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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttaaaaaaaactgttctaattgctttaacagattatcatctcatcacttgctattttgttagcaatctatattttcgctgaccttaagtgtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGGCCATTGGAACAGGAAAGGTTGCAACTCCTGCTCAGGCTCAAGAG

Basic information

species Glycine max
transcript GLYMA13G41120.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G41120.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g62420.3 (Oryza sativa), 3'ss of exon 5
gttaaaaaaaactgttctaatt-gctttaacagattatcatctcatcacttgctattttgttagcaatctatattttcgctgaccttaagtgta----tttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGGCCATTGGAACAGGAAAGGTTGCAACTCCTGCTCAGGCTCAAGAG-----
  |    |   || || |  |    | ||      |  |||   |   |||   ||||    | |   |||  |||| |      |||   ||     ||| |||  || |||||  |||||  |||||| |||||||| ||||| |||||||||||||||||||| || ||||||||||| |||||||||||||| |||     
--tctttatggcttttgtggtccattgtactgtgctgacatagaagt-cttctcatttctccacc--cctaactttttgtcttttttactcgtcatatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAGGTATT

upper sequence: GLYMA13G41120.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g62420.5 (Oryza sativa), 3'ss of exon 4
gttaaaaaaaactgttctaattgctttaacag-attatcatctcatcacttgctattttgttagcaatctatattttcgctgaccttaagtgta----tttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGGCCATTGGAACAGGAAAGGTTGCAACTCCTGCTCAGGCTCAAGAG
  |    |   || || |  |   ||  || |   |  |||   |   |||   ||||    | |   |||  |||| |      |||   ||     ||| |||  || |||||  |||||  |||||| |||||||| ||||| |||||||||||||||||||| || ||||||||||| |||||||||||||| |||
--tctttatggcttttgtggtccattgtactgtgctgacatagaagt-cttctcatttctccacc--cctaactttttgtcttttttactcgtcatatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG

upper sequence: GLYMA13G41120.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G146206_T02 (Zea mays), 3'ss of exon 5
gttaaaaaaaactgttctaa---ttgctttaacagattatcatctcatcacttgctattttgttagcaatctatattttcgctgaccttaagtgtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGGCCATTGGAACAGGAAAGGTTGCAACTCCTGCTCAGGCTCAAGAG
  |   |    ||| | | |   ||  |    ||       ||        |    ||||   ||     || | |  |  ||  ||||  ||   |||||||  ||||||||| |||||   ||| | || ||||| ||||| ||||||||||| ||||| || || || ||||||||||||||||||||||| |||
cattctagctgctgctttgaattttattccttcacgcagaaatgagggacttctgaatttctctaattcactgtttactgcctctccttttgt---tttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGGCTATTGGTACCGGCAAAGTTGCAACTCCTGCTCAGGCTCAGGAG

upper sequence: GLYMA13G41120.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0004g04800.t01 (Vitis vinifera), 3'ss of exon 5
gttaaaaaaaactgttctaattgctttaacagattatcatctcatcacttgctattttgttagcaatctatattttcgctgacct--taagtgtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGGCCATTGGAACAGGAAAGGTTGCAACTCCTGCTCAGGCTCAAGAG
  || |  ||  |||  |  | ||  || |   || |  |  |   |  || | | |    |   || | | |  |   | |  |  ||  |    || |||  ||| | ||||  ||||| ||| | |||||||| ||||| || |||||||||||||| || |||||||||||||| ||||||||||| || || 
-ctacatgaatttgtaattgt-gccatatcccttttttctagctgtatgtgttctctatgaacggatatgtttgatgaataatttgctattttctctttcagAAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAA

upper sequence: GLYMA13G41120.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ37925 (Selaginella moellendorffii), 3'ss of exon 5
gttaaaaaaaactgttctaattgctttaacagattatcatctcatcacttgctattttgttagcaatctatattttcgctgaccttaagtgtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGGCCATTGGAACAGGAAAGGTTGCAACTCCTGCTCAGGCTCAAGAG-----
                                 ||    | ||||   ||  | ||   |    ||   | |     ||  | ||   || | |   |||  ||  |     | ||| | ||||| ||  | || || |||||||| ||||| |||||||||||||| ||||| || ||||| ||||| || |||     
--------------------------------gtttgggtttcatgtttttatcttgcatccaaaacacacacccaagcataactcttgtttgtg-acagACAAGGTCAAGGACTGGAAGAATGTGGTGATAGCATACGAGCCAGTGTGGGCGATTGGAACAGGAAAAGTTGCCACCCCTGCGCAGGCCCAGGAGGTCCA

upper sequence: GLYMA13G41120.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ31929 (Selaginella moellendorffii), 3'ss of exon 5
gttaaaaaaaactgttctaattgctttaacagattatcatctcatcacttgctattttgttagcaatctatattttcgctgaccttaagtgtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGGCCATTGGAACAGGAAAGGTTGCAACTCCTGCTCAGGCTCAAGAG-----
                                 ||    | ||||   ||  | ||   |    |    | | |   ||  || |   |  |  | ||||  ||  |     | ||| | ||||| ||  | || || |||||||| ||||| |||||||||||||| ||||| || ||||| |||||||| |||     
--------------------------------gtttgggtttcatgtttttatcttgcatccaaagctcacactcaagcatacttcttg-attgtggcagACAAGGTCAAGGACTGGAAGAATGTGGTGATAGCATACGAGCCAGTGTGGGCGATTGGAACAGGAAAAGTTGCCACCCCTGCGCAGGCTCAGGAGGTCCA

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|207829294|gb|GD798942.1|GD798942
EST:     AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAG                         CTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGG
genomic: AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAGgtagcttttt ... gtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGG
EST: gi|208180403|gb|GD977608.1|GD977608
EST:     AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAG                         CTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGG
genomic: AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAGgtagcttttt ... gtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGG
EST: gi|6071447|gb|AW100834.1|AW100834
EST:     AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAG                         CTAANATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGNG
genomic: AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAGgtagcttttt ... gtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGG
EST: gi|18040397|gb|BM308691.1|BM308691
EST:     AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAG                         CTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGG
genomic: AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAGgtagcttttt ... gtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGG
EST: gi|193542030|gb|FK494504.1|FK494504
EST:     AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAG                         CTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGG
genomic: AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAGgtagcttttt ... gtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGG
EST: gi|207707167|gb|GD687645.1|GD687645
EST:     AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAG                         CTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGG
genomic: AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAGgtagcttttt ... gtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGG
EST: gi|193513329|gb|FK470093.1|FK470093
EST:     AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAG                         CTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGG
genomic: AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAGgtagcttttt ... gtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGG
EST: gi|207830106|gb|GD801462.1|GD801462
EST:     AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAG                         CTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGG
genomic: AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAGgtagcttttt ... gtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGG
EST: gi|208279834|gb|GE078464.1|GE078464
EST:     AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAG                         CTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGG
genomic: AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAGgtagcttttt ... gtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGG
EST: gi|10843979|gb|BF067325.1|BF067325
EST:     AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAG                         CTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGG
genomic: AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAGgtagcttttt ... gtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGG
EST: gi|207698002|gb|GD681067.1|GD681067
EST:     AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAG                         CTAAAATATCAAATTGGGACAATGTCGTTT
genomic: AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAGgtagcttttt ... gtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTT
EST: gi|192308239|gb|FK002751.1|FK002751
EST:     AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAG                         CTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGA
genomic: AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAGgtagcttttt ... gtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGG
EST: gi|193390433|gb|FK356409.1|FK356409
EST:     AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAG                         CTAAAATATCAAATTGGGACAAT
genomic: AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAGgtagcttttt ... gtatttgcagCTAAAATATCAAATTGGGACAAT
EST: gi|208184964|gb|GD981170.1|GD981170
EST:     AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAG                         CTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGG
genomic: AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAGgtagcttttt ... gtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGG
EST: gi|208308523|gb|GE102923.1|GE102923
EST:     AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAG                         CTAAAATATCAAATTGGGACAATGTCG-TTTGGCCTATGAGCCAGTTTGGG
genomic: AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAGgtagcttttt ... gtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGG
EST: gi|192300263|gb|FG987840.1|FG987840
EST:     AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAG                         CTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGG
genomic: AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAGgtagcttttt ... gtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGG
EST: gi|193308287|gb|FK277292.1|FK277292
EST:     AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAG                         CTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGG
genomic: AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAGgtagcttttt ... gtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGG
EST: gi|37997347|gb|CF808936.1|CF808936
EST:     AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAG                         CTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAG
genomic: AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAGgtagcttttt ... gtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAG
EST: gi|151409950|gb|EV279758.1|EV279758
EST:     AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAG                         CTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGG
genomic: AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAGgtagcttttt ... gtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGG
EST: gi|208308386|gb|GE110122.1|GE110122
EST:     AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAG                         CTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGG
genomic: AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAGgtagcttttt ... gtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGG
EST: gi|193508667|gb|FK465823.1|FK465823
EST:     AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAG                         CTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGG
genomic: AGCTGGTACAACAACGGCTGTTGTTGCTGAGCAAACAAAAGCAATTGCAGgtagcttttt ... gtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacttgctattttgttagcaatctatattttcgctgaccttaagtgtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGGCCATTGGAACAGGAAAGGTTGCAACTCCTGCTCAGGCTCAAGAG
                               cgctgac  putative branch site (score: 3)
                   aatctatatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaaaaaaaactgttctaattgctttaacagattatcatctcatcacttgctattttgttagcaatctatattttcgctgaccttaagtgtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGGCCATTGGAACAGGAAAGGTTGCAACTCCTGCTCAGGCTCAAGAG

- -aaaaaaa
- - - - - - - - - - -tgcttta
- - - - - - - - - - - - - - - - - - - - - - -cacttgc