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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAATCCTAGAAATTTGACAAAATGTGAACACCATTTTCACTTATCATGCATTCTTGAGTGGATGGAAAGAAGTGACTCATGTCCTATATGTGATCAGGtttggcttttgcattaactctattacatgaaaagcctcatcttagatttgtttccaatttgcattaaatgcatgtttggtaatgcttaaatttggaaaaa...

Basic information

species Glycine max
transcript GLYMA18G46990.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G46990.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv15s0046g01820.t01 (Vitis vinifera), 5'ss of exon 3
-GAAAATCCTAGAAATTTGACAAAATGTGAACACCATTTTCACTTATCATGCATTCTTGAGTGGATGGAAAGAAGTGACTCATGTCCTATATGTGATCAGGtttggcttttgcattaactctattacatgaaaagcctcatcttagatttgtttccaat-ttgcattaaatgcatgtttgg---taatgcttaaatttggaaaaa-
 || || || | ||   | ||||||||  | || ||||||||  | || |||||||||||||||||||||||||||||  | || ||| | |||||||||||||| || |  || ||| | |||  |||| |  || |        ||||  | |  ||  |  | || ||| |||  |||   |  || |    | |   |  | 
GGAGAACCCAAAAACAATCACAAAATGCAACCATCATTTTCATCTTTCGTGCATTCTTGAGTGGATGGAAAGAAGTGAAACCTGCCCTGTGTGTGATCAGgtttgcctct--cagtaa-tttat--catgcagtgcttagataagaatttcatccatatacttaactagatg-atgactggggctcttgatctgctctatgagtat
















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|58023269|gb|CX710010.1|CX710010
EST:     CATTCTTGAGTGGATGGAAAGAAGTGACTCATGTCCTATATGTGATCAGG                         AGATGATATTTTGACCAGACAATGAATTAGTTTGATTGTTCTAAAATCAAG
genomic: CATTCTTGAGTGGATGGAAAGAAGTGACTCATGTCCTATATGTGATCAGGtttggctttt ... atgttacaggAGATGATATTTTGACCAGACAATGAATTAGTTTGATTGTTCTAAAATCAAG
EST: gi|57575190|gb|CX548165.1|CX548165
EST:     CATTCTTGAGTGGATGGAAAGAAGTGACTCATGTCCTATATGTGATCAGG                         AGATGATATTTTGACCAGACAATGAATTAGTTTGATTGTTCTAAAATCAAG
genomic: CATTCTTGAGTGGATGGAAAGAAGTGACTCATGTCCTATATGTGATCAGGtttggctttt ... atgttacaggAGATGATATTTTGACCAGACAATGAATTAGTTTGATTGTTCTAAAATCAAG
EST: gi|8670491|gb|BE191598.1|BE191598
EST:     CATTCTTGAGTGGATGGAAAGAAGTGACTCATGTCCTATATGTGATCAGG                         AGATGATATTNTGACCAGACAATGAATTAGTTTGATTGTTCTAAAATCAAG
genomic: CATTCTTGAGTGGATGGAAAGAAGTGACTCATGTCCTATATGTGATCAGGtttggctttt ... atgttacaggAGATGATATTTTGACCAGACAATGAATTAGTTTGATTGTTCTAAAATCAAG
EST: gi|254333187|gb|GR850437.1|GR850437
EST:     CATTCTTGAGTGGATGGAAAGAAGTGACTCATGTCCTATATGTGATCAGG                         AGATGATATTTTGACCAGACAATGAATTAGTTTGATTGTTCTAAAATCAAG
genomic: CATTCTTGAGTGGATGGAAAGAAGTGACTCATGTCCTATATGTGATCAGGtttggctttt ... atgttacaggAGATGATATTTTGACCAGACAATGAATTAGTTTGATTGTTCTAAAATCAAG
EST: gi|9903230|gb|BE612198.1|BE612198
EST:     CATTCTTGAGTGGATGGAAAGAAGTGACTCATGTTCTATATGTGATCAAG                         AGATGATATTT
genomic: CATTCTTGAGTGGATGGAAAGAAGTGACTCATGTCCTATATGTGATCAGGtttggctttt ... atgttacaggAGATGATATTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAAATCCTAGAAATTTGACAAAATGTGAACACCATTTTCACTTATCATGCATTCTTGAGTGGATGGAAAGAAGTGACTCATGTCCTATATGTGATCAGGtttggcttttgcattaactctattacatgaaaagcctcatcttagatttgtttccaatttgcattaaatgcatgtttggtaatgcttaaatttggaaaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT