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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgaagtgtttctttataatttgacatttacttccattgaatttctaatattaacttgaattgtatatattgcgatgtcatatatttctttgttttcgtgaaacagCTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATCATGTCGACTCTTTTGGTGAGAAAGCAATTGCCGAGATTAAGAAGCAATA

Basic information

species Glycine max
transcript GLYMA05G37300.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G37300.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0025g00640.t01 (Vitis vinifera), 3'ss of exon 4
gtaatgaagtgtttctttataatttgacatttact--tccattgaatttctaatattaacttgaattgtatatattgcgatgtcatatatttctttgttttcgtgaaacagCTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATCATGTCGACTCTTTTGGTGAGAAAGCAATTGCCGAGATTAAGAAGCAATA
|||||||  | | | |||||  ||| | |   | |  |  ||||| ||| |||   ||  || ||| || | |       || |||  | || | || |||| | |||||| |||||||||||||||||| ||||||||||| |||||||||||||| || |  || ||||| ||||  ||||| ||||| |  ||||| ||||  || ||
gtaatgatttttatttttatt-tttaaaaaaaattaatttattgattttttaaacata--tttaatagttttt-------tgacattgacttttatgatttcctaaaacagTTTTTGTTTTGCTTCACACCGTGCCTGTGCTGTATGAGAAATATGAGGACCCAGTGGACTCATTTGCAGAGAAGGCAATGGTGGAGATCAAGAGACAGTA
















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|207713175|gb|GD697159.1|GD697159
EST:     TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAG                         CTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
genomic: TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAGgtaatgaagt ... cgtgaaacagCTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
EST: gi|192308804|gb|FK000138.1|FK000138
EST:     TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAG                         CTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
genomic: TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAGgtaatgaagt ... cgtgaaacagCTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
EST: gi|15662661|gb|BI700032.1|BI700032
EST:     TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAG                         CTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
genomic: TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAGgtaatgaagt ... cgtgaaacagCTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
EST: gi|192304897|gb|FG996071.1|FG996071
EST:     TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAG                         CTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGGTC
genomic: TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAGgtaatgaagt ... cgtgaaacagCTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
EST: gi|254333646|gb|GR848564.1|GR848564
EST:     TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAG                         CTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
genomic: TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAGgtaatgaagt ... cgtgaaacagCTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
EST: gi|151395586|gb|EV265463.1|EV265463
EST:     TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAG                         CTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
genomic: TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAGgtaatgaagt ... cgtgaaacagCTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
EST: gi|192298967|gb|FG987712.1|FG987712
EST:     TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAG                         CTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
genomic: TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAGgtaatgaagt ... cgtgaaacagCTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
EST: gi|14991971|gb|BI317644.1|BI317644
EST:     TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAG                         CTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
genomic: TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAGgtaatgaagt ... cgtgaaacagCTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
EST: gi|208193014|gb|GD988413.1|GD988413
EST:     TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAG                         CTTTTGTTTTGCTTCAC
genomic: TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAGgtaatgaagt ... cgtgaaacagCTTTTGTTTTGCTTCAC
EST: gi|207738118|gb|GD715126.1|GD715126
EST:     TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACAAAG                         CTTTTGTTTTG
genomic: TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAGgtaatgaagt ... cgtgaaacagCTTTTGTTTTG
EST: gi|207835434|gb|GD807895.1|GD807895
EST:     TCTCTATTCTGGGTTTGTTTGGGCCAACTTCTTGACCTTGTTCTACATAG                         CTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
genomic: TCTCTATTCTGGG-TTG-TTGGGCCAACTTCTTGACCTTGTTCTACATAGgtaatgaagt ... cgtgaaacagCTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
EST: gi|192330925|gb|FK023098.1|FK023098
EST:     TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAG                         CTTTTGTTTTGCTCCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
genomic: TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAGgtaatgaagt ... cgtgaaacagCTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
EST: gi|254335900|gb|GR847428.1|GR847428
EST:     GCCAACTTCTTGACCTTGTTCTACATAG                         CTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
genomic: GCCAACTTCTTGACCTTGTTCTACATAGgtaatgaagt ... cgtgaaacagCTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
EST: gi|193720285|gb|FK659321.1|FK659321
EST:     TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAG                         CTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
genomic: TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAGgtaatgaagt ... cgtgaaacagCTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
EST: gi|213602678|gb|DB956614.1|DB956614
EST:     TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAG                         CTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAA-TATGAAGATC
genomic: TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAGgtaatgaagt ... cgtgaaacagCTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
EST: gi|208199358|gb|GE001560.1|GE001560
EST:     TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAG                         CTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATNTGAAGATC
genomic: TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAGgtaatgaagt ... cgtgaaacagCTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
EST: gi|6667541|gb|AW278992.1|AW278992
EST:     TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAG                         CTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
genomic: TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAGgtaatgaagt ... cgtgaaacagCTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
EST: gi|26059213|gb|CA802127.1|CA802127
EST:     TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAG                         CTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
genomic: TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAGgtaatgaagt ... cgtgaaacagCTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
EST: gi|163918183|gb|EH039899.1|EH039899
EST:     TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAG                         CTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
genomic: TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAGgtaatgaagt ... cgtgaaacagCTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
EST: gi|193545509|gb|FK499984.1|FK499984
EST:     TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAG                         CTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
genomic: TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAGgtaatgaagt ... cgtgaaacagCTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
EST: gi|38191865|gb|CF921071.1|CF921071
EST:     TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAG                         CTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
genomic: TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAGgtaatgaagt ... cgtgaaacagCTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
EST: gi|193583654|gb|FK541104.1|FK541104
EST:     TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAG                         CTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAA
genomic: TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAGgtaatgaagt ... cgtgaaacagCTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAA
EST: gi|193658368|gb|FK605461.1|FK605461
EST:     TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAG                         CTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
genomic: TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAGgtaatgaagt ... cgtgaaacagCTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
EST: gi|192327130|gb|FK015522.1|FK015522
EST:     TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAG                         CTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC
genomic: TTTCTCTATTCTGGGTTGTTGGGCCAACTTCTTGACCTTGTTCTACATAGgtaatgaagt ... cgtgaaacagCTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taacttgaattgtatatattgcgatgtcatatatttctttgttttcgtgaaacagCTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATCATGTCGACTCTTTTGGTGAGAAAGCAATTGCCGAGATTAAGAAGCAATA
 tattaac  putative branch site (score: 1)
                               tatttctttgttttc  putative PPT
                            atatatttctttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgaagtgtttctttataatttgacatttacttccattgaatttctaatattaacttgaattgtatatattgcgatgtcatatatttctttgttttcgtgaaacagCTTTTGTTTTGCTTCACACTGTGCCTGTGCTTTATGAGAAATATGAAGATCATGTCGACTCTTTTGGTGAGAAAGCAATTGCCGAGATTAAGAAGCAATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA