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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTGCTGCAGTTTGCCAGTCTTGGAGGAATATGTGCAAGGACATCGTTAAGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAGgttaggttcattatttttcatagcagactgtttcacttttattaaccaaactattacatttatgtggtgataacaatgatagttgatgttatgggttgaagcagcaccctgattgtttgctcctttcacttttcag

Basic information

species Glycine max
transcript GLYMA15G05490.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G05490.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G046816_T04 (Zea mays), 5'ss of exon 2
ATGTGCTGCAGTTTGCCAGTCTTGGAGGAATATGTGCAAGGACATCGTTAAGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAGgttaggttcattatttttcatagcagactgtttcacttttattaacca---aactattacatttatgtggtg-ataacaatgata-gttgatgttatg-ggttgaagcagcaccctgattgtttgctcctttcacttttcag
 ||||| || || |||    | |||||  | ||||| |  || || || |||||||||||||||| ||| ||| | || || ||||| |||||||||||||| |   |     | | | ||| |  | | |  ||  | || | |       ||  ||     ||     || | |  | || || |   ||  |||  || | |   |  |  || ||  | | |  |||    | | |||
TTGTGCAGCTGTCTGCAGAACATGGAGAGAGATGTGTAGAGAGATTGTCAAGAGCCCAGAGTTTTCTGGAAAAATCACTTTTCCTGTTTCCTTGAAGCAGgtaatcatgcagctatgttataccttattatc-catatatactgattccgttaccgttgtcaatactccatgtacagtattggtatgccaatcatatttggataatctaataagctcatgctgttcctcttctg-tctacag

upper sequence: GLYMA15G05490.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv12s0055g00460.t01 (Vitis vinifera), 5'ss of exon 3
ATGTGCTGCAGTTTGCCAGTCTTGGAGGAATATGTGCAAGGACATCGTTAAGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAGgttaggttcattatttttcatagcagactgtttcacttttattaaccaaactattacatttatgtggtgataacaatgatagttgatgttatgggttgaagcagcaccctgattgtttgctcctttcacttttcag
||| ||||| ||||||| ||| ||||||| |||||| || || || ||||  || ||||||||||||| ||||||||| || || |||||| ||||||||||  | | ||||   | |  |       |||||   |||| |         || |  | ||| | ||  | ||  |  | | ||  |   ||  ||     |||                                
ATGCGCTGCTGTTTGCCGGTCATGGAGGACTATGTGTAAAGAAATTGTTAGAAGTCCAGAGTTTTGTGCCAAACTTACCTTTCCAGTGTCCCTGAAGCAGgtaggatccatttgctctgct--ttatttgttttttttttttccggttccgtaatgaagttacg-ggcaacaaatacta-aattctttccatttgtattttcag--------------------------------
















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|193684875|gb|FK623207.1|FK623207
EST:     AGAG-CCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAG                         CCTGGGCCACGGGATGGAATCATTCAATGTTTTATCAAAAGAGATAAATCT
genomic: AGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAGgttaggttca ... cacttttcagCCTGGGCCACGGGATGGAATCATTCAATGTTTTATCAAAAGAGATAAATCT
EST: gi|207816550|gb|GD787419.1|GD787419
EST:     AGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAG                         CCTGGGCCACGGGATGGAATCATTCAATGTTTTATCAAAAGAGATAAATCT
genomic: AGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAGgttaggttca ... cacttttcagCCTGGGCCACGGGATGGAATCATTCAATGTTTTATCAAAAGAGATAAATCT
EST: gi|254325987|gb|GR838868.1|GR838868
EST:     AGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAG                         CCTGGGCCACGGGATGGAATCATTCAATGTTTTATCAAAAGAGATAAATCT
genomic: AGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAGgttaggttca ... cacttttcagCCTGGGCCACGGGATGGAATCATTCAATGTTTTATCAAAAGAGATAAATCT
EST: gi|207806804|gb|GD778385.1|GD778385
EST:     AGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAG                         CCTGGGCCACGGGATGGAATCATTCAATGTTTTANCAAAAGAGATAAATCT
genomic: AGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAGgttaggttca ... cacttttcagCCTGGGCCACGGGATGGAATCATTCAATGTTTTATCAAAAGAGATAAATCT
EST: gi|193420570|gb|FK390521.1|FK390521
EST:     AGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAG                         CCTGGGCCACGGGATGGAATCATTCAATGTTTTATCAAAAGAGATGAATCT
genomic: AGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAGgttaggttca ... cacttttcagCCTGGGCCACGGGATGGAATCATTCAATGTTTTATCAAAAGAGATAAATCT
EST: gi|193529709|gb|FK487336.1|FK487336
EST:     AGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGGAGCAG                         CCTGGGCCACGGGATGGAATCATTCAATGTTTTATCAAAAGAGATAA
genomic: AGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAGgttaggttca ... cacttttcagCCTGGGCCACGGGATGGAATCATTCAATGTTTTATCAAAAGAGATAA
EST: gi|9440416|gb|BE440921.1|BE440921
EST:     AGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAG                         CCTGGGCCACGGGATGGAATCATTCAATGTTTTATCAAAAGAGATAAATCT
genomic: AGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAGgttaggttca ... cacttttcagCCTGGGCCACGGGATGGAATCATTCAATGTTTTATCAAAAGAGATAAATCT
EST: gi|208084291|gb|GD882281.1|GD882281
EST:     AGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAG                         CCTGGGCCACGGGATGGAATCATTCAATGTTTTATCAAAAG
genomic: AGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAGgttaggttca ... cacttttcagCCTGGGCCACGGGATGGAATCATTCAATGTTTTATCAAAAG
EST: gi|208308909|gb|GE104087.1|GE104087
EST:     AGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAG                         CCTGGGCCACGGGATGGAATCATTCAATGTTTTATCAAAAGAGATAAATCT
genomic: AGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAGgttaggttca ... cacttttcagCCTGGGCCACGGGATGGAATCATTCAATGTTTTATCAAAAGAGATAAATCT
EST: gi|208037728|gb|GD833642.1|GD833642
EST:     AGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAG                         CCTGGGCCACGGGATGGAATCATTCAATGTTTTATC
genomic: AGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAGgttaggttca ... cacttttcagCCTGGGCCACGGGATGGAATCATTCAATGTTTTATC
EST: gi|208325460|gb|GE120122.1|GE120122
EST:     AGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAG                         CCTGGGCCACGGGATGGAATCATTCAATGTTTTATCAAAAGAGATAAATCT
genomic: AGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAGgttaggttca ... cacttttcagCCTGGGCCACGGGATGGAATCATTCAATGTTTTATCAAAAGAGATAAATCT
EST: gi|208183773|gb|GD985705.1|GD985705
EST:     AGACCCAAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAG                         CCTGGGCCACGGGATGGAATCATTCAATGTTTTATCAAAAGAGATAAATCT
genomic: AG-CCC-AGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAGgttaggttca ... cacttttcagCCTGGGCCACGGGATGGAATCATTCAATGTTTTATCAAAAGAGATAAATCT
EST: gi|193641904|gb|FK591120.1|FK591120
EST:     AGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAG                         CCTGGGCCACGGGATGGAATCATTCAATGTTTTATCAAAAGAGATAAATCT
genomic: AGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAGgttaggttca ... cacttttcagCCTGGGCCACGGGATGGAATCATTCAATGTTTTATCAAAAGAGATAAATCT
EST: gi|192295815|gb|FG990867.1|FG990867
EST:     AGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAG                         CCTGGGCCACGGGATGGAATCATTCAATGTTTTATCAAAAGAGATAAATCT
genomic: AGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAGgttaggttca ... cacttttcagCCTGGGCCACGGGATGGAATCATTCAATGTTTTATCAAAAGAGATAAATCT
EST: gi|151394349|gb|EV264220.1|EV264220
EST:     AGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAG                         CCTGGGCCACGGGATGGAATCATTCAATGTTTTATCAAAAGAGATAAATCT
genomic: AGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAGgttaggttca ... cacttttcagCCTGGGCCACGGGATGGAATCATTCAATGTTTTATCAAAAGAGATAAATCT
EST: gi|208069109|gb|GD869087.1|GD869087
EST:     AGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAG                         CCTGGGCCACGGGATGGAATCATTCAATGTTTTATCAAAAGAGATAAATCT
genomic: AGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAGgttaggttca ... cacttttcagCCTGGGCCACGGGATGGAATCATTCAATGTTTTATCAAAAGAGATAAATCT
EST: gi|207771965|gb|GD743482.1|GD743482
EST:     AGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAG                         CCTGGGCCACGGGATGGAATCATTCAATGTTTTATCAAAAGAGATAAATCT
genomic: AGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAGgttaggttca ... cacttttcagCCTGGGCCACGGGATGGAATCATTCAATGTTTTATCAAAAGAGATAAATCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGTGCTGCAGTTTGCCAGTCTTGGAGGAATATGTGCAAGGACATCGTTAAGAGCCCAGAGTTTTGTGGCAAACTTACATTCCCTGTGTCCTTGAAGCAGgttaggttcattatttttcatagcagactgtttcacttttattaaccaaactattacatttatgtggtgataacaatgatagttgatgttatgggttgaagcagcaccctgattgtttgctcctttcacttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC