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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcatggcatgttcttgtgcatctactatgaggtagttgttttaaccttcctatgtttaatatttactgaatattattcttccaattgtggtttcccctagCCATTGCTGTTTCTCGAGATCACAAACCAGACCAAACTGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCAG

Basic information

species Glycine max
transcript GLYMA04G06250.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G06250.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G166035_T02 (Zea mays), 3'ss of exon 4
------gcatggcatgttcttgtgcatctactatgaggtagttgttttaaccttcctatgtttaatatttactgaatattattcttccaattgtggtttcccctagCCATTGCTGTTTCTCGAGATCACAAACCAGACCAAACTGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCAG
       ||      |||  |    |||   | | |||       | ||| |    ||   ||   |   | |  ||  | || | || ||  ||   | |   ||| ||||| |||||  | ||||||||||| || || || |||||||||||||| ||||| || ||||| ||||||||||||||||| |
gctgaatcagaatcagtttct-caaatcgtttgtcaggattccaatctaatcgcattacactt--caacaattttatgatgttttccccatcttgacctgc---agCAATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAAGAATTGAGGATGCAGGGGGCTTTGTTATGTGGGCTG

upper sequence: GLYMA04G06250.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM5G829894_T01 (Zea mays), 3'ss of exon 3
gcatggcatgttcttgtgcatctactatgaggtagttgttttaacc---ttcc---tatgtttaatatttactgaatattattcttccaattgtggtttcccctagCCATTGCTGTTTCTCGAGATCACAAACCAGACCAAACTGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCAG
   ||  | |      |  |   | ||| |||         |||||   ||||   | | ||  ||||||  ||  |  | || | || ||   ||     |  ||| ||||| |||||  | ||||||||||| || || || |||||||| ||||| ||||| || ||||| ||||||||||||||||| |
--ttgtgacgaatggataaactgaatatcaggattccaagctaaccacgttccacttgtattcgatattttttg--ttatgttttccccatctcggagctgc--agCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG

upper sequence: GLYMA04G06250.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G056572_T02 (Zea mays), 3'ss of exon 4
gcatggcatgttcttgtgcatctactatgaggtagttgttttaaccttccta----tgtttaat-atttactgaatattattcttccaattgtggtttcccctagCCATTGCTGTTTCTCGAGATCACAAACCAGACCAAACTGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCAG
   |          |  |  |  | | |  ||  | | ||| ||| ||  |      ||||||  | || |  ||  | || | | |   ||    ||     ||| |||||||||||    |||||||| || || |||||||||||| ||||  | |||||||| || ||||| ||||| ||||||||||
--ctactgctaagctaggagttgattctacggctgatatttcaacattggtgacaccgtttaaccactttcctaacttgatgcattc---tgcttctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAG

upper sequence: GLYMA04G06250.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 5
----gcatggcatgttcttgtgcatctactatgaggtagttgttttaaccttcctatgtttaatatttactgaatattattcttccaattgtggtttcccctagCCATTGCTGTTTCTCGAGATCACAAACCAGACCAAACTGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCAG
     | |   ||    |  |    ||  |    |  | |||   |||  |  || |||||  |||      ||| | ||  ||    || | ||||  |  ||| |||||||| || ||||||||||| || || |||| ||| ||| | ||||| ||||| || |||||||| ||||| |||||||| |
acatacttataatcacatgatagcccttgttcatgaaatttgcaataag-tcgctctgttttgtatggtactaatttgatatttt---tttttgtttgtcaaagCTATTGCTGTATCCCGAGATCACAAGCCTGATCAAAGTGACGAGCGCCAAAGAATTGAGGATGCAGGAGGATTTGTCATGTGGGCTG

upper sequence: GLYMA04G06250.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0008g07320.t01 (Vitis vinifera), 3'ss of exon 5
gcatggcatgttcttgtgcatctactatgaggtagttgttt----taaccttc-ctatgtttaatatttactgaatattattcttccaa-ttgtggtttcccctagCCATTGCTGTTTCTCGAGATCACAAACCAGACCAAACTGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCAG
    |     ||   |  | ||| |||||  | | ||| ||    ||   ||| ||   || | | |||  | | | | ||     ||  ||||  ||||| | ||||||||||||||||||||||||||| |||||||||||||||||| ||||  | ||||| || || ||||| ||||| |||||||| |
----gatgaattaaagatcttct-ctatggagaatttgcttcgtctagtgttcactggtttcagtgtttgatca-tctgatgaaaacatcttgtaatttcctccagCCATTGCTGTTTCTCGAGATCACAAGCCAGACCAAACTGATGAGCGGCAGCGTATTGAGGATGCTGGAGGGTTTGTGATGTGGGCTG

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|192313213|gb|FK003333.1|FK003333
EST:     TGTTGCAAATGTTGGGGATTCCAGAGCTGTTATATGCAGGGGTGGTAATG                         CCATTGCTGTTTCTCGAGATCACAAACCAGACCAAACTGATGAGAGGCAAA
genomic: TGTTGCAAATGTTGGGGATTCCAGAGCTGTTATATGCAGGGGTGGTAATGgtaagggtgt ... tttcccctagCCATTGCTGTTTCTCGAGATCACAAACCAGACCAAACTGATGAGAGGCAAA
EST: gi|5509507|gb|AI856065.1|AI856065
EST:     TGTTGCAAATGTTGGGGATTCCAGAGCTGTTATATGCAGGGGTGGTAATG                         CCATTGCTGTTTCTCGAGATCACAAACCA
genomic: TGTTGCAAATGTTGGGGATTCCAGAGCTGTTATATGCAGGGGTGGTAATGgtaagggtgt ... tttcccctagCCATTGCTGTTTCTCGAGATCACAAACCA
EST: gi|254334939|gb|GR844724.1|GR844724
EST:     TGTTGCAAATGTTGGGGATTCCAGAGCTGTTATATGCAGGGGTGGTAATG                         CCATTGCTGTTTCTCGAGATCACAAACCAGACCAAACTGATGAGAGGCAAA
genomic: TGTTGCAAATGTTGGGGATTCCAGAGCTGTTATATGCAGGGGTGGTAATGgtaagggtgt ... tttcccctagCCATTGCTGTTTCTCGAGATCACAAACCAGACCAAACTGATGAGAGGCAAA
EST: gi|11412749|gb|BF424760.1|BF424760
EST:     TGTTGCAAATGTTGGGGATTCCAGAGCTGTTATATGCAGGGGTGGTAATG                         CCATTGCTGTTTCTCGAGATCACAAACCAGACCAAACTGATGAGAGGCAAA
genomic: TGTTGCAAATGTTGGGGATTCCAGAGCTGTTATATGCAGGGGTGGTAATGgtaagggtgt ... tttcccctagCCATTGCTGTTTCTCGAGATCACAAACCAGACCAAACTGATGAGAGGCAAA
EST: gi|193496826|gb|FK463770.1|FK463770
EST:     TGTTGCAAATGTTGGGGATTCCAGAGCTGTTATATGCAGGGGTGGTAATG                         CCATTGCTGTTTCTCGAGATCACAAACCAGACCAAACTGATGAGAGGCAAA
genomic: TGTTGCAAATGTTGGGGATTCCAGAGCTGTTATATGCAGGGGTGGTAATGgtaagggtgt ... tttcccctagCCATTGCTGTTTCTCGAGATCACAAACCAGACCAAACTGATGAGAGGCAAA
EST: gi|192313214|gb|FK003334.1|FK003334
EST:     TGTTGCAAATGTTGGGGATTCCAGAGCTGTTATATGCAGGGGTGGTAATG                         CCATTGCTGTTTCTCGAGATCACAAACCAGACCAAACTGATGAGAGGCAAA
genomic: TGTTGCAAATGTTGGGGATTCCAGAGCTGTTATATGCAGGGGTGGTAATGgtaagggtgt ... tttcccctagCCATTGCTGTTTCTCGAGATCACAAACCAGACCAAACTGATGAGAGGCAAA
EST: gi|11412737|gb|BF424748.1|BF424748
EST:     TGTTGCAAATGTTGGGGATTCCAGAGCTGTTATATGCAGGGGTGGTAATG                         CCATTGCTGTTTCTCGAGATCACAAACCAGACCAAACTGATGAGAGGCAAA
genomic: TGTTGCAAATGTTGGGGATTCCAGAGCTGTTATATGCAGGGGTGGTAATGgtaagggtgt ... tttcccctagCCATTGCTGTTTCTCGAGATCACAAACCAGACCAAACTGATGAGAGGCAAA
EST: gi|209722645|gb|BW654652.1|BW654652
EST:     TGTTGCAAATGTTGGGGATTCCAGAGCTGTTATATGCAGGGGTGGTAATG                         CCATTGCTGTTTCTCGAGATCACAAACCAGACCAAACTGATGAGAGGCAAA
genomic: TGTTGCAAATGTTGGGGATTCCAGAGCTGTTATATGCAGGGGTGGTAATGgtaagggtgt ... tttcccctagCCATTGCTGTTTCTCGAGATCACAAACCAGACCAAACTGATGAGAGGCAAA
EST: gi|120491886|gb|EH220053.1|EH220053
EST:     TGTTGCAAATGTTGGGGATTCCAGAGCTGTTATATGCAGGGGTGGTAATG                         CCATTGCTGTTTCTCGAGATC
genomic: TGTTGCAAATGTTGGGGATTCCAGAGCTGTTATATGCAGGGGTGGTAATGgtaagggtgt ... tttcccctagCCATTGCTGTTTCTCGAGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcctatgtttaatatttactgaatattattcttccaattgtggtttcccctagCCATTGCTGTTTCTCGAGATCACAAACCAGACCAAACTGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCAG
        gtttaat  putative branch site (score: 4)
                                             tttcccct  putative PPT
     tatgtttaatatttac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatggcatgttcttgtgcatctactatgaggtagttgttttaaccttcctatgtttaatatttactgaatattattcttccaattgtggtttcccctagCCATTGCTGTTTCTCGAGATCACAAACCAGACCAAACTGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
gcatggc
- - - - - - cttgtgc
- - - - - - - - - - - - ctatgag
- - - - - - - - - - - - - - - - - - - - - - ccttcct