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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGAGCAACTACAACTCTTTTGAGGGAGTTCTTTATTGTAAGCCACACTTTGACCAACTGTTCAAAAGAACAGGGAGCCTTGACAAAAGCTTTGAAggtaacaaaggatcaagaatctaattattaaatttctcactaagcttgtcttcttagttactcaaccccacttccttttgtctaacta

Basic information

species Glycine max
transcript GLYMA17G35290.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G35290.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G004959_T01 (Zea mays), 5'ss of exon 2
GCTGAGCAACTACAACTCTTTTGAGGGAGTTCTTTATTGTAAGCCACACTTTGACCAACTGTTCAAAAGAACAGGGAGCCTTGACAAAAGCTTTGAAggtaacaaaggatcaagaatctaattattaaatttctcactaagc---ttgtcttcttagttactcaaccccacttccttttgtctaacta
 ||   |||||||||||| || |||||||| || || || | ||| ||||| ||||| |||||||| || ||||||||| | ||||| ||||| ||||||| ||  |  |        |   | |  | |     |   | |   | || |||||   |      || ||| | |   || ||     
-CTCGCCAACTACAACTCCTTCGAGGGAGTGCTCTACTGCAGGCCTCACTTCGACCAGCTGTTCAAGAGGACAGGGAGCTTGGACAAGAGCTTCGAAGgtatcatcgttttccccccttccctttgcagtacgaaatagatccagtggtgttcttgcgtgtct--cctcacctacaaatggcttcag-

upper sequence: GLYMA17G35290.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv18s0001g09040.t01 (Vitis vinifera), 5'ss of exon 2
GCTGAGCAACTACAACTCTTTTGAGGGAGTTCTTTATTGTAAGCCACACTTTGACCAACTGTTCAAAAGAACAGGGAGCCTTGACAAAAGCTTTGAAggtaacaaaggatcaagaatctaattattaaatttctcactaagcttgtcttcttagttactcaaccccacttccttttgtctaacta-
 ||  | |||||||| || ||||||||||| |||||||| | |||||||||||| ||||| ||||| || || || || || |||||||||||||||||||||||   |   |||      | |||   | |    | ||  || |  |||  | |  | |      |||     | | |    | 
-CTTGGAAACTACAATTCCTTTGAGGGAGTACTTTATTGCAGGCCACACTTTGATCAACTCTTCAAGAGGACTGGCAGTCTAGACAAAAGCTTTGAAGgtaacaactaaatgagagc----taattcgctctgatgcaaaatttcttctctctgctcatgatttttccttttcaattttttttcag
















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|192317453|gb|FK011271.1|FK011271
EST:     ACTTTGACCAACTGTTCAAAAGAACAGGGAGCCTTGACAAAAGCTTTGAA                         GGAACACCAAAAATTGCCAAGCCAGAGAAAAATTTGGAAGA
genomic: ACTTTGACCAACTGTTCAAAAGAACAGGGAGCCTTGACAAAAGCTTTGAAggtaacaaag ... tgtctaactaGGAACACCAAAAATTGCCAAGCCAGAGAAAAATTTGGAAGA
EST: gi|21678062|gb|BQ630413.1|BQ630413
EST:     ACTTTGACCAACTGTTCAAAAGAACAGGGAGCCTTGACAAAAGCTTTGAA                         GGAACACCAAAAATTGCCAAGCCAGAGAAAAATTTGGAAGA
genomic: ACTTTGACCAACTGTTCAAAAGAACAGGGAGCCTTGACAAAAGCTTTGAAggtaacaaag ... tgtctaactaGGAACACCAAAAATTGCCAAGCCAGAGAAAAATTTGGAAGA
EST: gi|22930611|gb|BU547758.1|BU547758
EST:     TCAAAAGAACAGGGAGCCTTGACAAAAGCTTTGAA                         GGAACACCAAAAATTGCCAAGCCAGAGAAAAATTTGGAAGA
genomic: TCAAAAGAACAGGGAGCCTTGACAAAAGCTTTGAAggtaacaaag ... tgtctaactaGGAACACCAAAAATTGCCAAGCCAGAGAAAAATTTGGAAGA
EST: gi|192313493|gb|FK005545.1|FK005545
EST:     ACTTTGACCAACTGTTCAAAAGAACAGGGAGCCTTGACAAAAGCTTTGAA                         GGAACACCAAAAATTGCCAAGCCAGAGAAAAATTTGGAAGA
genomic: ACTTTGACCAACTGTTCAAAAGAACAGGGAGCCTTGACAAAAGCTTTGAAggtaacaaag ... tgtctaactaGGAACACCAAAAATTGCCAAGCCAGAGAAAAATTTGGAAGA
EST: gi|6719641|gb|AW307288.1|AW307288
EST:     ACTTTGACCAACTGTTCAAAAGAACAGGGAGCCTTGACAAAAGCTTTGAA                         GGAACACCAAAAATTGCCAAGCCAGAGAAAAATTTGGAAGA
genomic: ACTTTGACCAACTGTTCAAAAGAACAGGGAGCCTTGACAAAAGCTTTGAAggtaacaaag ... tgtctaactaGGAACACCAAAAATTGCCAAGCCAGAGAAAAATTTGGAAGA
EST: gi|151409626|gb|EV279434.1|EV279434
EST:     ACTTTGACCAACTGTTCAAAAGAACAGGGAGCCTTGACAAAAGCTTTGAA                         GGAACACCAAAAATTGCCAAGCCAGAGAAAAATTTGGAAGA
genomic: ACTTTGACCAACTGTTCAAAAGAACAGGGAGCCTTGACAAAAGCTTTGAAggtaacaaag ... tgtctaactaGGAACACCAAAAATTGCCAAGCCAGAGAAAAATTTGGAAGA
EST: gi|192293922|gb|FG986131.1|FG986131
EST:     ACTTTGACCAACTGTTCAAAAGAACAGGGAGCCTTGACAAAAGCTTTGAA                         GGAACACCAAAAATTGCCAAGCCAGAGAAAAATTTGGAAGA
genomic: ACTTTGACCAACTGTTCAAAAGAACAGGGAGCCTTGACAAAAGCTTTGAAggtaacaaag ... tgtctaactaGGAACACCAAAAATTGCCAAGCCAGAGAAAAATTTGGAAGA
EST: gi|192313492|gb|FK005544.1|FK005544
EST:     ACTTTGACCAACTGTTCAAAAGAACAGGGAGCCTTGACAAAAGCTTTGAA                         GGAACACCAAAAATTGCCAAGCCAGAGAAAAATTTGGAAGA
genomic: ACTTTGACCAACTGTTCAAAAGAACAGGGAGCCTTGACAAAAGCTTTGAAggtaacaaag ... tgtctaactaGGAACACCAAAAATTGCCAAGCCAGAGAAAAATTTGGAAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGAGCAACTACAACTCTTTTGAGGGAGTTCTTTATTGTAAGCCACACTTTGACCAACTGTTCAAAAGAACAGGGAGCCTTGACAAAAGCTTTGAAggtaacaaaggatcaagaatctaattattaaatttctcactaagcttgtcttcttagttactcaaccccacttccttttgtctaacta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC