From 8168766a11f05879104978baea8f711d66521f51 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Wed, 9 Sep 2015 12:55:16 +0100 Subject: [PATCH] JAL-1684 aligned proteins and citation for for Estrogen cDNA/Protein --- examples/applets.html | 9 +- examples/estrogenReceptorProtein.aln | 162 ++++++++++++++++++++++++++++++++++ 2 files changed, 169 insertions(+), 2 deletions(-) create mode 100644 examples/estrogenReceptorProtein.aln diff --git a/examples/applets.html b/examples/applets.html index a101d65..ff97475 100644 --- a/examples/applets.html +++ b/examples/applets.html @@ -168,7 +168,7 @@ Try out JalviewLite by pressing one of the buttons below.

-

Linked amino acid and cDNA alignments for homologous proteins

+

Linked Protein and cDNA alignments for a family of Steroid Receptors

@@ -191,6 +191,11 @@ Try out JalviewLite by pressing one of the buttons below.
value="http://www.jalview.org/services/launchApp"/> - +
Displays a split window view of protein and its related cDNADisplays a split window view of protein + and its related cDNA.
Data retrieved from Uniprot and ENA, + after Thornton, Need and Crews, Science 19 + September 2003: 301 (5640), 1714-1717 +
diff --git a/examples/estrogenReceptorProtein.aln b/examples/estrogenReceptorProtein.aln new file mode 100644 index 0000000..cfe7d80 --- /dev/null +++ b/examples/estrogenReceptorProtein.aln @@ -0,0 +1,162 @@ +CLUSTAL + +UNIPROT|Q7LCB3/1-530 -------MDIKNSPSSLNSPSSYNCSQSILPLEHG-----------SIYIPSSYVDSHHE +UNIPROT|Q9VSE9/1-484 ----------------------------------M-----------SDGVSILHIKQEVD +UNIPROT|Q9IBD5/1-710 -----MDNNHQDKMESLYTPARASPTPDAESIKRARNLIKTYSESFGSYVEEIVRDDSNN +UNIPROT|Q7LCB3/1-530 -------MDIKNSPSSLNSPSSYNCSQSILPLEHG-----------SIYIPSSYVDSHHE +UNIPROT|Q9YGV9/1-848 MEIPVGLGGVSDATNAVFRGPYQNVFHSLQ----------------VAFQSHGAVSRSLD +UNIPROT|Q90ZM7/1-438 -----------------------------------------------------GVEFQLP +UNIPROT|Q91445/1-344 ------------------------------------------------------------ +UNIPROT|Q9VSE9/1-484 ----------------------------------M-----------SDGVSILHIKQEVD +UNIPROT|Q90ZM8/1-554 ARGFSEAHGYEYSGASLYQPLPPSCTEFSI----------------GAHQQQQHQHQHHQ + +UNIPROT|Q7LCB3/1-530 YPAM--------------------------------------------TFYSPAVMNYSI +UNIPROT|Q9VSE9/1-484 TPSA--------------------------------------------SCFSPSSKSTAT +UNIPROT|Q9IBD5/1-710 IQSLSSVPLLMRNFGNMDTLTCAPGSGSDSEIWKDFVVPGNSVVSKD-TCGHVEISTKAE +UNIPROT|Q7LCB3/1-530 YPAM--------------------------------------------TFYSPAVMNYSI +UNIPROT|Q9YGV9/1-848 FPNTKYGFLQNRHFCEMRQENKQPPCKGLGLFYGNHRNSDTGTNEDDIACFSRQSDAEAR +UNIPROT|Q90ZM7/1-438 YSASA-------------------------------------------TSFRPSVATSSA +UNIPROT|Q91445/1-344 ------------------------------------------------------------ +UNIPROT|Q9VSE9/1-484 TPSA--------------------------------------------SCFSPSSKSTAT +UNIPROT|Q90ZM8/1-554 HQHQ--------------------------------------------QHHHQQQQQQPQ + +UNIPROT|Q7LCB3/1-530 P---------SNVTNLEGGP-------GRQTTSPNVLWPTPGHLSPLVVHRQLSHLYAEP +UNIPROT|Q9VSE9/1-484 Q---------SGTNGLKSSP----------SVSPERQLCSS--TTSLSCDLHNVSLSNDG +UNIPROT|Q9IBD5/1-710 NLSWAAAPL-SREETLAKGTVTVPATVPKESFTATSNTSSASGIS--IKDEQQSLLKMEP +UNIPROT|Q7LCB3/1-530 P---------SNVTNLEGGP-------GRQTTSPNVLWPTPGHLSPLVVHRQLSHLYAEP +UNIPROT|Q9YGV9/1-848 PGIFSESSLDTGDEITCKLQSDNQGVRASGPLLPGSSGCNSGQKSSLACTSQQRETTSQS +UNIPROT|Q90ZM7/1-438 ----------SGISNFSNGN---------------------------------------- +UNIPROT|Q91445/1-344 ------------------------------------------------------------ +UNIPROT|Q9VSE9/1-484 Q---------SGTNGLKSSP----------SVSPERQLCSS--TTSLSCDLHNVSLSNDG +UNIPROT|Q90ZM8/1-554 P---------QQNGVLGEGQSSHLSYLPPSTELPQYVPSSPSAPYSMELGAGRPHGYDPG + +UNIPROT|Q7LCB3/1-530 QKSPWCE---------------------------------------------------AR +UNIPROT|Q9VSE9/1-484 DS--------------------------------------------------------LK +UNIPROT|Q9IBD5/1-710 QSSDFCPYTANIPKLNP-----------------------------------------SY +UNIPROT|Q7LCB3/1-530 QKSPWCE---------------------------------------------------AR +UNIPROT|Q9YGV9/1-848 DTCAGESCSEHQATTISETARELCNAVSVSLGLNLDLNDMNDLSSNQISSTESDTSQAIY +UNIPROT|Q90ZM7/1-438 ----------------------------------------------------------NF +UNIPROT|Q91445/1-344 ------------------------------------------------------------ +UNIPROT|Q9VSE9/1-484 DS--------------------------------------------------------LK +UNIPROT|Q90ZM8/1-554 PQSLYRGGVE------------------------------------------------SS + +UNIPROT|Q7LCB3/1-530 SLEHTLPVNRETLKRKVSGNRCASPV---------------------------------- +UNIPROT|Q9VSE9/1-484 GSGTSGGNGGGGGGGTSGGNATNASA---------------------------------- +UNIPROT|Q9IBD5/1-710 LTNTASTKQLGYGEQPDTSAHSSPPA---------------------------------- +UNIPROT|Q7LCB3/1-530 SLEHTLPVNRETLKRKVSGNRCASPV---------------------------------- +UNIPROT|Q9YGV9/1-848 LFESSPGYTGVGLNALVRDCKCQSAREGTSTQQYDRGAMFKINRVNDLPLQPAPPRHTSI +UNIPROT|Q90ZM7/1-438 GFLSPNGVQQDGFPYPGFTSPAQSSV---------------------------------- +UNIPROT|Q91445/1-344 ------------------------------------------------------------ +UNIPROT|Q9VSE9/1-484 GSGTSGGNGGGGGGGTSGGNATNASA---------------------------------- +UNIPROT|Q90ZM8/1-554 APPYSEQQQVVGGGGAMSAMGLTEPR---------------------------------- + +UNIPROT|Q7LCB3/1-530 ------------------------------------------------------------ +UNIPROT|Q9VSE9/1-484 ------------------------------------------------------------ +UNIPROT|Q9IBD5/1-710 QKIVLDTARYSADLCSDNPLPQATNIKTDPCSSFSSFVGEGILTRASMGYSQQAIQTLPV +UNIPROT|Q7LCB3/1-530 ------------------------------------------------------------ +UNIPROT|Q9YGV9/1-848 SDAKWDMEAGLCAQMEHKDSEKCANMDGAHSTSVFSQFDQLLPVNASHYSQNVSVRVEPQ +UNIPROT|Q90ZM7/1-438 ------------------------------------------------------------ +UNIPROT|Q91445/1-344 ------------------------------------------------------------ +UNIPROT|Q9VSE9/1-484 ------------------------------------------------------------ +UNIPROT|Q90ZM8/1-554 ------------------------------------------------------------ + +UNIPROT|Q7LCB3/1-530 ------------------------------------------------------------ +UNIPROT|Q9VSE9/1-484 ------------------------------------------------------------ +UNIPROT|Q9IBD5/1-710 HKSEPFRLSASSAPADSPFW---------------------------------------- +UNIPROT|Q7LCB3/1-530 ------------------------------------------------------------ +UNIPROT|Q9YGV9/1-848 SDFSPILYKSPGIQKNAEKYNVQYDATIKSEDGKTTSEREWGFQYRYNESCSTPSAPPRH +UNIPROT|Q90ZM7/1-438 ------------------------------------------------------------ +UNIPROT|Q91445/1-344 ------------------------------------------------------------ +UNIPROT|Q9VSE9/1-484 ------------------------------------------------------------ +UNIPROT|Q90ZM8/1-554 ------------------------------------------------------------ + +UNIPROT|Q7LCB3/1-530 --------------------------------------------TGPGSKRDA------- +UNIPROT|Q9VSE9/1-484 -------------------------------------------GAGSGSVRDELR----- +UNIPROT|Q9IBD5/1-710 -------------------------------------------CQSTGPSEDHHLQIDYL +UNIPROT|Q7LCB3/1-530 --------------------------------------------TGPGSKRDA------- +UNIPROT|Q9YGV9/1-848 CAHQNRAGPYNQFFFNPFEYAKRGVVSREGYSLEHGFPNNLARTPYSGSLKNELGDRLSG +UNIPROT|Q90ZM7/1-438 ------------------------------------------------------------ +UNIPROT|Q91445/1-344 ------------------------------------------------------------ +UNIPROT|Q9VSE9/1-484 -------------------------------------------GAGSGSVRDELR----- +UNIPROT|Q90ZM8/1-554 -------------------------------------------HVSSGSLPSSTRPE--- + +UNIPROT|Q7LCB3/1-530 --------------------------HFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGH +UNIPROT|Q9VSE9/1-484 --------------------------RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGN +UNIPROT|Q9IBD5/1-710 SPAGLHSTCKYSSTNAYSSYLGVLPQRVCVICGDEASGCHYGVLTCGSCKVFFKRAVEGH +UNIPROT|Q7LCB3/1-530 --------------------------HFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGH +UNIPROT|Q9YGV9/1-848 PYPDVSYRYEGERENVFPVEFFFPPQRTCLICGDEASGCHYGALTCGSCKVFFKRAAEGK +UNIPROT|Q90ZM7/1-438 -----------------------PPQKACLICSDEASGCHYGVLTCGSCKVFFKRAVEGQ +UNIPROT|Q91445/1-344 ----------------------------------EASGCHYGALTCGSCKVFFKRAAEGK +UNIPROT|Q9VSE9/1-484 --------------------------RLCLVCGDVASGFHYGVASCEACKAFFKRTIQGN +UNIPROT|Q90ZM8/1-554 -----------------------RSTQFCAVCSDYASGYHYGVWSCEGCKAFFKRSTQGH + +UNIPROT|Q7LCB3/1-530 NDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMVKCGSRRER-CGYRLVRRQRSADEQL +UNIPROT|Q9VSE9/1-484 IEYTCPANNECEINKRRRKACQACRFQKCLLMGMLKEGVRLDRVRGGRQKYRRNPVSNSY +UNIPROT|Q9IBD5/1-710 HNYLCAGRNDCIVDKIRRKNCPACRLRKCYQAGMI---------LGGRKLKKLGALKAAG +UNIPROT|Q7LCB3/1-530 NDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMVKCGSRRER-CGYRLVRRQRSADEQL +UNIPROT|Q9YGV9/1-848 QKYLCASINDCTIDKLRRKNCPSCRLKRCFAAGMT---------LGARKLKKIGQMRAPE +UNIPROT|Q90ZM7/1-438 HNYLCAGRNDCIIDKIRRKNCPACRLRKCIQAGMT---------LGARKLKKQGRVKGEN +UNIPROT|Q91445/1-344 QKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMT---------LGARKLKKLGNLKAQD +UNIPROT|Q9VSE9/1-484 IEYTCPANNECEINKRRRKACQACRFQKCLLMGMLKEGVRLDRVRGGRQKYRRNPVSNSY +UNIPROT|Q90ZM8/1-554 NDYMCPATNQCTIDRNRRKSCQACRLRKCYEVGMVK-GVRKDR-KGFRGVKHKRKRPIPQ + +UNIPROT|Q7LCB3/1-530 HCAGKAKRSGGH------------------------APRVRELLLDALSPE--------Q +UNIPROT|Q9VSE9/1-484 QTMQLLYQSNTTSLCDVKILEVLNSYEPDALSVQTPPPQVHTTSITNDEASSSSGSI--K +UNIPROT|Q9IBD5/1-710 LTQALVAHSLTPRR---------LSGDSQALMPLGCLPGVRELHLS-------------P +UNIPROT|Q7LCB3/1-530 HCAGKAKRSGGH------------------------APRVRELLLDALSPE--------Q +UNIPROT|Q9YGV9/1-848 DGQGQGPAEAELSV----------------------SPKYDLGFHTQ------------S +UNIPROT|Q90ZM7/1-438 QRSPASSTATTSSA--------------------TPQPSSNSTAVTTFSPPPTGEPIFSP +UNIPROT|Q91445/1-344 DIEGASSSSPTEEQ----------------------APKLVMTRIDGYECQ--------P +UNIPROT|Q9VSE9/1-484 QTMQLLYQSNTTSLCDVKILEVLNSYEPDALSVQTPPPQVHTTSITNDEASSSSGSI--K +UNIPROT|Q90ZM8/1-554 KNGGEGGAGGGQDV-----------SETRPQGERPSGPRDRESAVSSLEAD--------Q + +UNIPROT|Q7LCB3/1-530 LVLTLLEA-EPPHVLISR-PSAPFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLF +UNIPROT|Q9VSE9/1-484 LESSVVTP-NGTCIFQNNNNNDP---NEILSVLSDIYDKELVSVIGWAKQIPGFIDLPLN +UNIPROT|Q9IBD5/1-710 QIISVLESIEPEVVYSGYDNSQPDMPNMLLNSLNRLCERQLLRIVKWSKSLPGFRSLHIN +UNIPROT|Q7LCB3/1-530 LVLTLLEA-EPPHVLISR-PSAPFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLF +UNIPROT|Q9YGV9/1-848 MFLNILEAIEPEVVNAGHDYGQPDSAASLLTSLNELGERQLVKVVKWAKGMPGFRSLYVD +UNIPROT|Q90ZM7/1-438 TLIAILQAIEPEVVMSGYDNTRSQTTAYMLSSLNRLCDKQLVSIVKWAKSLPGFRNLHID +UNIPROT|Q91445/1-344 IFLNVLEAIEPGVVCAGHDNSQPDSFSNLLTSLNELGERQLVYVVKWAKALPGFRNLHVD +UNIPROT|Q9VSE9/1-484 LESSVVTP-NGTCIFQNNNNNDP---NEILSVLSDIYDKELVSVIGWAKQIPGFIDLPLN +UNIPROT|Q90ZM8/1-554 VISALLEA-EPPTVLSSYDPDKPVTEASLMAALTSLADRELVHMITWAKKIPGFTAIGLS + +UNIPROT|Q7LCB3/1-530 DQVRLLESCWMEVLMMGLMWRSIDH--PGKLIFAPDLVLDRDEGKCVEGILEIFDMLLA- +UNIPROT|Q9VSE9/1-484 DQMKLLQVSWAEILTLQLTFRSLPF--NGKLCFATDVWMDEHLAKEC-GYTEFYYHCVQ- +UNIPROT|Q9IBD5/1-710 DQMALIQYSWMSLMVFSLGWRSFQNVTSDYLYFAPDLILNEEYMRRS----PIFDLCMAM +UNIPROT|Q7LCB3/1-530 DQVRLLESCWMEVLMMGLMWRSIDH--PGKLIFAPDLVLDRDEGKCVEGILEIFDMLLA- +UNIPROT|Q9YGV9/1-848 DQMTVIQHSWMAVMVFALGWRSFKNVKSRMLYFAPDLVFNEHRMQVS----TMYEHCIRM +UNIPROT|Q90ZM7/1-438 DQMVLIQYSWMGLMSFAMSWRSFQHTNSKLLYFAPDLVFDETRMQQS----AMYQLCVEM +UNIPROT|Q91445/1-344 DQMSIIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHKS----RMYSQCIRM +UNIPROT|Q9VSE9/1-484 DQMKLLQVSWAEILTLQLTFRSLPF--NGKLCFATDVWMDEHLAKEC-GYTEFYYHCVQ- +UNIPROT|Q90ZM8/1-554 DQVQLLECCWLEILIVGLIWRSIDR--PGQLHFAPNLILGREDARNVEGMLDMFDMLLV- + +UNIPROT|Q7LCB3/1-530 --TTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSRKL-AHLLNAVTDALVW +UNIPROT|Q9VSE9/1-484 --IAQRMERISPRREEYYLLKALLLANC------DILLDDQSSLRAFRDTILNSLNDVVY +UNIPROT|Q9IBD5/1-710 QFIPQEFANLQVTKEEFLCMKVLLLLN-------TVPLEGLKSQPQFDEMRQNYIHELTK +UNIPROT|Q7LCB3/1-530 --TTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSRKL-AHLLNAVTDALVW +UNIPROT|Q9YGV9/1-848 KNFSQEFAMLQVSQEEFLCMKALLLFS-------TIPVEGLKGQNFFDELRRSYINELDR +UNIPROT|Q90ZM7/1-438 RQVSEDFMKLQVTSEEFLCMKAILLLS-------TVPQEGLKSQGCFEEMRISYIRELNR +UNIPROT|Q91445/1-344 RHLSQEFGWLQITPQGFLCMKALLFFS-------IIPVDGLKNQKLFDELRMNYIKELDR +UNIPROT|Q9VSE9/1-484 --IAQRMERISPRREEYYLLKALLLANC------DILLDDQSSLRAFRDTILNSLNDVVY +UNIPROT|Q90ZM8/1-554 --TVSRFRELHLRREEYVCLKAMILLNSGVFFCLSNSAGEQTNVQLIQQILEKVMDALGS + +UNIPROT|Q7LCB3/1-530 VIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNV-----VPVYDLLLEM +UNIPROT|Q9VSE9/1-484 LLRHSSAVSHQQ-----QLLLLLPSLRQADDILRRFWRGIARDEV-----ITMKKLFLEM +UNIPROT|Q9IBD5/1-710 AIHLRENGVVACSQRFYHLTKLMDHMHDIVKKLHLYCLSTFIQADAMR--VEFPEMMSEV +UNIPROT|Q7LCB3/1-530 VIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNV-----VPVYDLLLEM +UNIPROT|Q9YGV9/1-848 LVSFRSK--SSCSERFQQLTRLLDSLQPVLKKLHQFTFDLFVQSQNLSNQVCFPEMISEI +UNIPROT|Q90ZM7/1-438 TIARTEKNAVQCWQRFYQLTKLLXCMQDLVSKLLEFCFATFTQTQVWS--VEFPDMMAEI +UNIPROT|Q91445/1-344 IIACKRKNPTSCSRRFYQLTKVLDSVTPIAKDLHQFTFDLLIKAHMVS--VDYPEMMAEI +UNIPROT|Q9VSE9/1-484 LLRHSSAVSHQQ-----QLLLLLPSLRQADDILRRFWRGIARDEV-----ITMKKLFLEM +UNIPROT|Q90ZM8/1-554 TIGHIEASPPQHSRRLSQLLLLLSQIRHISNKGIEHLNSMKRKNV-----IPLYDLLLEL + +UNIPROT|Q7LCB3/1-530 LNAHVLRGCKSSITGSECSPAEDSKSKEGSQNPQSQ--- +UNIPROT|Q9VSE9/1-484 LE------------------------------PLAR--- +UNIPROT|Q9IBD5/1-710 IASQL------------------PRVLAGMVKPLLFHTK +UNIPROT|Q7LCB3/1-530 LNAHVLRGCKSSITGSECSPAEDSKSKEGSQNPQSQ--- +UNIPROT|Q9YGV9/1-848 ISVHV------------------PKILAGTVKPILFHK- +UNIPROT|Q90ZM7/1-438 ISAQL------------------ASHHGREARALHFHKK +UNIPROT|Q91445/1-344 ISVQV------------------PKILS----------- +UNIPROT|Q9VSE9/1-484 LE------------------------------PLAR--- +UNIPROT|Q90ZM8/1-554 LDAHSLQN-----TGLRTSPP--PQDFRATLVP------ + -- 1.7.10.2