro_rnor_2999, retro_rnor_836, retro_rnor_953,
Sorex araneus	ENSSARG00000003173	2 retrocopies	retro_sara_680, retro_sara_690,
Sorex araneus	ENSSARG00000007736	5 retrocopies	retro_sara_195, retro_sara_279, retro_sara_354, retro_sara_427, retro_sara_74,
Ictidomys tridecemlineatus	ENSSTOG00000006129	6 retrocopies	retro_itri_1309, retro_itri_402, retro_itri_459, retro_itri_541, retro_itri_701, retro_itri_810,
Tupaia belangeri	ENSTBEG00000013307	30 retrocopies	retro_tbel_1050, retro_tbel_1052, retro_tbel_1178, retro_tbel_1595, retro_tbel_1642, retro_tbel_1785, retro_tbel_1883, retro_tbel_1924, retro_tbel_2245, retro_tbel_2290, retro_tbel_2532, retro_tbel_2979, retro_tbel_3092, retro_tbel_3100, retro_tbel_3340, retro_tbel_3469, retro_tbel_3483, retro_tbel_3520, retro_tbel_3583, retro_tbel_3598, retro_tbel_3986, retro_tbel_4045, retro_tbel_4278, retro_tbel_4283, retro_tbel_4563, retro_tbel_4623, retro_tbel_539, retro_tbel_701, retro_tbel_98, retro_tbel_991,
Tarsius syrichta	ENSTSYG00000001295	7 retrocopies	retro_tsyr_1360, retro_tsyr_1388, retro_tsyr_212, retro_tsyr_707, retro_tsyr_878, retro_tsyr_90, retro_tsyr_954,
Tarsius syrichta	ENSTSYG00000013635	3 retrocopies	retro_tsyr_1576, retro_tsyr_1822, retro_tsyr_2045,
Tursiops truncatus	ENSTTRG00000007290	2 retrocopies	retro_ttru_1883, retro_ttru_391,
Vicugna pacos	ENSVPAG00000009607	2 retrocopies	retro_vpac_185, retro_vpac_467,