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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttctcttcccagagtcgtagtttaattttcagattagctttggtttcagtattgataatttctattcttaatatattcacagCCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCGAGGATAAGAAACCAGAG

Basic information

species Glycine max
transcript GLYMA20G23080.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G23080.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g61670.1 (Oryza sativa), 3'ss of exon 4
----------------gtacttctcttcccagagtcgtagtttaattttca-gattagctttggtttcagtattgataatttctattctta-atat----attcacagCCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCGAGGATAAGAAACCAGAG
                  |||  |  | |     ||  | |    | |  | | |   || |  || |||   | |||| || |||  | | || |     ||  ||||||||||| ||||| ||||| ||||  ||||||||||| ||||| ||||| || |||
gtaacttagagataattcactggttgttctgacttctgaataggctgtctatgctcttctatttttacagaggtcataacttatatggtaatatgttactgtttgcagCCAGAAGACTGGGACGACAATGAATACATTCCTGATCCTGAGGACAAGAAGCCTGAG
















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|254332429|gb|GR843906.1|GR843906
EST:     ATTGGGATCTTCTCCCTCCAAAGACA-TCAAAGATCCCGAGGCTAAAAAA                         CCAGAAGATTGG-ATGACAAAGAATTTATTCCTGATCCCGAG
genomic: ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAAgtacttctct ... atattcacagCCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCGAG
EST: gi|4289620|gb|AI437497.1|AI437497
EST:     ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAA                         CCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCGAGGATAAGAAA
genomic: ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAAgtacttctct ... atattcacagCCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCGAGGATAAGAAA
EST: gi|298193745|gb|HO040393.1|HO040393
EST:     ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAA                         CCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCGAGGATAAGAAG
genomic: ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAAgtacttctct ... atattcacagCCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCGAGGATAAGAAA
EST: gi|13790097|gb|BG652688.1|BG652688
EST:     ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAA                         CCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCGAGGATAAGAAA
genomic: ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAAgtacttctct ... atattcacagCCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCGAGGATAAGAAA
EST: gi|7147510|gb|AW509432.1|AW509432
EST:     ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAA                         CCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCGAGGATAAGAAA
genomic: ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAAgtacttctct ... atattcacagCCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCGAGGATAAGAAA
EST: gi|22521717|gb|BU080528.1|BU080528
EST:     ATTGGGATCTTTTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAA                         CCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCGAGGATAAGAAA
genomic: ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAAgtacttctct ... atattcacagCCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCGAGGATAAGAAA
EST: gi|207836291|gb|GD806960.1|GD806960
EST:     ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAA-                         CCAGAAGATTGGGATGACAAAGAAATTTATTCCTGATC
genomic: ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAAgtacttctct ... atattcacagCCAGAAGATTGGGATGACAAAGAA-TTTATTCCTGATC
EST: gi|213615216|gb|DB965024.1|DB965024
EST:     ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAA                         CCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCGAGGATAAGAAA
genomic: ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAAgtacttctct ... atattcacagCCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCGAGGATAAGAAA
EST: gi|208339532|gb|GE138594.1|GE138594
EST:     ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAA                         CCAGAAGATTGGGATGACAAAGAAATTTAATTCCTGACTCCCG
genomic: ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAAgtacttctct ... atattcacagCCAGAAGATTGGGATGACAAAGAA-TTTA-TTCCTGA-TCCCG
EST: gi|193404716|gb|FK369601.1|FK369601
EST:     ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAA                         CCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCGAGGATAAGAAA
genomic: ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAAgtacttctct ... atattcacagCCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCGAGGATAAGAAA
EST: gi|208330230|gb|GE132203.1|GE132203
EST:     ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAA                         CCAGAAGATTGGGATGACAAAGAATTTAATTCCTGATCCCG
genomic: ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAAgtacttctct ... atattcacagCCAGAAGATTGGGATGACAAAGAATTTA-TTCCTGATCCCG
EST: gi|24136456|gb|BU926966.1|BU926966
EST:     ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAA                         CCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCGAGGATAAGAAA
genomic: ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAAgtacttctct ... atattcacagCCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCGAGGATAAGAAA
EST: gi|193448512|gb|FK412467.1|FK412467
EST:     ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAA                         CCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCGAGGATAAGAAA
genomic: ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAAgtacttctct ... atattcacagCCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCGAGGATAAGAAA
EST: gi|208188492|gb|GD985178.1|GD985178
EST:     ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAA                         CCNGAAGATTGGGATGACAAAGAATTT
genomic: ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAAgtacttctct ... atattcacagCCAGAAGATTGGGATGACAAAGAATTT
EST: gi|6718756|gb|AW306403.1|AW306403
EST:     ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAA                         CCAGAAGATTGNGATGACAAAGAATNTATTCCTGATCCCGAGGATAAGAAA
genomic: ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAAgtacttctct ... atattcacagCCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCGAGGATAAGAAA
EST: gi|208203090|gb|GD997522.1|GD997522
EST:     ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAA                         CCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCG
genomic: ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAAgtacttctct ... atattcacagCCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCG
EST: gi|18692767|gb|BM521615.1|BM521615
EST:     ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAA                         CCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCGAGGATAAGAAA
genomic: ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAAgtacttctct ... atattcacagCCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCGAGGATAAGAAA
EST: gi|26045988|gb|CA783372.1|CA783372
EST:     ATTGGGATCTTCTCCCTCTTTTTACAATCAAAGATCCCGAGGCTAAAAAA                         CCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCGAGGATAAGAAA
genomic: ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAAgtacttctct ... atattcacagCCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCGAGGATAAGAAA
EST: gi|207755558|gb|GD730419.1|GD730419
EST:     ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAA                         CCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCGAGGATAA
genomic: ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAAgtacttctct ... atattcacagCCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCGAGGATAA
EST: gi|22524331|gb|BU083142.1|BU083142
EST:     ATTGGGATCTTCTCCCTCCAAAGACAATCATTTATCCCGAGGCTAAAAAA                         CCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCGAGGATAAGAAA
genomic: ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAAgtacttctct ... atattcacagCCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCGAGGATAAGAAA
EST: gi|14990999|gb|BI316672.1|BI316672
EST:     ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAA                         CCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCGAGGATAAGAAA
genomic: ATTGGGATCTTCTCCCTCCAAAGACAATCAAAGATCCCGAGGCTAAAAAAgtacttctct ... atattcacagCCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCGAGGATAAGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagattagctttggtttcagtattgataatttctattcttaatatattcacagCCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCGAGGATAAGAAACCAGAG
                                      tcttaat  putative branch site (score: 3)
                tttcagtattgataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttctcttcccagagtcgtagtttaattttcagattagctttggtttcagtattgataatttctattcttaatatattcacagCCAGAAGATTGGGATGACAAAGAATTTATTCCTGATCCCGAGGATAAGAAACCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA