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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggaacttatggagtaaaatgaatattaaaatttgtttttattgcttattgtaacaagggatggctaatatgtatttcatcatgcttataatttgcagATGCGTGCAGATCAGAAATTGGTTTGATTACCGAAATCACATATGCATT

Basic information

species Glycine max
transcript GLYMA06G08480.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G08480.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0008g04220.t01 (Vitis vinifera), 3'ss of exon 4
gtatggaacttatggagtaaaatgaatattaaaatttgtttttattgcttattgtaacaagggatggctaatatgtatttcatcatgcttataatttgcagATGCGTGCAGATCAGAAATTGGTTTGATTACCGAAATCACATATGCATT
     | || |||  | || | |   |  | || |      ||   |||  |||     | |    |||   |||| | | |   | |||    | | |||||| ||||||||     | |||||||||||||| |||||||||||||| 
-----gtacatatccactagattttctgctgaa-tggaaggttgacgctagttggctttatgccctgctctaatgtttatgaattttcttgctttctacagATGTGTGCAGATTCAGCACTGGTTTGATTACCGGAATCACATATGCATA
















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|193465134|gb|FK432039.1|FK432039
EST:     GAGATTGATGTGCTTCAACAACTAGCGAAGAATGATAGAGGAAGCTCGCG                         ATGCGTGCAGATCAGAAATTGGTTTGATTACCGAAATCACATATGCATTGT
genomic: GAGATTGATGTGCTTCAACAACTAGCGAAGAATGATAGAGGAAGCTCGCGgtatggaact ... taatttgcagATGCGTGCAGATCAGAAATTGGTTTGATTACCGAAATCACATATGCATTGT
EST: gi|193358158|gb|FK319730.1|FK319730
EST:     GAGATTGATGTGCTTCAACAACTAGCGAAGAATGATAGAGGAAGCTCGCG                         ATGCGTGCAGATCAGAAATTGGTTTGATTACCGAAATCACATATGCATT
genomic: GAGATTGATGTGCTTCAACAACTAGCGAAGAATGATAGAGGAAGCTCGCGgtatggaact ... taatttgcagATGCGTGCAGATCAGAAATTGGTTTGATTACCGAAATCACATATGCATT
EST: gi|208265222|gb|GE065018.1|GE065018
EST:     GAGATTGATGTGCTTCAACAACTAGCGAAGAATGATAGAGGAAGCTCGCG                         ATGCGTGCAGATCAGAAATTGGTTTGATTACCGAAATCACATATGCATT
genomic: GAGATTGATGTGCTTCAACAACTAGCGAAGAATGATAGAGGAAGCTCGCGgtatggaact ... taatttgcagATGCGTGCAGATCAGAAATTGGTTTGATTACCGAAATCACATATGCATT
EST: gi|193661905|gb|FK606051.1|FK606051
EST:     GAGATTGATGTGCTTCAACAACTAGCGAAGAATGATAGAGGAAGCTCGCG                         ATGCGTGCAGATCGGAAATTGGTTTGATTACCGAAATCACATATGCATT
genomic: GAGATTGATGTGCTTCAACAACTAGCGAAGAATGATAGAGGAAGCTCGCGgtatggaact ... taatttgcagATGCGTGCAGATCAGAAATTGGTTTGATTACCGAAATCACATATGCATT
EST: gi|193553037|gb|FK507448.1|FK507448
EST:     GAGATTGATGTGCTTCAACAACTAGCGAAGAATGATAGAGGAGGCTCGCG                         ATGCGTGCAGATCAGAAATTGGTTTAATTACCGAAATCACATATGCATT
genomic: GAGATTGATGTGCTTCAACAACTAGCGAAGAATGATAGAGGAAGCTCGCGgtatggaact ... taatttgcagATGCGTGCAGATCAGAAATTGGTTTGATTACCGAAATCACATATGCATT
EST: gi|208200175|gb|GD996048.1|GD996048
EST:     GAGATTGATGTGCTTCAACAACTAGCGAAGAATGATAGAGGAAGCTCGCG                         ATGCGTGCAGATCAGAAATTGGTTTGATTACCGAAATCACATATGCATT
genomic: GAGATTGATGTGCTTCAACAACTAGCGAAGAATGATAGAGGAAGCTCGCGgtatggaact ... taatttgcagATGCGTGCAGATCAGAAATTGGTTTGATTACCGAAATCACATATGCATT
EST: gi|193609602|gb|FK564424.1|FK564424
EST:     GAGATTGATGTGCTTCAACAACTAGCGAAGAATGATAGAGGAGGCTCGCG                         ATGCGTGCAGATCAGAAATTGGTTTAATTACCGAAATCACATATGCATT
genomic: GAGATTGATGTGCTTCAACAACTAGCGAAGAATGATAGAGGAAGCTCGCGgtatggaact ... taatttgcagATGCGTGCAGATCAGAAATTGGTTTGATTACCGAAATCACATATGCATT
EST: gi|193546835|gb|FK501374.1|FK501374
EST:     AGATTGATGTGCTTCAACAACTAGCGAAGAATGATAAGAGGAGGCTCGCG                         ATGCGTGCAGATCAGAAATTGGTTTAATTACCGAAATCACATATGCATT
genomic: AGATTGATGTGCTTCAACAACTAGCGAAGAATGATA-GAGGAAGCTCGCGgtatggaact ... taatttgcagATGCGTGCAGATCAGAAATTGGTTTGATTACCGAAATCACATATGCATT
EST: gi|208202898|gb|GD995300.1|GD995300
EST:     GAGATTGATGTGCTTCAACAACTAGCGAAGAATGATAGAGGAAGCTCGCG                         ATGCGTGCAGATCAGAAATTGGTTTGATTACCGAAATCACATATGCATT
genomic: GAGATTGATGTGCTTCAACAACTAGCGAAGAATGATAGAGGAAGCTCGCGgtatggaact ... taatttgcagATGCGTGCAGATCAGAAATTGGTTTGATTACCGAAATCACATATGCATT
EST: gi|193382442|gb|FK349027.1|FK349027
EST:     GAGATCGATGTGCTTCAACAACTAGCGAAGAATGGTAGAGGAAGCTCGCG                         ATGCGTGCAGATCAGAAATTGGTTTGATTACCGAAATCACATATGCATT
genomic: GAGATTGATGTGCTTCAACAACTAGCGAAGAATGATAGAGGAAGCTCGCGgtatggaact ... taatttgcagATGCGTGCAGATCAGAAATTGGTTTGATTACCGAAATCACATATGCATT
EST: gi|207811844|gb|GD783093.1|GD783093
EST:     GAGATTGATGTGCTTCAACAACTAGCGAAGAATGATAGAGGAAGCTCGCG                         ATGCGTGCAGATCAGAAATTGGTTTGATTACCGAAATCACATATGCATT
genomic: GAGATTGATGTGCTTCAACAACTAGCGAAGAATGATAGAGGAAGCTCGCGgtatggaact ... taatttgcagATGCGTGCAGATCAGAAATTGGTTTGATTACCGAAATCACATATGCATT
EST: gi|193679060|gb|FK620232.1|FK620232
EST:     GAGATTGATGTGCTTCAACAACTAGCGAAGAATGATAGAGGAAGCTCGCG                         ATGCGTGCAGATCAGAAATTGGTTTGATTACCGAAATCACATATGCATT
genomic: GAGATTGATGTGCTTCAACAACTAGCGAAGAATGATAGAGGAAGCTCGCGgtatggaact ... taatttgcagATGCGTGCAGATCAGAAATTGGTTTGATTACCGAAATCACATATGCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttattgtaacaagggatggctaatatgtatttcatcatgcttataatttgcagATGCGTGCAGATCAGAAATTGGTTTGATTACCGAAATCACATATGCATT
                      taatatgtatttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggaacttatggagtaaaatgaatattaaaatttgtttttattgcttattgtaacaagggatggctaatatgtatttcatcatgcttataatttgcagATGCGTGCAGATCAGAAATTGGTTTGATTACCGAAATCACATATGCATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA