# STOCKHOLM 1.0 #=GF AC RFxxx (* ___currently_unassigned____ *) #=GF ID SmY #=GF DE SmY spliceosomal RNA; probably involved in trans-splicing #=GF AU Tom Jones # #=GF CC SmY appears to be a component of a splicesomal complex involved in #=GF CC nematode trans-splicing. In C. elegans, SmY associates in a #=GF CC SmY/Sm/SL75p/SL26p complex with three proteins, whereas the better #=GF CC known SL trans-spliced leader RNA is found associated in a #=GF CC SmY/kiSm/SL75p/SL21p complex; SL26p is a paralog of SL21p [1]. # #=GF CC SmY RNA was first identified in the nematode Ascaris suum #=GF CC biochemically by co-purification from spliceosome-enriched extracts, #=GF CC where it appeared as an unexpected band in addition to the known #=GF CC spliceosomal small RNAs, and a second unexpected RNA species named SmX #=GF CC [2]. # #=GF CC The "Sm" in the name comes from the presence of a consensus Sm protein #=GF CC binding site in the sequence, which is a feature of many spliceosome #=GF CC RNAs. The eukaryotic Sm protein is a highly conserved RNA binding #=GF CC protein. # #=GF CC At least six of the C. elegans SmY homologs are enriched by #=GF CC immunoprecipitation with antibodies against 2,2,7-trimethylguanosine #=GF CC cap structures [3]. 5' trimethyl-G caps are a feature of many #=GF CC polII-transcribed small functional RNAs. # #=GF RN [1] #=GF RM 17283210 #=GF RT A novel family of C. elegans snRNPs contains proteins associated #=GF RT with trans-splicing. #=GF RA MacMorris M, Kumar M, Lasda E, Larsen A, Kraemer B, Blumenthal T. #=GF RL RNA 2007;13:511-520. # #=GF RN [2] #=GF RM 8752084 #=GF RT Direct analysis of nematode cis- and trans-spliceosomes: #=GF RT a functional role for U5 snRNA in spliced leader addition #=GF RT trans-splicing and the identification of novel Sm snRNPs. #=GF RA Maroney PA, Yu YT, Jankowska M, Nilsen TW; #=GF RL RNA 1996;2:735-745. # #=GF RN [3] #=GF RM 17903271 #=GF RT Systematic identification of non-coding RNA 2,2,7-trimethylguanosine #=GF RT cap structures in Caenorhabditis elegans. #=GF RA Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R; #=GF RL BMC Mol Biol. 2007;8:86. # #=GF RN [4] #=GF RM 16344563 #=GF RT Organization of the Caenorhabditis elegans small non-coding transcriptome: #=GF RT genomic features, biogenesis, and expression. #=GF RA Deng W, Zhu X, Skogerbo G, Zhao Y, Fu Z, Wang Y, He H, Cai L, Sun H, Liu C, #=GF RA Li B, Bai B, Wang J, Jia D, Sun S, He H, Cui Y, Wang Y, Bu D, Chen R; #=GF RL Genome Res. 2006;16:20. ##### Member sequence provenance # --------------------------------------------------------------------------- # Ascaris lumbricoides SmY is the founding member. # (Uniprot taxonomy considers A. lumbricoides == A. suum and assigns _ASCSU name to both) #=GS SMY_ASCSU DE validated SmY gene; GB:U52372.1/141-212; RNA 2:735 (1996) # --------------------------------------------------------------------------- # Caenorhabditis elegans coordinates: WS150 assembly, WormBase. # Gene names follow MacMorris et. al. RNA 13:511 (2007) # 9 of 12 known C. elegans SmY RNAs included in seed as representatives. #=GS SMY1_CAEEL DE validated SmY gene; CHROMOSOME_IV/9511816-9511740; CeN32; AY948626.1; ends determined by [4] #=GS SMY2_CAEEL DE validated SmY gene; CHROMOSOME_IV/9511446-9511370; CeN25-1; AY948618.1; ends determined by [4] #=GS SMY3_CAEEL DE validated SmY gene; CHROMOSOME_V/14095158-14095239; CeN25-2; AY948619.1; ends determined by [4] ### SMY4_CAEEL [not included in seed] predicted SmY gene; CHROMOSOME_V/14097288-14097208; NR_003471.1 ### SMY5_CAEEL [not included in seed] validated SmY gene; CHROMOSOME_V/14099054-14098978; CeN25-3; NR_003470.1; ends determined by [4] (but this included 1 nontemplated 5' G, not in accessioned sequence) ### SMY6_CAEEL [not included in seed] validated SmY gene; CHROMOSOME_V/14100106-14100024; CeN25-5; AM286190.1 #=GS SMY7_CAEEL DE predicted SmY gene; CHROMOSOME_IV/6460748-6460667; NR_003463.1; published in wrong ori. #=GS SMY8_CAEEL DE validated SmY gene; CHROMOSOME_IV/13600816-13600894; CeN31; AY948625.1; ends determined by [4] #=GS SMY9_CAEEL DE validated SmY gene; CHROMOSOME_IV/13602171-13602247; CeN25-7; AM286192.1 #=GS SMY10_CAEEL DE validated SmY gene; CHROMOSOME_IV/13601605-13601694; CeN112; AY948610.1; ends determined by [4] #=GS SMY11_CAEEL DE validated SmY gene; CHROMOSOME_IV/14863949-14864026; CeN25-4; AY948621.1; ends determined by [4] #=GS SMY12_CAEEL DE validated SmY gene; CHROMOSOME_IV/14864706-14864786; CeN25-6; AM286191.1; 3' estimated (8bp added to accessioned 3' end) # --------------------------------------------------------------------------- # Caenorhabditis briggsae coordinates: v1.0(cb3) assembly (Jan 2007), WashU GSC. # Gene names follow MacMorris et al RNA 13:511 (2007), except Smy-11 and Smy-12, which we assigned. # All sequence bounds re-predicted by us, modifying bounds predicted by MacMorris et al. #=GS SMY1_CAEBR DE predicted SmY gene; chrIV/9065594-9065671 #=GS SMY2_CAEBR DE predicted SmY gene; chrV/12863240-12863160 ### SMY3_CAEBR [not included in seed] predicted SmY gene; chrIV/9066035-9065959 #=GS SMY4_CAEBR DE predicted SmY gene; chrV/12588531-12588614 #=GS SMY5_CAEBR DE predicted SmY gene; chrV/12563358-12563441 ### SMY6_CAEBR [not included in seed] predicted SmY gene; chrV/12574816-12574731 ### SMY7_CAEBR [not included in seed] predicted SmY gene; chrV/12537216-12537133 #=GS SMY8_CAEBR DE predicted SmY gene; chrV/12591313-12591397 #=GS SMY9_CAEBR DE predicted SmY gene; chrIV/9100165-9100244 ### SMY10_CAEBR [not included in seed] is likely NOT an SmY RNA; MacMorris et al. assigned cbSmY-10 to chrIII/1407520-1407623 #=GS SMY11_CAEBR DE predicted SmY gene; chrIV/9104344-9104422 #=GS SMY12_CAEBR DE predicted SmY gene; chrV/12592018-12592102 # --------------------------------------------------------------------------- # Other sequences in the seed: #=GS Contig0/3332057-3331977 DE predicted SmY gene; (Caenorhabditis remanei); SRC: GSC genome WGS v15.0.1 (May 2007) #=GS Contig200/106745-106823 DE predicted SmY gene; (Caenorhabditis remanei); SRC: GSC genome WGS v15.0.1 (May 2007) #=GS Contig200/88734-88656 DE predicted SmY gene; (Caenorhabditis remanei); SRC: GSC genome WGS v15.0.1 (May 2007) #=GS Contig200/88250-88173 DE predicted SmY gene; (Caenorhabditis remanei); SRC: GSC genome WGS v15.0.1 (May 2007) #=GS Contig10/510122-510205 DE predicted SmY gene; (Caenorhabditis remanei); SRC: GSC genome WGS v15.0.1 (May 2007) #=GS Contig11/252917-252995 DE predicted SmY gene; (Caenorhabditis remanei); SRC: GSC genome WGS v15.0.1 (May 2007) #=GS Contig254/12038-12116 DE predicted SmY gene; (Caenorhabditis remanei); SRC: GSC genome WGS v15.0.1 (May 2007) #=GS Contig137/142319-142239 DE predicted SmY gene; (Caenorhabditis remanei); SRC: GSC genome WGS v15.0.1 (May 2007) #=GS Contig2/1581908-1581989 DE predicted SmY gene; (Caenorhabditis remanei); SRC: GSC genome WGS v15.0.1 (May 2007) #=GS Contig2/1595709-1595790 DE predicted SmY gene; (Caenorhabditis remanei); SRC: GSC genome WGS v15.0.1 (May 2007) #=GS Contig2/1874843-1874925 DE predicted SmY gene; (Caenorhabditis remanei); SRC: GSC genome WGS v15.0.1 (May 2007) #=GS Contig2/1589250-1589173 DE predicted SmY gene; (Caenorhabditis remanei); SRC: GSC genome WGS v15.0.1 (May 2007) #=GS Contig2/1578235-1578154 DE predicted SmY gene; (Caenorhabditis remanei); SRC: GSC genome WGS v15.0.1 (May 2007) #=GS Contig258/103352-103272 DE predicted SmY gene; (Caenorhabditis japonica); SRC: WashU Assembly v3.0.2 (Mar 2008) #=GS Contig370/26489-26409 DE predicted SmY gene; (Caenorhabditis japonica); SRC: WashU Assembly v3.0.2 (Mar 2008) #=GS Contig1440/27718-27794 DE predicted SmY gene; (Caenorhabditis japonica); SRC: WashU Assembly v3.0.2 (Mar 2008) #=GS Contig1440/26106-26025 DE predicted SmY gene; (Caenorhabditis japonica); SRC: WashU Assembly v3.0.2 (Mar 2008) #=GS Contig1440/25238-25158 DE predicted SmY gene; (Caenorhabditis japonica); SRC: WashU Assembly v3.0.2 (Mar 2008) #=GS Contig1440/27517-27436 DE predicted SmY gene; (Caenorhabditis japonica); SRC: WashU Assembly v3.0.2 (Mar 2008) #=GS Contig1484/2759-2837 DE predicted SmY gene; (Caenorhabditis japonica); SRC: WashU Assembly v3.0.2 (Mar 2008) #=GS Contig3/56758-56837 DE predicted SmY gene; (Caenorhabditis brenneri); SRC: GSC genome WGS v6.0.1 (Feb 2008) #=GS Contig3/54041-54120 DE predicted SmY gene; (Caenorhabditis brenneri); SRC: GSC genome WGS v6.0.1 (Feb 2008) #=GS Contig3/280402-280481 DE predicted SmY gene; (Caenorhabditis brenneri); SRC: GSC genome WGS v6.0.1 (Feb 2008) #=GS Contig3/300557-300636 DE predicted SmY gene; (Caenorhabditis brenneri); SRC: GSC genome WGS v6.0.1 (Feb 2008) #=GS Contig3/54759-54838 DE predicted SmY gene; (Caenorhabditis brenneri); SRC: GSC genome WGS v6.0.1 (Feb 2008) #=GS Contig3/301521-301442 DE predicted SmY gene; (Caenorhabditis brenneri); SRC: GSC genome WGS v6.0.1 (Feb 2008) #=GS Contig72/83389-83465 DE predicted SmY gene; (Caenorhabditis brenneri); SRC: GSC genome WGS v6.0.1 (Feb 2008) #=GS Contig105/113605-113684 DE predicted SmY gene; (Caenorhabditis brenneri); SRC: GSC genome WGS v6.0.1 (Feb 2008) #=GS Contig183/7569-7648 DE predicted SmY gene; (Caenorhabditis brenneri); SRC: GSC genome WGS v6.0.1 (Feb 2008) #=GS Contig185/160297-160218 DE predicted SmY gene; (Caenorhabditis brenneri); SRC: GSC genome WGS v6.0.1 (Feb 2008) #=GS Contig291/909-826 DE predicted SmY gene; (Caenorhabditis brenneri); SRC: GSC genome WGS v6.0.1 (Feb 2008) #=GS Contig585/6512-6592 DE predicted SmY gene; (Caenorhabditis brenneri); SRC: GSC genome WGS v6.0.1 (Feb 2008) #=GS Contig884/26438-26513 DE predicted SmY gene; (Caenorhabditis brenneri); SRC: GSC genome WGS v6.0.1 (Feb 2008) #=GS Contig884/25927-26005 DE predicted SmY gene; (Caenorhabditis brenneri); SRC: GSC genome WGS v6.0.1 (Feb 2008) #=GS Contig2/907373-907451 DE predicted SmY gene; (Pristionchus pacificus); SRC: GSC genome assembly v5.0.1 (Jan 2008) #=GS Contig2/389920-389842 DE predicted SmY gene; (Pristionchus pacificus); SRC: GSC genome assembly v5.0.1 (Jan 2008) #=GS Contig2/720515-720437 DE predicted SmY gene; (Pristionchus pacificus); SRC: GSC genome assembly v5.0.1 (Jan 2008) #=GS Contig48/288048-287970 DE predicted SmY gene; (Pristionchus pacificus); SRC: GSC genome assembly v5.0.1 (Jan 2008) #=GS Contig120/11483-11560 DE predicted SmY gene; (Pristionchus pacificus); SRC: GSC genome assembly v5.0.1 (Jan 2008) #=GS Contig122/156544-156622 DE predicted SmY gene; (Pristionchus pacificus); SRC: GSC genome assembly v5.0.1 (Jan 2008) #=GS contig025547/1209-1285 DE predicted SmY gene; (Haemonchus contortus); SRC: Sanger 2006 genome assembly (Jan 2006) #=GS ABLA01022309.1/286-367 DE predicted SmY gene; (Heterodera glycines); SRC: WGS v1 (Mar 2008) #=GS ABLA01020015.1/643-564 DE predicted SmY gene; (Heterodera glycines); SRC: WGS v1 (Mar 2008) #=GS Mh10g200708_Contig1500/18637-18561 DE predicted SmY gene; (Meloidogyne hapla); SRC: PNGG genome assembly (Nov 2008) #=GS CABB01001438;/775-852 DE predicted SmY gene; (Meloidogyne incognita); SRC: EBI genome assembly (Sep 2008) #=GS Contig6576.2/644-570 DE predicted SmY gene; (Ascaris suum); SRC: www.nematode.net/FTP/wgs_ftp/Ascaris_suum.WGS #=GS AUAC-aae50e10.b1/615-541 DE predicted SmY gene; (Ascaris suum); SRC: www.nematode.net/FTP/wgs_ftp/Ascaris_suum.WGS #=GS AUAC-aac93a10.b1/191-114 DE predicted SmY gene; (Ascaris suum); SRC: www.nematode.net/FTP/wgs_ftp/Ascaris_suum.WGS #=GS Contig5095.1/369-291 DE predicted SmY gene; (Ascaris suum); SRC: www.nematode.net/FTP/wgs_ftp/Ascaris_suum.WGS #=GS AAQA01004525.1/621-545 DE predicted SmY gene; (Brugia malayi); SRC: ftp.ncbi.nih.gov/genomes/Brugia_malayi/FASTA/Brugia_malayi.faa # A.lumbricoides (aka suum) (Clade III, Spirurina) =================================================================================== SMY_ASCSU .............AGCAACCACGAAGUUCAGGGCCUU...AUGAAGACCCGAAGG..ACAAUUUUUGGAG..GCCC..CUC.....CGAG.GAG..GUGC.GC. # C.elegans (Clade V, Rhabditina) ======================================================================================== SMY1_CAEEL .........GUUAAACCAUAACUA.ACUCAGGGCCUUG..UUAAAGACCCGAAGU..ACAAUUUUUGAAG..CCCUG.UCU.....CUCG.AGG.CAGGG.G.. SMY2_CAEEL .........CGAUUUCUUAUAAUACU.UCAGGGCCUUA..CUAAAGACCCAGUGU..ACAAUUUUUGCAG..CCCUG.UCU.....UCUG.AGG.CAGGG.G.. SMY3_CAEEL ..........GCUAUUUAUAAACGCUCUCAGGGCCUUG..CAAAAGACCCAGUGA..ACAAUUUUUGGAGAACCCUGUCCU.....UUCG.AGGUCAGGGUA.. SMY7_CAEEL .........CAGCACGAUUUAACACUCUCAGGGCCUUA..CAAAAGACCCAGUGA..ACAAUUUUUGCAA.ACCCUGUCCU.....UUCA.AGGUCAGGGUA.. SMY8_CAEEL .........GUUAAUUCAU..UAACUUCCAAGGCCUUA..CACAAGACCUAGUGG..ACAAUUUUUGGAG.ACCCUA..UC...UAGCCGUGA..UAGGGUG.. SMY9_CAEEL ..............UUCGCUAAACCU.CCAAGGCCUUU..CAUAAGACCUAGUGA..ACAAUUUUUGGGG.ACCCUA.UCU....UUUUA.AGG.UAGGGUUAA SMY10_CAEEL CAAUCCUAAACUUAAAUAACAAAAAACCCAAAGCCUAA..CUCAGGACUUGGU.A..ACAAUUUUUGGAG.ACCCUA.ACU....UUUAUUAGU.UAGGGUG.. SMY11_CAEEL ...........AUAUAAUAUAUCACUGUCAGGGCCUUA..CAAAAGACCCAGUGA..ACAAUUUUUGCAAA.CCCUG.UCU....UCUUGAAGG.CGGGG.... SMY12_CAEEL ..........AAUAUAAUAAAACACUGUCAGGGCCUUA..CAAAAGACCCACUGA..UCAAUUUUUGAAA.ACCUUG.UUC....UCUUGAGGG.CACGGUA.. # C.briggsae (Clade V, Rhabditina) ======================================================================================== SMY1_CAEBR .........UGUUCUAUUAAAA.UCAUUCAGGGCCUUA..CUUAAGACCCGGUGU..ACAAUUUUUGGA..GCCCUG.UCG.....CUUG.CGG.CAGGGUA.. SMY2_CAEBR .........UCAUUAAAUACUUGAGU.ACAGGGCCUUU..CACAAGACCCGAUGU..ACAAUUUUUGGAG.ACCCUG.UCC...UCUCUC.GGG.CAGGGUU.. SMY4_CAEBR .........CAGCAUCUAGCAUUUCA.UCGAGGCCUUC..AAUAAGACCUUCAGA..ACAAUUUUUGGAG.ACCCUGUCCU.AAUUUUUG.AGG.CAGGGAA.. SMY5_CAEBR .........CGGUAUCUAGCAUUUCA.UCGAGGUCUUC..UUUAAGACCUUUAGA..ACAAUUUUUGGAA.ACCCUG.UCUCAUUAAUUG.GGG.CAGGGUA.. SMY8_CAEBR .........GUAUCUAUCAUUUUAUUUUUGAGGCCUUC..UACAAGACCUUAAGA..ACAACUUUUGGAG.ACCCUG.UCCUAAUAUUUG.GGG.CAGAGUA.. SMY9_CAEBR .........UUUGCUAGUCUAUCUCUUGCCGGGCCUUC..CUCAAGACCCUAAGC..ACAAUUUUUGGGC.ACCC.G.UCG...CAGCAA.CGG.C.GGGUG.. SMY11_CAEBR .........UAAAAUCCUUCAUA....GCUGGGCCUUC..CUUAAGACCCUAAGC..ACAAUUUUUGGG..CGCCUG.UCG.UGCAACAG.CGG.CGGGUGA.. SMY12_CAEBR .........CAGUAUCUAGUAUUUCA.UCGAGGCCUUC..UUGAAGACCUUAAGU..AUAAUUUUUGGAA.ACCCUG.UUCUAAUAUUUUAGGA.CAGGGUA.. # C.remanei (Clade V, Rhabditina) ======================================================================================== Contig0/3332057-3331977 .........GUUAAAUCUAUAACACU.UCAGGGCCUUA..AUAAAGACCCGUCGU..ACAAUUUUUGGAC.GCCCU.UUCC....UUCACAGGAC.UGGGUG.. Contig200/106745-106823 .........UGGUGCACCUCGU-AUUCUAUGGGCCUUCU.UUCAAGACCCUGAAA..UAAAUU.UUGGAG.ACCCGU.CAU.....UCCG.AUG.GCGGGUG.. Contig200/88734-88656 .........UCGUUUAAUAUAACUUAUUCCGGGCCUUG..UAAAAGACCCCAAGA..ACAAUUUUUGCA..GCCCUGU.UC.....UUUG.GA.UCAGGGUA.. Contig200/88250-88173 .........UUUCUAACCAGAAAGACAGCAGGGCCUUA..CUAAAGACCCGUACU..ACAAUUUUUGCAG..CCCUG.UUC.....UUCG.GAG.CAGGG.G.. Contig10/510122-510205 .........CAUCGAACUACAAUACCUUUAAGGCCUUU..CCUAAGACCUCGACU..AGAAUUUUUGGAAAACCCUG.UCU...AUUCUUUAGG.CAGGGUG.. Contig11/252917-252995 .........UAAAUUGUAACAACAC..ACAAGGCCUUG..UUUAAGACCUGCUGU..AAAAUUUUUGGAGA.CCCUG.UCC....UUCAUUGGG.CAGGG.A.. Contig254/12038-12116 .........UCUAGUAUAGUUCUUCUUGCUGGGCCUUC..UUUAAGACCCUAAGA..UAAAUU.UUGGAC.GC.CUG.UCU....CUAAGGAGG.CAG.GUG.. Contig137/142319-142239 .........UUUAGUAAUAGUAGUCUUUCAGGGCCUUC..CUUAAGACCCGAAGAA.UUAAUUUUUGGAG.ACCCUUU.UC.....UUUG.GA.UUAGGGUG.. Contig2/1581908-1581989 .........GUGUAUUUUAUAUUGCCAUCAAGGCCUUA..CUUAAGACCUGAAGU..ACAAUUUUUGGAG.ACCCUG.UCC....UUUAUUGGG.CAGGGUG.. Contig2/1595709-1595790 .........UGUGAUGUUAUAUUGCUUUCAAGGCCUUC..CUUAAGACCUGAAGA..ACAAUUUUUGGAA.ACCCU.CUCC....UUCAUUGGGC.AGGGUG.. Contig2/1874843-1874925 .........CCAGAGAAAUUGAAAGU.GCAGGGCCUUU..CUCAAGACCCCAAGU..ACAAUUUUUGCA..ACCCUG.CCA.GAAUUUAGUUGG.UAGGGUA.. Contig2/1589250-1589173 .........AUGUAUGUUAUUUCUUCCUCAAGGCCUUC..CUUAAGACCUGUAGU..ACAAUUUUUGGAG.ACCCUG...U...CCUUUA.G...UAGGGUG.. Contig2/1578235-1578154 .........AUUCUUAUUAUUUCUUAUUCAGGGCCUUC..CUUAAGACUCAAAGU..ACAAUUUUUUGAG.AUCCUG.UCC....UUCAGUGGG.CAGAGUG.. # C.japonica (Clade V, Rhabditina) ======================================================================================== Contig258/103352-103272 .........AAUUAUAUCCCAUUG.UUACAGGGCCUUU..AAGAAGACCCACAGU..ACAAUUUUUGAAA.ACCCUGCUCU.....UUCU.AGAUCAGGGUG.. Contig370/26489-26409 .........UUCUUACACCUAGUGUGAACCGGGCCUUG..UUGAAGACCCUAAGC..ACAAUUUUUGCA..GCCCUGU.CC....UUCUUUGG.UCAGGGUA.. Contig1440/27718-27794 .........GUCAAAUAAUAAUAAAUUGCAGAGCCUUG..AAGAAGACUCGAAGC..ACAAUUUUUGCAA.ACCCUG..UU......UCC.AA..CAGGGUA.. Contig1440/26106-26025 .........GUUGUGAAAUAAUCAAAUUCAGAGCCUUC..AAGAAGACUCAAAGU..ACAAUUUUUGCAA.ACCCUAGCUU.....UUCC.AAGUCAGGGUA.. Contig1440/25238-25158 .........GUUGUGAAAUAAUAAAUUGCAGAGCCUUG..AAAAAGACUCCAAGU..ACAAUUUUUGCGA.ACCCUG.UUC....AAUUU.GGA.UAGGGUU.. Contig1440/27517-27436 .........GUUGUGAAAUAAUCAAAUACAGAGCCUUU..AAGAAGACUCGAAGA..ACAAUUUUUGCAA.ACUCUGAUCU.....UAUU.AGGUCGGGGUA.. Contig1484/2759-2837 .........GUUUUCAUAUAAAC.GAUGCAGGGCCUUA..CUGAAGACCCCUAGC..ACAAUUUUUGAA..ACCCUG.UCU....GUUUC.GGA.UGGGGUA.. # C.brenneri (Clade V, Rhabditina) ======================================================================================== Contig3/56758-56837 .........AAAUGAUCUAAAUAUCUCUCAGGGCCUUG..AAUAAGACCCAGUGA..ACAAUUUUUGGAG.ACCCUA.UUC.....CUAG.GAA.UAGGGUG.. Contig3/54041-54120 .........CAACUAACAACACACCUCUCAGGGCCUUG..AUCAAGACCCGGUGA..ACAAUUUUUGGAG.ACCCUA.UUC.....UUCG.GAG.UAGGGUG.. Contig3/280402-280481 .........AAUUCUAAUGAAUCACUCUCAGGGCCUUG..AAUAAGACCCAGUGA..ACAAUUUUUGGAG.ACCCUAA.UC.....UGAG.GA.AUAGGGUG.. Contig3/300557-300636 .........ACAAAUGAUCUAAAUAUCUCAGGGCCUUG..CAUAAGACCUAGUGA..ACAAUUUUUGGAG.ACCCUA.UUC.....UCAG.GAA.UAGGGUG.. Contig3/54759-54838 .........AAAAGAUCUGAAUCUCUGUCAGGGCUAUG..AUUAAGACCCAGUGC..GCAAUUUUUGGAC.ACCCUA.UUC.....UCAG.GAA.UAGGGUG.. Contig3/301521-301442 .........AGUGUAAUUGAAUGACUCUCAGGGCCUUG..AACAAGACCCAGUGA..ACAAUUUUUGGAG.ACCCUA.UUU.....UUCG.GAG.UAGGGUG.. Contig72/83389-83465 .........AUUCUUAUGAAU.AUACUGCAGGGCCUUC..AUCAAGACCCAGUGA..ACAAUUUUUGGG..ACCCUA.UUC.....UUU..GAA.UAGGGUA.. Contig105/113605-113684 .........CAAAUGAAAAAAAACCUCUCAGGGCCUUG..AAUAAGACCCAGUGA..ACUAUUUUUGGAG.ACCCUA.UUC.....GAAA.GGA.UAGGAUG.. Contig183/7569-7648 .........GUGUAAUUUUAAUUACUCUUAAGGCCUUG..AAUAAGACCCAGUGA..ACAAUUUUUGGAG.ACCCUA.UUC.....UCAG.GAA.UAGGGUG.. Contig185/160297-160218 .........CUAUUGAAUAACUCACUUUCAGGGCCUUG..CAUAAGACCCAGUGA..ACAAUUUUUGGAG.ACCCUUC.UC.....UUCG.GA.UUAGGGUG.. Contig291/909-826 .........GCUUCUAUCAAC.AUUAUUCAGGGCCUUA..CCCAAGACCCGGUGU..ACAAUUUUUGGAA.ACCCUG.UCC.GGUUUUAUAGGG.CAGGGUU.. Contig585/6512-6592 .........UAUUCUAAUGAAUACCUCUCAGGGCCUUU..UAUAAGACCCAGUGA..ACAAUUUUUGCAG.ACCCUCUUCC.....UUU..GGUUGAGGGUG.. Contig884/26438-26513 .........UGAUUUCUUAAAAA..UCACCGGGCCUUA..CUAAAGACCCCAAGU..ACAAUUUUUGCAA..CCCUGU.CC.....UUCG.GG.UCAGGG.A.. Contig884/25927-26005 .........GGUUAUAAAGAUUUUUAUACCGGGCCUUA..CAGAAGACCCCAAGU..ACAAUUUUUGCA..GCCCUUU.CC.....UUCG.GG.UCAGGGUA.. # P.pacificus (Clade V, Rhabditina) ======================================================================================== Contig2/907373-907451 .........UCGUAUUAAAUCAAUCUCUCAGGGCCUCG..AUAGAGACCCAGAAU..CCAGUUUUUGGA..GGUCUU.CCA.....CACU.UGG.GAGGUUA.. Contig2/389920-389842 .........AGGUGCAAUACAAG.CUCUCAGGGCCUUU..ACCAAGACCCAGAGU..CCAGUUUUUGGAG.AACCCU..CC....GGCUAAGG..GGGGUUG.. Contig2/720515-720437 .........GUAUUGAACAAAAUAAGUUCAGGGCCUCA..ACCGAGACCCGGUG...UCGAUUUUUGGUG.AGCUCU.UCA.....AUGC.UGA.AGAGCUU.. Contig48/288048-287970 .........AUCUGAGUCUUCGCACUUUCAGGGCCUCA..CUUGAGACCCAGUGA..CCAGUUUUUGGA..AACCUU.CCA.....UGCU.UGG.AAGGUUA.. Contig120/11483-11560 .........UGUUGUAUCAAAAAUGAUUCAGGGCCUCG..AACGAGACCCGUAG...CCAAUUUUUGGA..AGCCUC.UCC.....GCCA.GGA.GGGGUUA.. Contig122/156544-156622 .........CGUUUGUAAACCAAUCUAUCAGGGCCUCU..ACCGAGACCCAGAGU..CCAGUUUUUGGG..AACCUC.CCA.....CGCU.UGG.GGGGUUA.. # H.contortus (Clade V, Rhabditina) ======================================================================================== contig025547/1209-1285 .........GGAAACAACUAGCUUGGUGUAGGGCCUU...UAUAAGACCCACAGU..ACAAUUUUUGCAG.ACCUUU..GC.....UGGA.GC..AAAGGUA.. # (Clade IV, Tylenchina) ======================================================================================== ABLA01022309.1/286-367 .........GUGUACACCCUUUUGUGCGGAGGGCCUUUUGCUGAAGACCCUUUUUUGACAAUUUUUGGC..AGGCCC..AA.....CGGAAUU..GGGCCUU.. ABLA01020015.1/643-564 .........AAGCGUGUUAACUGAAUGUGA.GGCCUUGUUCUGAAGACC.CUUUUC.ACAAUUUUUGGC..AGGCUU.AAC.....CGAA.GUU.AGGCCUU.. Mh10g200708_Contig1500/18637-18561 .........AACGUUACCGUUUUUA.UCGCGGGCCUUAAGUUGAAGACCCAGCGUU.ACAUUUUUUGGA..GUCCCG...C.....GGGA.G...CGGGAUU.. CABB01001438;/775-852 .........AACGUUACCUUUUAUA.UCGCGGGCCUUGAGAUGAAGACCCAGCGUUUACAUUUUUUGGA..GUCUCA...C.....GGGA.G...UGAGAUU.. # (Other Clade III, Spirurina) ======================================================================================== Contig6576.2/644-570 .........CAUAAGCAACCGAUCAAUUCAGGGCCUU...CUGAAGACCCGAAAG..ACAGUUUUUGGAG..GCCC..CUU.....CGAA.GAG..GUGC.G.. AUAC-aae50e10.b1/615-541 .........GGUCAGCAGUCUUCCGCUUCAGGGCCUU...CUGAAGACCCGAAGG..ACAAUUUUUGGAG..GCCC..CUC.....CGAG.GAG..GUGC.G.. AUAC-aac93a10.b1/191-114 .........GGUCAGCAGACUUCCGCUUCAGGGCCUU...CUGAAGACCCGAAGG..ACAAUUUUUGGC..AGCGU.AUCC....GAGGA.GGA..GCGCUa.. Contig5095.1/369-291 .........AAUCGUGACUCAAGUAGUUCAGGGCCUUU..UUCAAGACCCGAAGG..ACAAUUUUUGGA..GGCUCA.CCG.....GGGA.UGG.UGAGCCa.. AAQA01004525.1/621-545 .........CGUGUCUAAGCUUUGA..CCAGGGCCUUG..UCCAAGACCCGGCGA..ACAAUUUUUGGC..UGCCUU.CCC.....AGGA.GGG.AGGGCAa.. # Annotation: ======================================================================================== #=GC SS_cons .........:::::::::::::::::::::<<<-<<<_..___>>>->>>-----..-------------.<<<<<<.<<<.....____.>>>.>>>>>>:.. #=GC RF .........auuuauaaaaaAuaacuuuCAGGGCCUUa..cuuAAGACCCaaaGa..ACAAUUUUUGGAG.ACCCug.cCc.....uuag.gGg.caGGGUa.. //