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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaactcacttttcattctcttctcttttatttctaacttattattattatgatggtgatggtgatgttgatgatgatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGCGACACATGGATGAACATCCATCTGCGAGAAGTCATTTGTACATCTAAA

Basic information

species Glycine max
transcript GLYMA03G37170.2
intron # 2
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 2
lower sequence: LOC_Os01g15310.1 (Oryza sativa), 3'ss of exon 2
-------gcaactcact-tttcattctcttctcttttatt-tctaactta-ttattattatgatggtgatggtgatgttgatg--atgatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGCGACACATGGATGAACATCCATCTGCGAGAAGTCATTTGTACATCTAAA
          |  | |   |||   || | |    |  || | |   ||  ||  |  |  | | | | | |  |  ||  ||   |  | |   || | ||||| || || || || ||||| || |||||||| ||||| || |||||||| |||||||||||||| || || || || ||||| || || || 
gtaagagaagatccgccgcttcgcgctgtgcgtggtggttgtttggtttggtttctgatcggctagggtttgaaacttttgtgtggtttttttttagCTCGTGGAGCTTAAGAACGGCGAGACGTACAACGGGCACTTGGTGAACTGCGACACGTGGATGAACATCCACCTCCGGGAGGTTATTTGCACCTCAAAG

upper sequence: GLYMA03G37170.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G038606_T03 (Zea mays), 3'ss of exon 2
---------------------gcaactcacttttcattctcttctct-----tttatttctaacttattattattatgatggtgatggtgatgttgatgatgatgtaa---cagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGCGACACATGGATGAACATCCATCTGCGAGAAGTCATTTGTACATCTAAA-
                     |    ||   |||| |  || | | |      | |||      | | | |  |  |  |  |||  ||    ||||   |  ||| |   ||| | ||||| ||||| ||||| |||||||| ||||||||| |||| ||||||||||| |||||||||||||||||  | || || ||||| || || ||  
gtaaggacgtaaggtcccgttggccttcttctttcgtcgtcgtttttggcgtctgattctccgttcaatctattgttagtcctgaccgttgaattgaaactattgtgatctcagCTCGTGGAGCTGAAGAATGGTGAGACATACAACGGGCATCTGGTCAATTGCGACACGTGGATGAACATCCATCTTAGGGAGGTTATTTGCACCTCAAAGG

upper sequence: GLYMA03G37170.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G038606_T02 (Zea mays), 3'ss of exon 2
---------------------gcaactcacttttcattctcttctct-----tttatttctaacttattattattatgatggtgatggtgatgttgatgatgatgtaa---cagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGCGACACATGGATGAACATCCATCTGCGAGAAGTCATTTGTACATCTAAA
                     |    ||   |||| |  || | | |      | |||      | | | |  |  |  |  |||  ||    ||||   |  ||| |   ||| | ||||| ||||| ||||| |||||||| ||||||||| |||| ||||||||||| |||||||||||||||||  | || || ||||| || || || 
gtaaggacgtaaggtcccgttggccttcttctttcgtcgtcgtttttggcgtctgattctccgttcaatctattgttagtcctgaccgttgaattgaaactattgtgatctcagCTCGTGGAGCTGAAGAATGGTGAGACATACAACGGGCATCTGGTCAATTGCGACACGTGGATGAACATCCATCTTAGGGAGGTTATTTGCACCTCAAAG

upper sequence: GLYMA03G37170.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G095114_T01 (Zea mays), 3'ss of exon 2
-----------gcaactcacttttcattctcttctcttttatttctaacttattatt-attatgatggtgatggtga-tgttgatgatga--------tgtaa---cagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGCGACACATGGATGAACATCCATCTGCGAGAAGTCATTTGTACATCTAAA
           |   ||  ||| |       |  | |||    | | | |  |  || | | |  || | ||  ||| |  |||   | |        |||     ||| | ||||| ||||| ||||| ||||| || ||||||||| |||| ||||||||||| |||||||||||||| ||  | || || ||||| || || || 
gtaagatcccggtgtctggcttctttcgtcgtcgtttttggcgtgtgattattcgttcagtctattgtttatcctgagtcctgaccgttaaaactttttgtgttctcagCTCGTGGAGCTGAAGAATGGTGAGACGTACAACGGGCATCTGGTCAATTGCGACACGTGGATGAACATCCACCTTAGGGAGGTTATTTGCACCTCAAAG

upper sequence: GLYMA03G37170.2 (Glycine max), 3'ss of exon 2
lower sequence: AT5G27720.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------------------------------gcaactcacttttcattctcttctcttttatt-tctaacttattattattatgatggtgatggtgatgttgatgatgatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGCGACACATGGATGAACATCCATCTGCGAGAAGTCATTTGTACATCTAAA
                                               | | || | |||   |   | |  | ||     |||||   |   ||  | | |  || ||  |||   |  |  || | |   || | ||||| || || ||||| |||||||| || ||||||||||| ||||| || || |||||||||||||||||||| |||||||| |||||||| || 
gtgagtaaaatttcgacccttgattacaattttgttatatatgaagtgaagctgagtttaagtgagcattgcattagggatctaaaggaac-ttccttttactgtaattttgaatcttgttttgttttggtagCTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGTGATACTTGGATGAACATCCATCTGCGTGAAGTCATATGTACATCAAAG

upper sequence: GLYMA03G37170.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0060g02240.t01 (Vitis vinifera), 3'ss of exon 2
---------gcaactcacttttcattctcttctcttttatttctaactta--ttattattatgatggtgatggt----gatgttgatgatgatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGCGACACATGGATGAACATCCATCTGCGAGAAGTCATTTGTACATCTAAA
           |  ||  || |  | ||||||| ||    |  | |  |   |   |||| |  |    ||  |    |   ||| |  |  |||  ||||||||||| |||||||||||||| || || || || ||||| || ||||| || ||||||||||||||||||||||| |||||||| || || || |||
acatatagcataggtctattattttcctcttcttttcctctggtgagatggctaggtattttagtatatattttacaagtcattgttattattgtggcagTTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAA

upper sequence: GLYMA03G37170.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0005g00230.t01 (Vitis vinifera), 3'ss of exon 4
------------gcaactcacttttcattctc---ttctcttttatttctaacttattattattatga--tggtgatggtgatgttgatgatgatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGCGACACATGGATGAACATCCATCTGCGAGAAGTCATTTGTACATCTAAA
             |||        ||  | |    || ||||| |    || | | | | | |  |||  ||    |  |  || |  | ||| ||| | |||||||||| || |||||||| || || || || |||||||||||||| || || || ||||||||||| ||||| || ||||| || ||||| || |||
cctcagatgaaaacaagcagagcctcgatgtaaaattttctttaagagttagcatctcact-tcgtgacctgtaacttatactgcttgt-atgttgtgatagTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGTGATACTTGGATGAACATTCATCTTCGGGAAGTTATCTGTACCTCAAAA

upper sequence: GLYMA03G37170.2 (Glycine max), 3'ss of exon 2
lower sequence: EFJ10085 (Selaginella moellendorffii), 3'ss of exon 1
gcaactcacttttcattctcttctcttttatttctaacttattattattatgatggtgatggtgatgttgatgatgatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGCGACACATGGATGAACATCCATCTGCGAGAAGTCATTTGTACATCTAAA-
                                  | | | ||  |  |  |     |  | ||  ||   ||   | |     || | ||||| || || ||||| ||||| || || ||||||||||| |  ||||| |  ||||||||||||||||| |||||||| ||||| || || ||  
---------------------------------gtgagtgatgttcttcgtttccttctttgtc-tgaaaatt-cgcttgggtagCTAGTGGAGCTCAAGAATGGAGAGACTTACAATGGGCATTTGGTGAGCTGCGATAGCTGGATGAACATCCATCTACGAGAAGTTATTTGCACTTCCAAGG

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:     CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATG                         TTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
genomic: CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATGgcaactcact ... gatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
EST: gi|22541271|gb|BU091114.1|BU091114
EST:     ACGACATGCTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATG                         TTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
genomic: ACGACATGCTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATGgcaactcact ... gatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
EST: gi|4306331|gb|AI443889.1|AI443889
EST:     CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATG                         TTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
genomic: CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATGgcaactcact ... gatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
EST: gi|298177576|gb|HO027243.1|HO027243
EST:     CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATG                         TTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
genomic: CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATGgcaactcact ... gatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
EST: gi|15285536|gb|BI469427.1|BI469427
EST:     CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATG                         TTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
genomic: CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATGgcaactcact ... gatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
EST: gi|20449577|gb|BQ253701.1|BQ253701
EST:     CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATG                         TTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
genomic: CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATGgcaactcact ... gatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
EST: gi|298188838|gb|HO035531.1|HO035531
EST:     CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATG                         TTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
genomic: CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATGgcaactcact ... gatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
EST: gi|298167205|gb|HO010644.1|HO010644
EST:     TTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATG                         TTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAGTTGC
genomic: CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATGgcaactcact ... gatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
EST: gi|15287452|gb|BI471343.1|BI471343
EST:     CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATG                         TTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
genomic: CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATGgcaactcact ... gatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
EST: gi|20449634|gb|BQ253758.1|BQ253758
EST:     CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATG                         TTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
genomic: CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATGgcaactcact ... gatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
EST: gi|11689790|gb|BF597466.1|BF597466
EST:     GCTTACTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATG                         TTGGTGGAACCGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
genomic: GCTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATGgcaactcact ... gatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
EST: gi|6227965|gb|AW156627.1|AW156627
EST:     CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATG                         TTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
genomic: CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATGgcaactcact ... gatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
EST: gi|298165378|gb|HO011427.1|HO011427
EST:     CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATG                         TTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
genomic: CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATGgcaactcact ... gatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
EST: gi|12773301|gb|BG238228.1|BG238228
EST:     CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATG                         TTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
genomic: CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATGgcaactcact ... gatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
EST: gi|298181583|gb|HO025758.1|HO025758
EST:     CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATG                         TTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
genomic: CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATGgcaactcact ... gatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
EST: gi|298177163|gb|HO027058.1|HO027058
EST:     CTTCCTCTTTCCCTTCTCAAGATTGCCCAAGGCCACCCTATG                         TTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
genomic: CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATGgcaactcact ... gatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
EST: gi|298169719|gb|HO021079.1|HO021079
EST:     CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATG                         TTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
genomic: CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATGgcaactcact ... gatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
EST: gi|298190031|gb|HO032152.1|HO032152
EST:     CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATG                         TTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
genomic: CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATGgcaactcact ... gatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
EST: gi|298180399|gb|HO025600.1|HO025600
EST:     CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATG                         TTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
genomic: CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATGgcaactcact ... gatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
EST: gi|298195412|gb|HO039243.1|HO039243
EST:     CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATG                         TTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
genomic: CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATGgcaactcact ... gatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
EST: gi|6724523|gb|AW308922.1|AW308922
EST:     CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATG                         TTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
genomic: CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATGgcaactcact ... gatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
EST: gi|24206235|gb|BU965488.1|BU965488
EST:     CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATG                         TTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC
genomic: CTTCCTCTTTCCCTTCTCAAGACTGCCCAAGGCCACCCTATGgcaactcact ... gatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctaacttattattattatgatggtgatggtgatgttgatgatgatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGCGACACATGGATGAACATCCATCTGCGAGAAGTCATTTGTACATCTAAA
     aacttattattattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaactcacttttcattctcttctcttttatttctaacttattattattatgatggtgatggtgatgttgatgatgatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGCGACACATGGATGAACATCCATCTGCGAGAAGTCATTTGTACATCTAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT