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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttacaatgcaatgtttcaaattgactaattattgttataacttatattgataatactttctattgatgttcttaccattttttttggaatttatccagATTGAGAGTAACATTGTTCGATGTCCAGACCCGGAGTATGCAGAGAAGATGATATCTGCAATTGATGCTGTGCGAGTGAGAGGTGATTCTGTTGGTGGTG

Basic information

species Glycine max
transcript GLYMA20G31980.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G31980.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os03g14990.1 (Oryza sativa), 3'ss of exon 7
atttacaatgcaatgtttcaaattgactaattattgttataacttatattgataatactttctattgatgttcttaccattttttttggaat-ttatccagATTGAGAGTAACATTGTTCGATGTCCAGACCCGGAGTATGCAGAGAAGATGATATCTGCAATTGATGCTGTGCGAGTGAGAGGTGATTCTGTTGGTGGTG
             | | |       || | ||     | ||||   | | || | | || |  |   || | || |  ||| | |||    | || ||||||| || || ||||||||| ||||||| || || || |||||| ||||||||||   |||||| |||   || ||||| |||||||||||  |||||||||
------------gtctgtggttcccaccattttcaagtttaacacttctggacagt-ctctgaaggcatttgctgaatattatatttattttattttccagATAGAAAGCAACATTGTTAGATGTCCTGATCCAGAATATGCACAGAAGATGATTGATGCAATCGATAAAGTACGAGTTAGAGGTGATTCGATTGGTGGTG

upper sequence: GLYMA20G31980.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G164562_T01 (Zea mays), 3'ss of exon 7
----atttacaatgcaatgtttcaaattgactaattattgttataacttatattgataatactttctattgatg-ttcttaccattttttttggaatttatccagATTGAGAGTAACATTGTTCGATGTCCAGACCCGGAGTATGCAGAGAAGATGATATCTGCAATTGATGCTGTGCGAGTGAGAGGTGATTCTGTTGGTGGTG
     ||       | |  |  |      |   ||||  |  |||   ||| | |    | |   |  |||||| || ||| | | || ||   |||||   ||||| ||||| ||||| ||| ||||||| || || || |||||||||||||||||  |||| |||||| | || ||||| ||||| |||||  ||||||| |
gtatcttcttgtcactacctccccctccaaagcattacagggatagtctat-tagtctttgcacacatttgatgatttttatcctattcttgtaaattt---cagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAATATGCAGAGAAGATGATTGCTGCCATTGATACGGTACGAGTTAGAGGAGATTCAATTGGTGGGG

upper sequence: GLYMA20G31980.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G036861_T01 (Zea mays), 3'ss of exon 7
--------atttaca---atgcaatgtttcaaattgactaattattgttataacttatat-tgataatactttctattgatgttctt----accattttttttggaatttatccagATTGAGAGTAACATTGTTCGATGTCCAGACCCGGAGTATGCAGAGAAGATGATATCTGCAATTGATGCTGTGCGAGTGAGAGGTGATTCTGTTGGTGGTG
        || | ||   ||||  ||   |       |    |     ||| |   |      || | |    | |  |   ||       |   |   || |    ||| | ||||| ||||| ||||| ||| ||||||| || || ||||| |||||||||||||||   ||||| ||    || |||||  |||| ||||| || ||||| |
gtcgacggatgtgcatgcatgctttgccacgcgccttcgttcttccactatgatacagccgccatgacagccccgacggtcatttaacaggattgtaccttgtttttttttttcagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAGTACGCAGAGAAGATGATAGACGCAATCGACAGAGTACGAGTTCGAGGGGATTCGGTCGGTGGAG

upper sequence: GLYMA20G31980.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G036861_T02 (Zea mays), 3'ss of exon 6
-----atttacaatgcaatgtttcaaattgacta-attattgttataacttatattgataatactttctattgatgttcttaccattttttttggaatttatccagATTGAGAGTAACATTGTTCGATGTCCAGACCCGGAGTATGCAGAGAAGATGATATCTGCAATTGATGCTGTGCGAGTGAGAGGTGATTCTGTTGGTGGTG
      ||| | | ||    |      |  ||||   ||  |     | | | |      |   |   |    | | |  |||| | ||||||     || | ||||| ||||| ||||| ||| ||||||| || || ||||| |||||||||||||||   ||||| ||    || |||||  |||| ||||| || ||||| |
gcatgctttgccacgcgccttcgttcttccactatgatacagccgcca-tgacagccccgacggtcatttaacaggattgtaccttgtttttt-----tttttcagATAGAGAGCAACATCGTTAGATGTCCTGATCCAGAGTACGCAGAGAAGATGATAGACGCAATCGACAGAGTACGAGTTCGAGGGGATTCGGTCGGTGGAG

upper sequence: GLYMA20G31980.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv13s0019g04190.t01 (Vitis vinifera), 3'ss of exon 7
-atttacaatgcaatgtttcaaattgactaattattgttataa-cttatattgata---atactttctattgatgttcttaccattttttttggaatttatccagATTGAGAGTAACATTGTTCGATGTCCAGACCCGGAGTATGCAGAGAAGATGATATCTGCAATTGATGCTGTGCGAGTGAGAGGTGATTCTGTTGGTGGTG
  |||    |    | ||||   || | |  || ||||||||  |||||  |||     | | || | ||| |||||||      | | | |||||  |  |||||| |||||||| |||||  | || ||||| || || |||||||||||||||||  ||||||||||||| || || ||||| || ||||||||||| ||||
cttttttctttttctttttcttttttagtcctttttgttatattcttatgatgaattgtagaattcccattaatgttctc-----tctctatggaacattgccagATAGAGAGTAATATTGTGAGGTGCCCAGATCCTGAATATGCAGAGAAGATGATTGCTGCAATTGATGCCGTTCGTGTGAGGGGAGATTCTGTTGGAGGTG

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|254322919|gb|GR835634.1|GR835634
EST:     TTGTTCTTCCAGAGGACCTTATTGATCATGACACTCTGACTCTTGATCAG                         ATTGAGAGTA-CATTGTTCGATGTCCAGACCCGGAGT
genomic: TTGTTCTTCCAGAGGACCTTATTGATCATGACACTCTGACTCTTGATCAGgtattaaagt ... atttatccagATTGAGAGTAACATTGTTCGATGTCCAGACCCGGAGT
EST: gi|23052733|gb|BU577224.1|BU577224
EST:     TTGTTCTTCCAGAGGACCTTATTGATCATGACACTCTGACTCTTGATCAG                         ATTGAGAGTAACATTGTTCGATGTCCAGACCCGGAGTATGCAGAGAAGATG
genomic: TTGTTCTTCCAGAGGACCTTATTGATCATGACACTCTGACTCTTGATCAGgtattaaagt ... atttatccagATTGAGAGTAACATTGTTCGATGTCCAGACCCGGAGTATGCAGAGAAGATG
EST: gi|208117633|gb|GD916419.1|GD916419
EST:     TTGTTCTTCCAGAGGACCTTATTGATCATGACACTCTGACTCTTGATCAG                         ATTGAGAGTAACATTGTTCGATGTCCAGACCCGGAGTATGCAGAGAAGATG
genomic: TTGTTCTTCCAGAGGACCTTATTGATCATGACACTCTGACTCTTGATCAGgtattaaagt ... atttatccagATTGAGAGTAACATTGTTCGATGTCCAGACCCGGAGTATGCAGAGAAGATG
EST: gi|16346555|gb|BI972150.1|BI972150
EST:     TTGTTCTTCCAGAGGACCTTATTGATCATGACACTCTGACTCTTGATCAG                         ATTGAGAGTAACATTGTTCGATGTCCAGACCCGGAGTATGCAGAGAAGATG
genomic: TTGTTCTTCCAGAGGACCTTATTGATCATGACACTCTGACTCTTGATCAGgtattaaagt ... atttatccagATTGAGAGTAACATTGTTCGATGTCCAGACCCGGAGTATGCAGAGAAGATG
EST: gi|120533980|gb|EH262113.1|EH262113
EST:     TTGTTCTTCCAGAGGACCTTATTGATCATGACACTCTGACTCTTGATCAG                         ATTGAGAGTAACATTGTTCGATGTCCAGACCCGGAGTATGCAGAGAAGATG
genomic: TTGTTCTTCCAGAGGACCTTATTGATCATGACACTCTGACTCTTGATCAGgtattaaagt ... atttatccagATTGAGAGTAACATTGTTCGATGTCCAGACCCGGAGTATGCAGAGAAGATG
EST: gi|19934393|gb|BQ079423.1|BQ079423
EST:     TTGTTCTTCCAGAGGACCTTATTGATCATGACACTCTGACTCTTGATCAG                         ATTGAGAGTAACATTGTTCGATGTCCAGACCCGGAGTATGCAGAGAAGATG
genomic: TTGTTCTTCCAGAGGACCTTATTGATCATGACACTCTGACTCTTGATCAGgtattaaagt ... atttatccagATTGAGAGTAACATTGTTCGATGTCCAGACCCGGAGTATGCAGAGAAGATG
EST: gi|192325343|gb|FK017144.1|FK017144
EST:     TTGTTCTTCCAGAGGACCTTATTGATCATGACACTCTGACTCTTGATCAG                         ATTGAGAGTAACATTGTTCGATGTCCAGACCCGGAGTATGCAGAGA-GATG
genomic: TTGTTCTTCCAGAGGACCTTATTGATCATGACACTCTGACTCTTGATCAGgtattaaagt ... atttatccagATTGAGAGTAACATTGTTCGATGTCCAGACCCGGAGTATGCAGAGAAGATG
EST: gi|192296954|gb|FG991950.1|FG991950
EST:     TTGTTCTTCCAGAGGACCTTATTGGTCATGACACTCTGACTCTTGATCAG                         ATTGAGAGTAACATTGTTCGATGTCCAGACCCGGAGTATGCAGAGAAGATG
genomic: TTGTTCTTCCAGAGGACCTTATTGATCATGACACTCTGACTCTTGATCAGgtattaaagt ... atttatccagATTGAGAGTAACATTGTTCGATGTCCAGACCCGGAGTATGCAGAGAAGATG
EST: gi|254340228|gb|GR858353.1|GR858353
EST:     TTGTTCTTCCAGAGGACCTTATTGATCATGACACTCTGACTCTTGATCAG                         ATTGAGAGTAACATTGTTCGATGTCCAGACCCGGAGTATGCAGAGAAGATG
genomic: TTGTTCTTCCAGAGGACCTTATTGATCATGACACTCTGACTCTTGATCAGgtattaaagt ... atttatccagATTGAGAGTAACATTGTTCGATGTCCAGACCCGGAGTATGCAGAGAAGATG
EST: gi|9900006|gb|BE608974.1|BE608974
EST:     TTGTTCTTCCAGAGGACCTTATTGATCATGACACTCTGACTGTTGATCAG                         ATTGAGAGTAACATTGTTCGATGTCCAGACCCGGAGTATGCAGAGAAGATG
genomic: TTGTTCTTCCAGAGGACCTTATTGATCATGACACTCTGACTCTTGATCAGgtattaaagt ... atttatccagATTGAGAGTAACATTGTTCGATGTCCAGACCCGGAGTATGCAGAGAAGATG
EST: gi|208044536|gb|GD837936.1|GD837936
EST:     TTGTTCTTCCAGAGGACCTTATTGATCATGACACTCTGACTCTTGATCAG                         ATTGAGAGTAACATTGTTCGATGTCCAGACCCGGAGTATGCAGAGA
genomic: TTGTTCTTCCAGAGGACCTTATTGATCATGACACTCTGACTCTTGATCAGgtattaaagt ... atttatccagATTGAGAGTAACATTGTTCGATGTCCAGACCCGGAGTATGCAGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattgataatactttctattgatgttcttaccattttttttggaatttatccagATTGAGAGTAACATTGTTCGATGTCCAGACCCGGAGTATGCAGAGAAGATGATATCTGCAATTGATGCTGTGCGAGTGAGAGGTGATTCTGTTGGTGGTG
                         ttcttac  putative branch site (score: 2)
                                              tttatcc  putative PPT
                                 attttttttggaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttacaatgcaatgtttcaaattgactaattattgttataacttatattgataatactttctattgatgttcttaccattttttttggaatttatccagATTGAGAGTAACATTGTTCGATGTCCAGACCCGGAGTATGCAGAGAAGATGATATCTGCAATTGATGCTGTGCGAGTGAGAGGTGATTCTGTTGGTGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - -caatgca