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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaaaatgctaatttagccgtatattatgaactgctattcatgcttccttccagttgctgaaaaaactagacattctctgattaatatcacctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAGGTCCTGGTGGGCGCCCAACAAAAGGAATTGGGCGTGGTCTTGATGATGG

Basic information

species Glycine max
transcript GLYMA03G37170.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G37170.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0060g02240.t01 (Vitis vinifera), 3'ss of exon 5
--tgaaaatgct--aatttagccgta--tattatgaactgctattcatgcttccttccagttgctgaaaaaactagacattctctgattaatatcacctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAGGTCCTGGTGGGCGCCCAACAAAAGGAATTGGGCGTGGTCTTGATGATGG
  || |  |||   |||||| | |||  | ||||| | ||  ||  || |  ||||  |  |  ||  ||  ||      |   | ||| |  |  |  ||||||||| | || ||||| || ||||||||||| || |||||||| |||||||||||| |||||||  | ||| |||| || || ||||||||  | ||||| ||
tgtggatgtgcatgaatttatcagtaggtcttatgga-tgtcatgtattcagcctttaa--tattgctaattct---tgcttcttaattgaattttcaattttcagATAGAAAGCCACCAGGAGTTGGGCGTGGGAGAGGAAGAGGTAGAGAGGAAGGTGCTGGTGGAAGGCCAGCAAAGGGCATAGGGCGTGGCATAGATGAAGG

upper sequence: GLYMA03G37170.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0005g00230.t01 (Vitis vinifera), 3'ss of exon 7
tgaaaatgctaatttagccgtatattatgaactgctattcatgcttccttccagttgctgaaaaaactagacattctctgattaatatcac----ctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAGGTCCTGGTGGGCGCCCAACAAAAGGAATTGGGCGTGGTCTTGATGATGG
     |   |  |  |    | ||  ||  | | || ||||   || | | ||  | || |  ||  | ||  || | ||  |    | |     ||||||||||| | || |||||||| || ||||||||||| || |||||||||||||| ||| || ||||| | ||| | || || ||||||||||| || ||||||||
cttggacaattttgcacttttctagcattgaattct-ttcagaattgcataca--tact-aggaatttggattttttatgtgttgctttatttggctttttcagATAGGAAGCCACCTGGGGTAGGGCGTGGAAGAGGCAGAGGCAGAGAGGACGGTTCTAGTGGGAGGCCAGCGAAGGGCATTGGGCGTGGCCTAGATGATGG
















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|298181980|gb|HO026155.1|HO026155
EST:     GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAG                         ATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
genomic: GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAGgtaagctttg ... cctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
EST: gi|22541271|gb|BU091114.1|BU091114
EST:     GTTATTGATAAAGTCCAAGAAGAAACCAAGAGCCGTGCAT                         ATCGCAAACCACCTGGTGTTGGGCGTGGA
genomic: GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAGgtaagctttg ... cctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGA
EST: gi|4306331|gb|AI443889.1|AI443889
EST:     GTTATTGATAAAGTTCAAGAAGAAACCAAAGAGC-GTGCAG                         ATCGCAAACCA
genomic: GTTATTGATAAAGTTCAAGAAGAAACCAA-GAGCCGTGCAGgtaagctttg ... cctttttcagATCGCAAACCA
EST: gi|298177576|gb|HO027243.1|HO027243
EST:     GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAG                         ATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
genomic: GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAGgtaagctttg ... cctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
EST: gi|15285536|gb|BI469427.1|BI469427
EST:     GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAG                         ATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
genomic: GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAGgtaagctttg ... cctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
EST: gi|20449577|gb|BQ253701.1|BQ253701
EST:     GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAG                         ATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
genomic: GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAGgtaagctttg ... cctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
EST: gi|298188838|gb|HO035531.1|HO035531
EST:     GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAG                         ATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
genomic: GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAGgtaagctttg ... cctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
EST: gi|298167205|gb|HO010644.1|HO010644
EST:     GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAG                         ATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
genomic: GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAGgtaagctttg ... cctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
EST: gi|15287452|gb|BI471343.1|BI471343
EST:     GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAG                         ATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
genomic: GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAGgtaagctttg ... cctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
EST: gi|20449634|gb|BQ253758.1|BQ253758
EST:     GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAG                         ATCGCAAACCACCTGGTGTTGGGCGTGGAAGGTGAAGAGGCAGAGAGGAAG
genomic: GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAGgtaagctttg ... cctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
EST: gi|6227965|gb|AW156627.1|AW156627
EST:     GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAG                         ATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
genomic: GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAGgtaagctttg ... cctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
EST: gi|298165378|gb|HO011427.1|HO011427
EST:     GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAG                         ATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
genomic: GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAGgtaagctttg ... cctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
EST: gi|12773301|gb|BG238228.1|BG238228
EST:     GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAG                         ATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
genomic: GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAGgtaagctttg ... cctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
EST: gi|298181583|gb|HO025758.1|HO025758
EST:     GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAG                         ATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
genomic: GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAGgtaagctttg ... cctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
EST: gi|298169719|gb|HO021079.1|HO021079
EST:     GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAG                         ATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
genomic: GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAGgtaagctttg ... cctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
EST: gi|298190031|gb|HO032152.1|HO032152
EST:     GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAG                         ATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
genomic: GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAGgtaagctttg ... cctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
EST: gi|298180399|gb|HO025600.1|HO025600
EST:     GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAG                         ATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
genomic: GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAGgtaagctttg ... cctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
EST: gi|298195412|gb|HO039243.1|HO039243
EST:     GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAG                         ATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
genomic: GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAGgtaagctttg ... cctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
EST: gi|6724523|gb|AW308922.1|AW308922
EST:     GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAG                         ATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
genomic: GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAGgtaagctttg ... cctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
EST: gi|208176841|gb|GD977690.1|GD977690
EST:     GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAG                         ATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAAGGAA
genomic: GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAGgtaagctttg ... cctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGA-GGAA
EST: gi|24206235|gb|BU965488.1|BU965488
EST:     GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAG                         ATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG
genomic: GTTATTGATAAAGTTCAAGAAGAAACCAAGAGCCGTGCAGgtaagctttg ... cctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccttccagttgctgaaaaaactagacattctctgattaatatcacctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAGGTCCTGGTGGGCGCCCAACAAAAGGAATTGGGCGTGGTCTTGATGATGG
                                  gattaat  putative branch site (score: 3)
                                          tcacctttttc  CT-rich tract
                                 tgattaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaaaatgctaatttagccgtatattatgaactgctattcatgcttccttccagttgctgaaaaaactagacattctctgattaatatcacctttttcagATCGCAAACCACCTGGTGTTGGGCGTGGAAGGGGAAGAGGCAGAGAGGAAGGTCCTGGTGGGCGCCCAACAAAAGGAATTGGGCGTGGTCTTGATGATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - aatgcta
- - - - - - - - - - - - -tatgaac
- - - - - - - - - - - - - - - - tgctatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaactag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cattctc