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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCTgtaagaatttcatccttctactgttaatttggtagtttttcagaacacaatcaaaatatgtgtagtcctatttcatggccctgcatattaacattccatt...

Basic information

species Glycine max
transcript GLYMA04G36600.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G36600.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os03g36750.1 (Oryza sativa), 5'ss of exon 5
GTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCTgtaaga-atttcatccttctactgttaatttggtagtttttcagaacacaatcaaaatatgtgtagtcctatttcatggccctgcatattaacattccatt
|| || |||||||| ||||  || ||||| |||||  | ||||||||||| |  |||||||| ||||| |||||||| |||||||| |||||||| |||||  ||||  |  ||| |    || |       |    ||  |  | ||| |  | | | | |    |     |    |    | |  |      |  
GTTTCGGCAATAGTTTCATGTTTACTGGGCCCTGATCGTGCAGAAAAAATTACCATATTTGCTGGAGATGTGGTTCCTCGTAAAAAACCTGATCCAgtaagttattttttaattcaataaatactaattctatcaaacaatattctatctagttctttatgggaagaaaaattatttcgaagtgtatagggcatag-

upper sequence: GLYMA04G36600.1 (Glycine max), 5'ss of exon 5
lower sequence: AT3G48420.1 (Arabidopsis thaliana), 5'ss of exon 5
GTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCTgtaagaatttcatccttc-tactgtta----atttggta-gtttttcagaacacaatcaaaatatgtgtagtcctatttcatggccctgcatattaacattccatt
|| ||||| ||||| |||| |||||| ||||| ||  ||||||| |||||||||||||| ||||||||||| || |||   || || |||||||| |||||    |||   | | | || | |    || || |  | ||       |    | |||    | ||  ||  | ||  ||   ||  | |             
GTTTCTGCTATAGTTTCATGCTTGCTTGGACCAGAACGAGCAGAGAAAATCAAGATATTCGCAGGAGACGTAGTCCCCAAAAAGAAACCTGATCCAgtaagttactcactttccatgctatcacaacatatgttttgcttgcttcgtcttggttaaagaccgagtcatcaaactttttgtttcttaacag------------

upper sequence: GLYMA04G36600.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv17s0000g09910.t01 (Vitis vinifera), 5'ss of exon 5
GTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCTgtaagaatttcatccttct-actgttaatttggtagtttttcagaacacaatcaaaatatgtgtagtcctatttcatggccctgcatat-taacattccatt
|||||||||||||| |||| ||||||||| |||||| |||||||||||||||||||||||||||| ||||||||||| || |||||||||||||| ||||   ||||||||  || | |||| ||   ||   | |  |  || || ||||  ||  |||     || |   | ||  |    |    ||||   |  
GTCTCTGCAATAGTTTCATGCTTGCTGGGGCCTGAGCGAGCAGAAAAAATCAAGATATTTGCAGGCGACGTGGTTCCTCGAAAAAAGCCTGATCCAgtaaacttttcatcccacttaatgttgatgcagtcagtgta-accactcattcaacttaaatgttcatgtagtcagttgctttctggagaccacatggaag-

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|213595680|gb|DB977962.1|DB977962
EST:     AAATCAAGATATTTGCATTAGACGTGGTTCCCCGTAAAAAGCCTGATCCT                         GCCATCTACCTATTAGCAGCCAGCACTCTGAATGTTGAACCTTCAAG
genomic: AAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCTgtaagaattt ... ttcctgacagGCCATCTACCTATTAGCAGCCAGCACTCTGAATGTTGAACCTTCAAG
EST: gi|120495078|gb|EH223245.1|EH223245
EST:     AAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCT                         GCCATCTACCTATTAGCAGCCAGCACTCTGAATGTTGAACCTTCAAG
genomic: AAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCTgtaagaattt ... ttcctgacagGCCATCTACCTATTAGCAGCCAGCACTCTGAATGTTGAACCTTCAAG
EST: gi|8670194|gb|BE191301.1|BE191301
EST:     AAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCT                         GCCATCTACCTATTAGCAGCCAGCACTCTGAATGTTGAACCTTCAAG
genomic: AAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCTgtaagaattt ... ttcctgacagGCCATCTACCTATTAGCAGCCAGCACTCTGAATGTTGAACCTTCAAG
EST: gi|20811539|gb|BQ296017.1|BQ296017
EST:     AAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCT                         GCCATCTACCTATTAGCAGCCAGCACTCTGAATGTTGAACCTTCAAG
genomic: AAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCTgtaagaattt ... ttcctgacagGCCATCTACCTATTAGCAGCCAGCACTCTGAATGTTGAACCTTCAAG
EST: gi|9258673|gb|BE346820.1|BE346820
EST:     AAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCT                         GCCATCTACCTATTAGCAGCCAGCACTCTGAATGTTGAACCTTCAAG
genomic: AAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCTgtaagaattt ... ttcctgacagGCCATCTACCTATTAGCAGCCAGCACTCTGAATGTTGAACCTTCAAG
EST: gi|209718041|gb|BW671874.1|BW671874
EST:     AAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCT                         GCCATCTACCTATTAGCAGCCAGCACTCTGAATGTTGAACCTTCAAG
genomic: AAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCTgtaagaattt ... ttcctgacagGCCATCTACCTATTAGCAGCCAGCACTCTGAATGTTGAACCTTCAAG
EST: gi|19269931|gb|BM886187.1|BM886187
EST:     AAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCT                         GCCATCTACCTATTAGCAGCCAGCACTCTGAATGTTGAACCTTCAAG
genomic: AAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCTgtaagaattt ... ttcctgacagGCCATCTACCTATTAGCAGCCAGCACTCTGAATGTTGAACCTTCAAG
EST: gi|31311871|gb|CD397074.1|CD397074
EST:     AGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCT                         GCCATCTACCTATTAGCAGCCAGCACTCTGAATGTTGAACCTTCAAG
genomic: AGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCTgtaagaattt ... ttcctgacagGCCATCTACCTATTAGCAGCCAGCACTCTGAATGTTGAACCTTCAAG
EST: gi|31310757|gb|CD395960.1|CD395960
EST:     AGCCTGATCCT                         GCCATCTACCTATTAGCAGCCAGCACTCTGAATGTTGAACCTTCAAG
genomic: AGCCTGATCCTgtaagaattt ... ttcctgacagGCCATCTACCTATTAGCAGCCAGCACTCTGAATGTTGAACCTTCAAG
EST: gi|8669990|gb|BE191097.1|BE191097
EST:     AAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCT                         GCCATCTACCTATTAGCAGCCAGCACTCTGAATGTTGAACCTTCAAG
genomic: AAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCTgtaagaattt ... ttcctgacagGCCATCTACCTATTAGCAGCCAGCACTCTGAATGTTGAACCTTCAAG
EST: gi|192318370|gb|FK011026.1|FK011026
EST:     NNNTCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCT                         GCCATCTACCTATTAGCAGCCAGCACTCTGAATGTTGAACCTTCAAG
genomic: AAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCTgtaagaattt ... ttcctgacagGCCATCTACCTATTAGCAGCCAGCACTCTGAATGTTGAACCTTCAAG
EST: gi|6718650|gb|AW306297.1|AW306297
EST:     AAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCT                         GCCATCTACCTATTAGCAGCCAGCACTCTGAATGTTGAACCTTCAAG
genomic: AAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCTgtaagaattt ... ttcctgacagGCCATCTACCTATTAGCAGCCAGCACTCTGAATGTTGAACCTTCAAG
EST: gi|31307094|gb|CD392297.1|CD392297
EST:     AAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCT                         GCCATCTACCTATTAGCAGCCAGCACTCTGAATGTTGAACCTTCAAG
genomic: AAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCTgtaagaattt ... ttcctgacagGCCATCTACCTATTAGCAGCCAGCACTCTGAATGTTGAACCTTCAAG
EST: gi|9564563|gb|BE474072.1|BE474072
EST:     AAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCT                         GCCATCTACCTATTAGCAGCCAGCACTCTGAATGTTGAACCTTCAAG
genomic: AAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCTgtaagaattt ... ttcctgacagGCCATCTACCTATTAGCAGCCAGCACTCTGAATGTTGAACCTTCAAG
EST: gi|11411417|gb|BF423428.1|BF423428
EST:     GTGGGTCCCCGTATAAAGCCTGATCCT                         GCCATCTACCTATTAGCAGCCAGCACTCTGAATGTTGAACCTTCAAG
genomic: GTGGTTCCCCGTAAAAAGCCTGATCCTgtaagaattt ... ttcctgacagGCCATCTACCTATTAGCAGCCAGCACTCTGAATGTTGAACCTTCAAG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTCTGCAATAGTATCATTCTTGCTGGGACCTGAGAGAGCAGAAAAAATCAAGATATTTGCAGGAGACGTGGTTCCCCGTAAAAAGCCTGATCCTgtaagaatttcatccttctactgttaatttggtagtttttcagaacacaatcaaaatatgtgtagtcctatttcatggccctgcatattaacattccatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA