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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagtggcctgattgttaacttaataatactgattaactgtagaatgtatgtgcattatctttttaatgcattctgatggcgtatagtatgccttaatcagTTGGCTGGGGTTACATGAGGAAATGAGACTCGACATGCAAAGAATTTGGAGAAGAAATTTAGGGAGAGATGATAGATGTATTGCTGATAATGGGAAGGAG

Basic information

species Glycine max
transcript GLYMA20G03040.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G03040.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv01s0011g00390.t01 (Vitis vinifera), 3'ss of exon 10
aagtggcctgattgttaa-cttaataatactgattaactgtag-aatgtatgtgcattatctttttaatgcattctgatggcgtatagtatgcct-taatcagTTGGCTGGGGTTACATGAGGAAATGAGACTCGACATGCAAAGAATTTGGAGAAGAAATTTAGGGAGAGATGATAGATGTATTGCTGATAATGGGAAGGAG
   | |  |   || ||  | | |  ||| | | | | |||      |||| | | |  || ||||    || | |    || | | | ||   | | ||||||||||| ||| || |||||||||||| | | |||||||| |||||||||| ||| ||  | ||||||||||||||||| |||||||||||||| ||||||
--ttagaatatgtgctattcctgaagatattcaattattgtgatggagtat-tacttattcattttgtctcactatctgtgccttttggatttgtattatcagTTGGCTTGGGCTAAATGAGGAAATGAAATTGGACATGCAGAGAATTTGGAAAAGGAACCTGGGGAGAGATGATAGATGCATTGCTGATAATGGCAAGGAG
















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|193510434|gb|FK469872.1|FK469872
EST:     GAGCAGTGTGCTGGGTATGGGAGACATAGAACAAGTTATAGACGTGGAAG                         TTGGCTGGGGTTACATGAGGAAATGAGACTCGACATGCAAAGAATTTGGAG
genomic: GAGCAGTGTGCTGGGTATGGGAGACATAGAACAAGTTATAGACGTGGAAGgtactactat ... ccttaatcagTTGGCTGGGGTTACATGAGGAAATGAGACTCGACATGCAAAGAATTTGGAG
EST: gi|193395009|gb|FK359112.1|FK359112
EST:     GAGCAGTGTGCTGGGTATGGGAGACATAGAACAAGTTATAGACGTGGAAG                         TTGGCTGGGGTTACATGAGGAAATGAGACTCGACATGCAAAGAATTTGGAG
genomic: GAGCAGTGTGCTGGGTATGGGAGACATAGAACAAGTTATAGACGTGGAAGgtactactat ... ccttaatcagTTGGCTGGGGTTACATGAGGAAATGAGACTCGACATGCAAAGAATTTGGAG
EST: gi|4397242|gb|AI496239.1|AI496239
EST:     GAGCAGTGTGCTGGGTATGGGAGACATAGAACAAGTTATAGACGTGGAAG                         TTGGCTGGGGTTACATGAGGAAATGAGACTCGACATGCAAAGAATTTGGAG
genomic: GAGCAGTGTGCTGGGTATGGGAGACATAGAACAAGTTATAGACGTGGAAGgtactactat ... ccttaatcagTTGGCTGGGGTTACATGAGGAAATGAGACTCGACATGCAAAGAATTTGGAG
EST: gi|120529547|gb|EH257681.1|EH257681
EST:     GAGCAGTGTGCTGGGTATGGGAGACATAGAACAAGTTATAGACGTGGAAG                         TTGGCTGGGGTTACATGAGGAAATGAGACTCGACATGCAAAGAATTTGGAG
genomic: GAGCAGTGTGCTGGGTATGGGAGACATAGAACAAGTTATAGACGTGGAAGgtactactat ... ccttaatcagTTGGCTGGGGTTACATGAGGAAATGAGACTCGACATGCAAAGAATTTGGAG
EST: gi|207736754|gb|GD711807.1|GD711807
EST:     GAGCAGTGTGCTGGGTATGGGAGACATAGAACAAGTTATAGACGTGGAAG                         TTGGCTGGGGTTACATGAGGAAATGAGACTCGACATGACAAAAGTAATTTG
genomic: GAGCAGTGTGCTGGGTATGGGAGACATAGAACAAGTTATAGACGTGGAAGgtactactat ... ccttaatcagTTGGCTGGGGTTACATGAGGAAATGAGACTCGACATG-CAAA-G-AATTTG
EST: gi|23064094|gb|BU578867.1|BU578867
EST:     GAGCAGTGTGCTGGGTATGGGAGACATAGAACAAGTTATAGACGTGGAAG                         TTGGCTGGGGTTACATGAGGAAATGAGAC
genomic: GAGCAGTGTGCTGGGTATGGGAGACATAGAACAAGTTATAGACGTGGAAGgtactactat ... ccttaatcagTTGGCTGGGGTTACATGAGGAAATGAGAC
EST: gi|208268149|gb|GE068990.1|GE068990
EST:     GAGCAGTGTGCTGGGTATGGGAGACATAGAACAAGTTATAGACGTGGAAG                         TTGGCTGGGGTTACATGAGGAAATGAGACTCGACATGCAAAGAATTTTGGA
genomic: GAGCAGTGTGCTGGGTATGGGAGACATAGAACAAGTTATAGACGTGGAAGgtactactat ... ccttaatcagTTGGCTGGGGTTACATGAGGAAATGAGACTCGACATGCAAAGAATTT-GGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatgtgcattatctttttaatgcattctgatggcgtatagtatgccttaatcagTTGGCTGGGGTTACATGAGGAAATGAGACTCGACATGCAAAGAATTTGGAGAAGAAATTTAGGGAGAGATGATAGATGTATTGCTGATAATGGGAAGGAG
                         ttctgat  putative branch site (score: 3)
        attatctttttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagtggcctgattgttaacttaataatactgattaactgtagaatgtatgtgcattatctttttaatgcattctgatggcgtatagtatgccttaatcagTTGGCTGGGGTTACATGAGGAAATGAGACTCGACATGCAAAGAATTTGGAGAAGAAATTTAGGGAGAGATGATAGATGTATTGCTGATAATGGGAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - ggcctga
- - - - - - - - - - - - - - - - - - - - - - - tatgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcattct