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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaaatatttttatatttattttttcttctcttgaatgaaaaaaggttttaacttgttttttatctctcttttttctttttccctttttgtctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGTGAAGCCTCTAGCGTCTGATTGAGAATCTTTAACCCATTCTCTGGCATGC

Basic information

species Glycine max
transcript GLYMA02G15540.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G15540.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0094g00490.t01 (Vitis vinifera), 3'ss of exon 3
----taaaatatttttatatttattttttcttctcttgaatgaaaaaaggttttaacttgttttttatctctcttttttctttttccctttttgtctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGTGAAGCCTCTAGCGTCTG-ATTGAGAATCTTTAACCCATTCTCTGGCATGC
    | |  ||  |||||    |    |   |   |||||||  ||||||||||   |  || |             ||||| ||  ||   | | | || ||| ||||| |||||||||||||| |||||||| || ||||||||||||||||| ||||||    | || | | |   |      |   ||     |  |    
ttttttaggtacctttatgggaaaagatatat---ttgaatgggaaaaggttttgcatcattatactcactatggcattcttattttctgcctttatttt-cagGATTGACAATTGGAAACGTGAACATATACTGCAATTCCTGAGAGAGAAGGTCAAGCCTGCTTCATCAGCAATCTAACCAGGCAGTTCAGCAAATAACCAA-
















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|298163443|gb|HO012176.1|HO012176
EST:     CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAG                         AATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGA
genomic: CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAGgtgagacttg ... tctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGA
EST: gi|10255966|gb|BE823732.1|BE823732
EST:     CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAG                         AATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAGgtgagacttg ... tctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
EST: gi|192330490|gb|FK022663.1|FK022663
EST:     CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAG                         AATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAGgtgagacttg ... tctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
EST: gi|17519610|gb|BM188652.1|BM188652
EST:     CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAG                         AATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAGgtgagacttg ... tctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
EST: gi|298167322|gb|HO010761.1|HO010761
EST:     CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAG                         AATTGATAATTGGAAACGTGAGCATATACTACAGTTCC
genomic: CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAGgtgagacttg ... tctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTCC
EST: gi|298199552|gb|HO042915.1|HO042915
EST:     CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAG                         AATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAGgtgagacttg ... tctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
EST: gi|192332058|gb|FK026338.1|FK026338
EST:     CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAG                         AATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAGgtgagacttg ... tctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
EST: gi|151397361|gb|EV267234.1|EV267234
EST:     CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAAACAG                         AATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAGgtgagacttg ... tctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
EST: gi|192297819|gb|FG988317.1|FG988317
EST:     CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAG                         AATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAGgtgagacttg ... tctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
EST: gi|151394659|gb|EV264530.1|EV264530
EST:     CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAG                         AATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAGgtgagacttg ... tctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
EST: gi|208300317|gb|GE100166.1|GE100166
EST:     CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAG                         AATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAGgtgagacttg ... tctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
EST: gi|58018535|gb|CX705277.1|CX705277
EST:     CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAG                         AATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAGgtgagacttg ... tctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
EST: gi|192330489|gb|FK022662.1|FK022662
EST:     CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAG                         AATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGA
genomic: CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAGgtgagacttg ... tctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGA
EST: gi|298192558|gb|HO036640.1|HO036640
EST:     CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAG                         AATTGATAATTGGAAACGTGAGCATATACTACAGTTC
genomic: CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAGgtgagacttg ... tctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTC
EST: gi|15203957|gb|BI426734.1|BI426734
EST:     CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAG                         AATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAGgtgagacttg ... tctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
EST: gi|298176175|gb|HO015580.1|HO015580
EST:     CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAG                         AATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTG
genomic: CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAGgtgagacttg ... tctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTG
EST: gi|209696840|gb|BW680462.1|BW680462
EST:     CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAG                         AATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAGgtgagacttg ... tctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
EST: gi|120492950|gb|EH221117.1|EH221117
EST:     CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAG                         AATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAGgtgagacttg ... tctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
EST: gi|151411054|gb|EV280865.1|EV280865
EST:     CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAG                         AATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAGgtgagacttg ... tctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
EST: gi|208309776|gb|GE105080.1|GE105080
EST:     CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAG                         AATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAGgtgagacttg ... tctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
EST: gi|10234082|gb|BE802970.1|BE802970
EST:     CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAG                         AATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAGgtgagacttg ... tctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
EST: gi|7147142|gb|AW509064.1|AW509064
EST:     CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCACAAGGAAACAATCAG                         AATTGATAATTGGAAACGTGAGCATATACTACAGTTGCTGAGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAGgtgagacttg ... tctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
EST: gi|298174830|gb|HO017939.1|HO017939
EST:     CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAG                         AATTGATAATT
genomic: CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAGgtgagacttg ... tctgttgcagAATTGATAATT
EST: gi|151408591|gb|EV278399.1|EV278399
EST:     CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAG                         AATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAGgtgagacttg ... tctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
EST: gi|298182792|gb|HO031527.1|HO031527
EST:     CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAG                         AATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTG
genomic: CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAGgtgagacttg ... tctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTG
EST: gi|298166885|gb|HO010324.1|HO010324
EST:     CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAG                         AATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAG
genomic: CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAGgtgagacttg ... tctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAG
EST: gi|208103597|gb|GD907704.1|GD907704
EST:     CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAG                         AATTGATAATT
genomic: CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAGgtgagacttg ... tctgttgcagAATTGATAATT
EST: gi|192331291|gb|FK021002.1|FK021002
EST:     CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAG                         AATTGATAATTGGAAACGTGAGTATATACTACAGTTCCTGAGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAGgtgagacttg ... tctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
EST: gi|192332059|gb|FK026339.1|FK026339
EST:     CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAG                         AATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAGgtgagacttg ... tctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
EST: gi|209696839|gb|BW680461.1|BW680461
EST:     CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAG                         AATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAGgtgagacttg ... tctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
EST: gi|298197039|gb|HO041726.1|HO041726
EST:     CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAG                         AATTGATAATTGGAAACATGAGCATATACTACAGTTCCTGAGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAGgtgagacttg ... tctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
EST: gi|193662354|gb|FK606950.1|FK606950
EST:     CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAG                         AATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAGgtgagacttg ... tctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
EST: gi|120493042|gb|EH221209.1|EH221209
EST:     CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAG                         AATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT
genomic: CCAAAGCTAATTATGCTGGATGAGGTGGGTCAGCAAAAGGAAACAATCAGgtgagacttg ... tctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttaacttgttttttatctctcttttttctttttccctttttgtctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGTGAAGCCTCTAGCGTCTGATTGAGAATCTTTAACCCATTCTCTGGCATGC
 ttttaac  putative branch site (score: 2)
       cttgttttttatctct  CT-rich tract
     aacttgttttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaaatatttttatatttattttttcttctcttgaatgaaaaaaggttttaacttgttttttatctctcttttttctttttccctttttgtctgttgcagAATTGATAATTGGAAACGTGAGCATATACTACAGTTCCTGAGAGAGAAGGTGAAGCCTCTAGCGTCTGATTGAGAATCTTTAACCCATTCTCTGGCATGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - -gaaaaaa