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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attcgaatttaaatataatgactaaaattgaaaaaagttgttgatagacaaaattaaatttagttgattatttgcttactttgaaagtcctgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAAAAATGCAAAGGGGAATCAAGGTTTCCAGCTCAG

Basic information

species Glycine max
transcript GLYMA19G25870.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G25870.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G011923_T01 (Zea mays), 3'ss of exon 3
---attcgaatttaaatataatgactaaaattgaaaaaagttgttgatagacaaaattaaatttagttgattatttgcttactttgaaagtcctgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAAAAATGCAAAGGGGAATCAAGGTTTCCAGCTCAG
    | || |  |   |  ||    | || |  ||  |   | ||| ||  || | ||||       | ||  |||  ||  ||  |||    | || |  |||| || ||||||||||| ||||| || ||||| ||||| ||||||||||| || || ||||| ||||| || || ||||| |||
tgattccgcaaatttgttgaagtttttaattccaatcacacttttggta--catatttaagaaactcttatctttttgttttttccaaacgaatttgct-tagGCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG

upper sequence: GLYMA19G25870.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0068g02040.t01 (Vitis vinifera), 3'ss of exon 3
attcgaatttaaatataatgactaaaattgaaaaaagttgttgatagacaaaattaaatttagtt-gattatttgcttactttgaaagtc--ctgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAAAAATGCAAAGGGGAATCAAGGTTTCCAGCTCAG
     ||| | ||  |  |    |    ||   |   |||   ||  |  | ||||   ||| || || |  ||  |   | |  || |    | | || |||||||| |||||||| ||||||||||| |||||||| || ||||| || |||||||||||||| ||||| |||||||| ||||||
---aaaatcttaaggttttatacatttatggttagttttgcgcatgaaagatattattattattttgaattcttaatagttctataatttgtttcttttacagGCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAAAAATGCAAAGGCGAATCGAGGTTTCCTGCTCAG

upper sequence: GLYMA19G25870.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S4_323V6.1 (Physcomitrella patens), 3'ss of exon 2
--attcgaatttaaatataatgactaaaattgaaaaaagttgttgatagacaaaattaaatttagttgattatttgcttactttgaaagtcctgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAAAAATGCAAAGGGGAATCAAGGTTTCCAGCTCAG
  |   | |  ||  |  |    ||   |         | |||  |         | | |  ||| |  | || |   |  | |  |  | |||| |  ||||||||||||||||| |||||||||||||||||||| |||||||| || || |||||    || || ||||| ||||| || |||
caaggaggacctacttggacgtcctctgacctgtgggtggtgtcaaggacttgcttcagacgtaggttctcatgta--tggtgtttacattctgtatgacagGCAGCAAGTTTTGGAGGCTCTAACATAGATCCAACCGCCTGGGAAGACAAGAAATGTCGGGGAGAGTCAAGATTTCCTGCCCAG

upper sequence: GLYMA19G25870.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S168_104V6.2 (Physcomitrella patens), 3'ss of exon 3
attcgaatttaaatataatgactaaaattgaaaaaagttgttg-atagacaaaattaaatttagttgattatttgcttactttgaaagtcctgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAAAAATGCAAAGGGGAATCAAGGTTTCCAGCTCAG
    | |   ||    |||  | | |  ||  |   ||||| | ||  |  | |||    |    |||     |  |   | |     | || | |  ||||||||||||||||| ||||| |||||||| ||||| |||||||| || || |||||   ||| ||||| || ||||| ||||||
---agcaaggaagatcaatttcaacatctgtgag--gttgtaggatgtattatattcttctggtatgaggtgctaatgcatgtcgtcattctttatgacaggcagCAAGTTTTGGAGGCTCAAACATAGACCCAACCGCCTGGGAAGACAAGAAATGTCGAGGAGAATCGAGATTTCCTGCTCAG

upper sequence: GLYMA19G25870.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S168_104V6.1 (Physcomitrella patens), 3'ss of exon 3
attcgaatttaaatataatgactaaaat-tgaaaaaagttgttg-atagacaaaattaaatttagttgattatttgcttactttgaaagtcctgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAAAAATGCAAAGGGGAATCAAGGTTTCCAGCTCAG
    |||   |   | |   | |  ||  |     | ||||| | ||  |  | |||    |    |||     |  |   | |     | || | |  ||||||||||||||||| ||||| |||||||| ||||| |||||||| || || |||||   ||| ||||| || ||||| ||||||
--gagaagcaaggaagatcaatttcaacatctgtgaggttgtaggatgtattatattcttctggtatgaggtgctaatgcatgtcgtcattctttatgacagGCAGCAAGTTTTGGAGGCTCAAACATAGACCCAACCGCCTGGGAAGACAAGAAATGTCGAGGAGAATCGAGATTTCCTGCTCAG

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|57574688|gb|CX547663.1|CX547663
EST:     CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... tgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|193664031|gb|FK609941.1|FK609941
EST:     CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... tgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|6726683|gb|AW311047.1|AW311047
EST:     CTTTATTTCTTAATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTACCATAGATCCAACTGCCTGGGAGGATAAA
genomic: CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... tgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|14205633|gb|BG839311.1|BG839311
EST:     CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... tgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|16345270|gb|BI970865.1|BI970865
EST:     CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTNNNGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... tgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|298165387|gb|HO011436.1|HO011436
EST:     CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... tgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|11275143|gb|BF325466.1|BF325466
EST:     CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... tgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|208279500|gb|GE080875.1|GE080875
EST:     CTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CTGCATGGTATTTTTGAGgtaagctatt ... tgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|254340597|gb|GR850899.1|GR850899
EST:     CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... tgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|15286212|gb|BI470103.1|BI470103
EST:     CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... tgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|10237029|gb|BE805917.1|BE805917
EST:     CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... tgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|6482567|gb|AW201818.1|AW201818
EST:     CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... tgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|16996811|gb|BM086183.1|BM086183
EST:     CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... tgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|15663461|gb|BI700832.1|BI700832
EST:     TTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... tgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|7233125|gb|AW568475.1|AW568475
EST:     CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... tgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|192334782|gb|FK025273.1|FK025273
EST:     CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... tgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|254339779|gb|GR857904.1|GR857904
EST:     CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... tgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|254335019|gb|GR844804.1|GR844804
EST:     CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... tgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|8283592|gb|BE021151.1|BE021151
EST:     CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... tgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|192304166|gb|FG993492.1|FG993492
EST:     CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... tgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|4289775|gb|AI437974.1|AI437974
EST:     CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... tgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|7693250|gb|AW761345.1|AW761345
EST:     CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... tgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|58019845|gb|CX706587.1|CX706587
EST:     CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... tgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|192316546|gb|FK009315.1|FK009315
EST:     CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CTTTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... tgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agacaaaattaaatttagttgattatttgcttactttgaaagtcctgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAAAAATGCAAAGGGGAATCAAGGTTTCCAGCTCAG
                           tgcttac  putative branch site (score: 2)
     aaattaaatttagttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attcgaatttaaatataatgactaaaattgaaaaaagttgttgatagacaaaattaaatttagttgattatttgcttactttgaaagtcctgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAAAAATGCAAAGGGGAATCAAGGTTTCCAGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - aaatataa
- - - - - - - - - - - - - - -gaaaaaa
- - - - - - - - - - - - - - - - - - gttgttg
- - - - - - - - - - - - - - - - - - - - - - - - - aaattaaa