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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

tactgttgcttgtgttattaaaagtaatcttttcagagattttccatgtttcagccatgcaaatcaagaggaatcagtcctctctctcccacgtgaatgatgagaataataatttgatatatttttttttcaatgcagaATTTGATGTTGAAAATCCTAGAAATTTGACAAAATGTGAACACCATTTTCACTTATCATGCATTCTTGAGTGGATGGAAAGAAGTGACTCATGTCCTATA

Basic information

species Glycine max
transcript GLYMA18G46990.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G46990.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv15s0046g01820.t01 (Vitis vinifera), 3'ss of exon 2
---------tactgttg-cttgtgttattaaaagta-atcttttcagagattttccatgtttcagccatgcaaatcaagaggaatcagtcctctctctcccacgtgaatgatgagaata------------ataatttgatatatttttttttcaatg----cagaATTTGATGTTGAAAATCCTAGAAATTTGACAAAATGTGAACACCATTTTCACTTATCATGCATTCTTGAGTGGATGGAAAGAAGTGACTCATGTCCTATA
         ||     | ||   | |  ||| | |  ||   ||     |||||  |  ||       ||    |  |    ||||||   |||   | |  |  |||| |||  |  |            |||| |   |||     ||| | | ||    |||| | |||| | || || || | ||   | ||||||||  | || ||||||||  | || |||||||||||||||||||||||||||||  | || ||| | 
gtgcagccctatcagagtctcaggatgctaacattttattcattttaccatttttaactttctttgtttgtttgtggaattaaatcagctgtcttcatgcgtcaagaattatgtaagcagctgagctcctcataactaattattcaactttgtgactgtttgcagAGTATGATTTGGAGAACCCAAAAACAATCACAAAATGCAACCATCATTTTCATCTTTCGTGCATTCTTGAGTGGATGGAAAGAAGTGAAACCTGCCCTGT-
















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|254333186|gb|GR850436.1|GR850436
EST:     CAAGAATTAGTGACAGAAGAAGAGGATGTCTGTCCAATTTGTCTTGAAGA                         ATTTGATGTTGAAAATCCTAGAAATTTGACAAA-TGTGAACACCATTTTCA
genomic: CAAGAATTAGTGACAGAAGAAGAGGATGTCTGTCCAATTTGTCTTGAAGGtactgttgct ... tcaatgcagaATTTGATGTTGAAAATCCTAGAAATTTGACAAAATGTGAACACCATTTTCA
EST: gi|58023269|gb|CX710010.1|CX710010
EST:     CAAGAATTAGTGACAGAAGAAGAGGATGTCTGTCCAATTTGTCTTGAAGA                         ATTTGATGTTGAAAATCCTAGAAATTTGACAAAATGTGAACACCATTTTCA
genomic: CAAGAATTAGTGACAGAAGAAGAGGATGTCTGTCCAATTTGTCTTGAAGGtactgttgct ... tcaatgcagaATTTGATGTTGAAAATCCTAGAAATTTGACAAAATGTGAACACCATTTTCA
EST: gi|57575190|gb|CX548165.1|CX548165
EST:     CAAGAATTAGTGACAGAAGAAGAGGATGTCTGTCCAATTTGTCTTGAAGA                         ATTTGATGTTGAAAATCCTAGAAATTTGACAAAATGTGAACACCATTTTCA
genomic: CAAGAATTAGTGACAGAAGAAGAGGATGTCTGTCCAATTTGTCTTGAAGGtactgttgct ... tcaatgcagaATTTGATGTTGAAAATCCTAGAAATTTGACAAAATGTGAACACCATTTTCA
EST: gi|8670491|gb|BE191598.1|BE191598
EST:     CAAGAATTAGTGACAGAAGAAGAGGATGTCTGTCCAATTTGTCTTGAAGA                         ATTTGATGTTGAAAATCCTAGAAATTTGACAAAATGTGAACACCATTTTCA
genomic: CAAGAATTAGTGACAGAAGAAGAGGATGTCTGTCCAATTTGTCTTGAAGGtactgttgct ... tcaatgcagaATTTGATGTTGAAAATCCTAGAAATTTGACAAAATGTGAACACCATTTTCA
EST: gi|254333187|gb|GR850437.1|GR850437
EST:     CAAGAATTAGTGACAGAAGAAGAGGATGTCTGTCCAATTTGTCTTGAA-G                         AATTGATGTTGAAAATCCTAGAAATTTGACAAAATGTGAACACCATTTTCA
genomic: CAAGAATTAGTGACAGAAGAAGAGGATGTCTGTCCAATTTGTCTTGAAGGtactgttgct ... tcaatgcagaATTTGATGTTGAAAATCCTAGAAATTTGACAAAATGTGAACACCATTTTCA
EST: gi|9903230|gb|BE612198.1|BE612198
EST:     CAAGAATTAGTGACAGAAGAAGAGGATGTCTGTCCAATATGTCTTGAAGA                         ATATGATGTTGAAAATCCTAGACATTTGACAAAATGTGAACACCATTTTCA
genomic: CAAGAATTAGTGACAGAAGAAGAGGATGTCTGTCCAATTTGTCTTGAAGGtactgttgct ... tcaatgcagaATTTGATGTTGAAAATCCTAGAAATTTGACAAAATGTGAACACCATTTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcccacgtgaatgatgagaataataatttgatatatttttttttcaatgcagaATTTGATGTTGAAAATCCTAGAAATTTGACAAAATGTGAACACCATTTTCACTTATCATGCATTCTTGAGTGGATGGAAAGAAGTGACTCATGTCCTATA
                           atttgat  putative branch site (score: 5)
                                 tatatttttttttc  CT-rich tract
           aatgatgagaataata  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tactgttgcttgtgttattaaaagtaatcttttcagagattttccatgtttcagccatgcaaatcaagaggaatcagtcctctctctcccacgtgaatgatgagaataataatttgatatatttttttttcaatgcagaATTTGATGTTGAAAATCCTAGAAATTTGACAAAATGTGAACACCATTTTCACTTATCATGCATTCTTGAGTGGATGGAAAGAAGTGACTCATGTCCTATA

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