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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

taatctaaaataggtcatacatttgttcactttctacttgttgatgcaccttctgatggtaatgaaaacttactgtaggCCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGCAGGCCAAGACCTTGAAGGTTGCCTGCAATCTGAACAATGCTGCTTGCAA

Basic information

species Glycine max
transcript GLYMA18G32830.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G32830.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv00s0958g00020.t01 (Vitis vinifera), 3'ss of exon 5
-taatctaaaataggtcatacattt-gttcactttctacttgttgatgca--ccttctgatggtaatgaaaactt-----------actgtaggCCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGCAGGCCAAGACCTTGAAGGTTGCCTGCAATCTGAACAATGCTGCTTGCAA
 |||  | | ||  |  |||   || ||  | |   ||   ||   |||    | ||||     |||  |   ||           | || |||| |  |||||||| || ||||||||||| |||||||| || ||||| ||||||||||| ||  | |||||| | ||||| || || ||||| ||||||| 
gtaaaatcatatgtggaatatgcttagtctattgattagcggtctctgccattcctctgtcctcaatttatctttcttttggttgcaatgcagGCTGCAAAGTACATTGAGTATGATTCCTCTTTTGGTGAAGAAGAGAAGAAGCAGGCCAAAACTCTCAAGGTTACTTGCAACCTCAATAATGCGGCTTGCA-

upper sequence: GLYMA18G32830.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv00s0769g00010.t01 (Vitis vinifera), 3'ss of exon 9
-taatctaaaataggtcatacatttgttc-actttctacttgttgatgca--ccttctgatggtaatgaaaactt-----------actgtaggCCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGCAGGCCAAGACCTTGAAGGTTGCCTGCAATCTGAACAATGCTGCTTGCAA
 |||  | | ||  |  |||   ||  || | |   ||   ||   |||    | ||||     |||  |   ||           | || |||| |  |||||||| || ||||||||||| |||||||| || ||||| ||||||||||| ||  | |||||| | ||||| || || ||||| || |||| 
gtaaaatcatatgtgggatatgcttaatctattgattagcggtctctgccattcctctgtcctcaatttatctttcttttggttgcaatgcagGCTGCAAAGTACATTGAGTATGATTCCTCTTTTGGTGAAGAAGAGAAGAAGCAGGCCAAAACTCTCAAGGTTACTTGCAACCTCAATAATGCAGCATGCA-
















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|193557923|gb|FK513706.1|FK513706
EST:     CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGG                         CCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
genomic: CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGGtaatctaaaa ... ttactgtaggCCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
EST: gi|298167977|gb|HO013240.1|HO013240
EST:     CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGG                         CCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
genomic: CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGGtaatctaaaa ... ttactgtaggCCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
EST: gi|207820812|gb|GD789695.1|GD789695
EST:     CAAGAGCTTCCAAAAGATATGAAAAGG                         CCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
genomic: CAAGAGCTTCCAAAAGATATGAAAAGGtaatctaaaa ... ttactgtaggCCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
EST: gi|208247941|gb|GE045357.1|GE045357
EST:     CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGG                         CCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
genomic: CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGGtaatctaaaa ... ttactgtaggCCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
EST: gi|208297825|gb|GE090968.1|GE090968
EST:     CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGG                         CCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
genomic: CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGGtaatctaaaa ... ttactgtaggCCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
EST: gi|14999653|gb|BI320481.1|BI320481
EST:     GTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGG                         CCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
genomic: GTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGGtaatctaaaa ... ttactgtaggCCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
EST: gi|17400187|gb|BM176969.1|BM176969
EST:     CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGG                         CCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
genomic: CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGGtaatctaaaa ... ttactgtaggCCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
EST: gi|13790585|gb|BG653176.1|BG653176
EST:     CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGG                         CCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
genomic: CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGGtaatctaaaa ... ttactgtaggCCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
EST: gi|208140662|gb|GD937846.1|GD937846
EST:     CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGG                         CCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
genomic: CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGGtaatctaaaa ... ttactgtaggCCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
EST: gi|193408318|gb|FK371888.1|FK371888
EST:     CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGG                         CCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
genomic: CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGGtaatctaaaa ... ttactgtaggCCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
EST: gi|11274268|gb|BF324636.1|BF324636
EST:     CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGG                         CCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
genomic: CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGGtaatctaaaa ... ttactgtaggCCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
EST: gi|151413161|gb|EV282969.1|EV282969
EST:     CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGG                         CCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
genomic: CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGGtaatctaaaa ... ttactgtaggCCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
EST: gi|193403025|gb|FK368971.1|FK368971
EST:     CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGG                         CCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
genomic: CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGGtaatctaaaa ... ttactgtaggCCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
EST: gi|207747134|gb|GD721197.1|GD721197
EST:     CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGG                         CTGTAAAGTACATAGAATATGATTCCTCATTCGGTGAGG
genomic: CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGGtaatctaaaa ... ttactgtaggCCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGG
EST: gi|151412679|gb|EV282491.1|EV282491
EST:     CTTGTCTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGG                         CCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
genomic: CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGGtaatctaaaa ... ttactgtaggCCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
EST: gi|208306374|gb|GE106651.1|GE106651
EST:     CTTGTTTAAAGCTAGTAAANATGCAAGAGCTTCCAAAAGATATGAAAAGG                         CCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
genomic: CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGGtaatctaaaa ... ttactgtaggCCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
EST: gi|192316447|gb|FK008180.1|FK008180
EST:     CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGG                         CCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
genomic: CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGGtaatctaaaa ... ttactgtaggCCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
EST: gi|193695631|gb|FK633445.1|FK633445
EST:     CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGG                         CCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
genomic: CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGGtaatctaaaa ... ttactgtaggCCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
EST: gi|208070310|gb|GD870847.1|GD870847
EST:     CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGG                         CCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
genomic: CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGGtaatctaaaa ... ttactgtaggCCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
EST: gi|6724715|gb|AW309048.1|AW309048
EST:     CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGG                         CCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
genomic: CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGGtaatctaaaa ... ttactgtaggCCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
EST: gi|193704914|gb|FK645720.1|FK645720
EST:     CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCC-AAAGATATG-AAAGG                         CCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
genomic: CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGGtaatctaaaa ... ttactgtaggCCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
EST: gi|192316448|gb|FK008181.1|FK008181
EST:     CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGG                         CCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
genomic: CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGGtaatctaaaa ... ttactgtaggCCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
EST: gi|208170991|gb|GD970184.1|GD970184
EST:     CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGG                         CCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
genomic: CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGGtaatctaaaa ... ttactgtaggCCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
EST: gi|193570780|gb|FK529911.1|FK529911
EST:     CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGG                         CCGTGAAGTACATAGAATATGATTCCT
genomic: CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGGtaatctaaaa ... ttactgtaggCCGTGAAGTACATAGAATATGATTCCT
EST: gi|193623836|gb|FK575130.1|FK575130
EST:     CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGG                         CCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGG
genomic: CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGGtaatctaaaa ... ttactgtaggCCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGG
EST: gi|9440155|gb|BE440665.1|BE440665
EST:     CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGG                         CCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC
genomic: CTTGTTTAAAGCTAGTAAATATGCAAGAGCTTCCAAAAGATATGAAAAGGtaatctaaaa ... ttactgtaggCCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcactttctacttgttgatgcaccttctgatggtaatgaaaacttactgtaggCCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGCAGGCCAAGACCTTGAAGGTTGCCTGCAATCTGAACAATGCTGCTTGCAA
                                          aacttac  putative branch site (score: 2)
                                   taatgaaaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatctaaaataggtcatacatttgttcactttctacttgttgatgcaccttctgatggtaatgaaaacttactgtaggCCGTGAAGTACATAGAATATGATTCCTCCTTTGGTGAGGAGGAGAAAAAGCAGGCCAAGACCTTGAAGGTTGCCTGCAATCTGAACAATGCTGCTTGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT