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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcttgcatcctttagtattattatttttaaccacttttcaaatataatggctaaaattgaaaaaatttagttgattatttgcttaccttgaaattgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAG

Basic information

species Glycine max
transcript GLYMA16G06100.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G06100.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G011923_T01 (Zea mays), 3'ss of exon 3
----ttcttgcatcctttagtattattatttttaaccacttttcaaatataatggctaaaattgaaaaaatttagttgattatttgcttaccttgaaattgc--agGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAG
    | |    ||   ||    || ||| ||  || |||  ||    || | |   ||| |     ||   |||  |  || |||  |      ||| ||||  |||| || ||||||||||| ||||| || ||||| ||||| ||||||||||| || || ||||| ||||| || || ||||| |||
tgattccgcaaatttgttgaagtttttaattccaatcacacttttggtaca-tatttaaga-----aactcttatctttttgttttttccaaacgaatttgcttagGCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG

upper sequence: GLYMA16G06100.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0068g02040.t01 (Vitis vinifera), 3'ss of exon 3
---ttcttgcatcctttagtattattatttttaaccacttttcaaatataatggctaaaattgaaaaaatttagttgattatttgcttaccttgaaattgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAG
    ||||      ||    |||  |  ||       |   | ||| ||| |   ||  |||   ||   ||| | | |   |   ||   |     || |||||||| |||||||| ||||||||||| |||||||| || ||||| || |||||||||||||||||||| |||||||| ||||||
aaaatcttaaggttttatacatttatggttagttttgcgcatgaaagata-ttattattattttgaattcttaatagttctataatttgtttctt--ttacagGCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAAAAATGCAAAGGCGAATCGAGGTTTCCTGCTCAG

upper sequence: GLYMA16G06100.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S4_323V6.1 (Physcomitrella patens), 3'ss of exon 2
ttcttgcatcctttagtattattatttttaaccacttttcaaatataatggctaaaattgaaaaaatttagttgattatt-tgcttaccttgaa-attgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAG
  |  | |     || |   |     | | |||  |          || | ||    |   |   |  |  |    |||  || |||| ||    ||  ||||||||||||||||| |||||||||||||||||||| |||||||| || || |||||    || || ||||| ||||| || |||
--caaggaggacctacttggacgtcctctgacctgtgggtggtgtcaaggacttgcttcagacgtaggttctcatgtatggtgtttacattctgtatgacagGCAGCAAGTTTTGGAGGCTCTAACATAGATCCAACCGCCTGGGAAGACAAGAAATGTCGGGGAGAGTCAAGATTTCCTGCCCAG

upper sequence: GLYMA16G06100.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S168_104V6.2 (Physcomitrella patens), 3'ss of exon 3
ttcttgcatcctttagtattattatttttaaccacttttcaaatataatggctaaaattgaaaaaatttagttgattatttgcttaccttgaaattgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAG
            | | | | |  || | | |    || |   || || |   |     ||  |  |  |  |     || |  | |   |  | |  ||||||||||||||||| ||||| |||||||| ||||| |||||||| || || |||||   ||| ||||| || ||||| ||||||
-agcaaggaagatcaatttcaacatctgtga--ggttgtaggatgtattatattcttctggtatgaggtgctaatgcatgtcgtcattcttta-tgacaggcagCAAGTTTTGGAGGCTCAAACATAGACCCAACCGCCTGGGAAGACAAGAAATGTCGAGGAGAATCGAGATTTCCTGCTCAG

upper sequence: GLYMA16G06100.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S168_104V6.1 (Physcomitrella patens), 3'ss of exon 3
---ttcttgcatcctttagtattattatttttaaccacttttcaaatataatggctaaaattgaaaaaatttagttgattatttgcttaccttgaaattgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAG
               | | | | |  || | | |    || |   || || |   |     ||  |  |  |  |     || |  | |   |  | |  ||||||||||||||||| ||||| |||||||| ||||| |||||||| || || |||||   ||| ||||| || ||||| ||||||
gagaagcaaggaagatcaatttcaacatctgtga--ggttgtaggatgtattatattcttctggtatgaggtgctaatgcatgtcgtcattcttta-tgacagGCAGCAAGTTTTGGAGGCTCAAACATAGACCCAACCGCCTGGGAAGACAAGAAATGTCGAGGAGAATCGAGATTTCCTGCTCAG

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|24206077|gb|BU965330.1|BU965330
EST:     CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... gaaattgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|208156515|gb|GD956825.1|GD956825
EST:     CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... gaaattgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|298190302|gb|HO032423.1|HO032423
EST:     CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... gaaattgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|14011483|gb|BG726405.1|BG726405
EST:     CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... gaaattgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|254341084|gb|GR854812.1|GR854812
EST:     CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... gaaattgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|4282613|gb|AI440553.1|AI440553
EST:     CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... gaaattgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|254320127|gb|GR831043.1|GR831043
EST:     CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... gaaattgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|192307583|gb|FG999622.1|FG999622
EST:     CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... gaaattgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|13563366|gb|BG551595.1|BG551595
EST:     CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... gaaattgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|15000111|gb|BI320925.1|BI320925
EST:     CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... gaaattgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|208137092|gb|GD934536.1|GD934536
EST:     CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... gaaattgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|192320601|gb|FK012011.1|FK012011
EST:     CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... gaaattgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|31307475|gb|CD392678.1|CD392678
EST:     ACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: ACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... gaaattgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|254336107|gb|GR841432.1|GR841432
EST:     CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... gaaattgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|192310236|gb|FK001934.1|FK001934
EST:     CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... gaaattgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|192300399|gb|FG987886.1|FG987886
EST:     ATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGAT
genomic: ATTATTTCTTTATAACTATACTACTCATCAGCTGCATGG-TATTTTTGAGgtaagctatt ... gaaattgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGAT
EST: gi|254336108|gb|GR841433.1|GR841433
EST:     TATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: TATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... gaaattgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|22522815|gb|BU081626.1|BU081626
EST:     CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... gaaattgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|22522894|gb|BU081705.1|BU081705
EST:     CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... gaaattgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|7232661|gb|AW568015.1|AW568015
EST:     CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... gaaattgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|4396720|gb|AI495717.1|AI495717
EST:     TTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: TTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... gaaattgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
EST: gi|7232641|gb|AW567995.1|AW567995
EST:     CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAG                         GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA
genomic: CATTATTTCTTTATAACTATACTACTCATCAGCTGCATGGTATTTTTGAGgtaagctatt ... gaaattgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatggctaaaattgaaaaaatttagttgattatttgcttaccttgaaattgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAG
                                   tgcttac  putative branch site (score: 2)
       taaaattgaaaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcttgcatcctttagtattattatttttaaccacttttcaaatataatggctaaaattgaaaaaatttagttgattatttgcttaccttgaaattgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - tgcatcc
- - - - - - - - - - - - - - - accactt
- - - - - - - - - - - - - - - - - - - - aaatataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaat