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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcaataaaagaaagcagtaatttatttcattctaaaggatcagtaaaatagactaatcttttttattattattatcattatttttaaaaaaatgtgcagGGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCAGCTAATAAAAACACTGTTCCTGGAGATGTGTCTGCCATGGTTCCTGGTG

Basic information

species Glycine max
transcript GLYMA18G27710.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G27710.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv00s0211g00090.t01 (Vitis vinifera), 3'ss of exon 4
atcaataaaagaaagcagtaatttatttcattctaaaggatcagtaaaatagactaatcttttttattattatta----tcattatttttaaaaaaat-----gtgcagGGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCAGCTAATAAAAACACTGTTCCTGGAGATGTGTCTGCCATGGTTCCTGGTG
      || | |    |||  ||   | |||| |||   ||  |||  ||    ||   ||| |||| |  |  |     || ||||| | |  |  |     || |||||||||||||||||||||||||| |||||||||||| | |||||||||| |||||| |||||||| ||||||||||||||||| |||||||||||| |||
-----aaatatatgagagttgttggctccatt-taatttatgtgtattat---ttagcttttattataaaaaggaagagccactatttcttatgattttctctgttcagGGTATTGATGGCTCCAGAGTTGAAAAGGTGTTGGAATCTGTTCATATTGTAGCTAACAAAAACACCGTTCCTGGAGATGTGTCGGCCATGGTTCCTAGTG

upper sequence: GLYMA18G27710.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 12
atcaataaaagaaagcagtaatttatttcattctaaaggatcagtaaaatagactaatcttttttattattatta----tcattatttttaaaaaaat-----gtgcagGGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCAGCTAATAAAAACACTGTTCCTGGAGATGTGTCTGCCATGGTTCCTGGTG
      || ||| |  |||  ||   | |||| |||   ||  |||  ||    ||   ||| |||| |  |  |     || ||||| | |  |  |     || |||||||||||||||||||||||||| |||||||||||| | ||||||||||||||||| || ||||| ||||||||||||||||| ||||||||||||||||
-----aaatagataagagttgttggctccatt-taatttatgtgtatcat---ttagcttttattataaaaaggaagagccactatttcttatgattttctctgttcagGGTATTGATGGCTCCAGAGTTGAAAAGGTGTTGGAATCTGTTCATATTGCAGCTAACAAGAACACCGTTCCTGGAGATGTGTCGGCCATGGTTCCTGGTG

upper sequence: GLYMA18G27710.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv00s0211g00070.t01 (Vitis vinifera), 3'ss of exon 12
atcaataaaagaaagcagtaatttatttcattctaaaggatcagtaaaatagactaatcttttttattattatta----tcattatttttaaaaaaat-----gtgcagGGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCAGCTAATAAAAACACTGTTCCTGGAGATGTGTCTGCCATGGTTCCTGGTG
      || |      |||  ||   | |||| |||   ||  |||  ||    |||  ||| |||| |  |  |     |||||||| | |  |  |     || |||||||||||||||||||||||||| |||||||| ||| | |||||||||| |||||| |||||||||||||||||||||||||| |||||||||||| |||
-----aaatatttgagagttgttggctccatt-taatttatgtgtattat---ttaacttttattataaaaaggaagagccattatttcttatgattttctctgttcagGGTATTGATGGCTCCAGAGTTGAAAAGGTGTTAGAATCTGTTCATATTGTAGCTAACAAAAACACTGTTCCTGGAGATGTGTCGGCCATGGTTCCTAGTG

upper sequence: GLYMA18G27710.1 (Glycine max), 3'ss of exon 13
lower sequence: PP1S79_54V6.1 (Physcomitrella patens), 3'ss of exon 12
-----atcaataaaagaaagcagtaat-ttatttcattctaaaggatcagtaaaatagactaatcttttttattattattatcattatttttaaaaaaatgtgcagGGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCAGCTAATAAAAACACTGTTCCTGGAGATGTGTCTGCCATGGTTCCTGGTG
       |  |  |      |  |||  | ||||||| |||  | | |  |  || | |  |     ||  ||  |||||| |   || ||| |     | |  ||||| | || ||||| ||||| |||   ||| ||||    | ||||||||| || || ||||||||||||||||||||||| |||||  | || ||||| |
gtatttcctgtgcattccctctataacatcatttcatgctattgcagctttcgaagaaagaa---cattgaatagttattaacgaaatctttcatt---tttttagGGTGTGGACGGCTCTAGAGTGGAGCGAGTGATGGAGCTTGCTCATATTGCGGCAAACAAAAACACTGTTCCTGGAGATGTATCTGCTCTAGTACCTGGAG

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|193322851|gb|FK288709.1|FK288709
EST:     TTTCTGGGGGAACTGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAG                         GGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATAT
genomic: TTTCTGGGGGAACTGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAGgtaataggaa ... aaatgtgcagGGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATAT
EST: gi|193413746|gb|FK380025.1|FK380025
EST:     TTTCTGGGGGAACTGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAG                         GGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATAT
genomic: TTTCTGGGGGAACTGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAGgtaataggaa ... aaatgtgcagGGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATAT
EST: gi|193328046|gb|FK296895.1|FK296895
EST:     TTTCTGGGGGAACTGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAG                         GGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATAT
genomic: TTTCTGGGGGAACTGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAGgtaataggaa ... aaatgtgcagGGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATAT
EST: gi|120533930|gb|EH262063.1|EH262063
EST:     TTTCTGGGGGAACTGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAG                         GGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCA
genomic: TTTCTGGGGGAACTGAGAATCACCTGGTTTTGGTGAATCTGAAGAATAAGgtaataggaa ... aaatgtgcagGGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaatagactaatcttttttattattattatcattatttttaaaaaaatgtgcagGGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCAGCTAATAAAAACACTGTTCCTGGAGATGTGTCTGCCATGGTTCCTGGTG
      gactaat  putative branch site (score: 2)
         taatcttttttattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcaataaaagaaagcagtaatttatttcattctaaaggatcagtaaaatagactaatcttttttattattattatcattatttttaaaaaaatgtgcagGGTATTGATGGCTCCAGAGTTGAGAAGGTGTTGGAAGCAGTTCATATTGCAGCTAATAAAAACACTGTTCCTGGAGATGTGTCTGCCATGGTTCCTGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- -aataaaa
- - - - - - - - - - - - - ttcattc