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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcattttttttattacccaagtttggtaagtgttggtttgtttttgggtattcaaccttttttttttctatgttgattttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCAGAATATGACCCTGTAGCCAAGATATCAATTATTCCTCGTGGCCAAGCTGGTGGTCTCACATTTTT

Basic information

species Glycine max
transcript GLYMA04G02100.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G02100.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g51029.1 (Oryza sativa), 3'ss of exon 2
---------gtatgcat-tttttttattacccaagtttggtaagtgttggtttgtttttgggtattcaaccttttttttttctatgttgattttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCAGAATATGACCCTGTAGCCAAGATATCAATTATTCCTCGTGGCCAAGCTGGTGGTCTCACATTTTT
         ||   ||| ||   || | ||   || |       |  |||| ||      |||    || |  |||||   || | |  |||| |||||||||| ||||| || || |||||  | ||||| |||||||||||||| || ||||| || || ||||||||||| ||||||||||| |||||||| ||
gtaaatcttgtcaccatattaacttgtgacttgagctgaaattatcctggtgtgcag--aggttcctaatccatttttgaacttt-tcaatttgcagAGGCTGGTCATGCCCTTGTTGGTGCCCTCATGCCTGAATATGACCCTGTTGCTAAGATTTCCATCATTCCTCGTGGTCAAGCTGGTGGACTCACATTCTT

upper sequence: GLYMA04G02100.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G126361_T03 (Zea mays), 3'ss of exon 3
---------gtatgcattttttttattacc-caagtttggtaagtgttggtttgtttttgggtattcaaccttttttttttctatgttgattttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCAGAATATGACCCTGTAGCCAAGATATCAATTATTCCTCGTGGCCAAGCTGGTGGTCTCACATTTTT
         ||    |||| | |||| |||  |||||||      | |     |  |   |||    || || || ||   || ||   ||||  ||||||||||||||| || || || ||  | |||||||| ||||| || ||||||||||| || || || ||||||||||| |||||||| |||||||| ||
gtaaatgttgt-caaatttatattataaccataagtttgactcccgcttacggggctc-aggttcctaatctgttgttgaactttgg-aatttgtagAGGCTGGCCATGCCCTTGTCGGCGCCCTCATGCCAGAGTATGATCCAGTAGCCAAGATTTCCATCATCCCTCGTGGCCAGGCTGGTGGACTCACATTCTT

upper sequence: GLYMA04G02100.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G42270.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgcattttttttattacccaagtttggtaagtgttggtttgtttttgggtattcaaccttttttttttctatgttg--attttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCAGAATATGACCCTGTAGCCAAGATATCAATTATTCCTCGTGGCCAAGCTGGTGGTCTCACATTTTT
         ||   || |||  |   | | ||  | |||  || || ||| ||   | ||    | ||     |  |||  |||| |||||||||| |||||| |||| |||||  | ||||| || ||||| || || ||||||||||| |||||||| ||||||||||||||||| ||||| |||||
--------gttagatactactgatcctagctacttcttgtgttattattgtgttgaccactcactgttcaataaaattgtaatttgcagAGGCTGGGCATGCTTTAGTTGGTGCACTTATGCCGGAGTATGATCCAGTGGCCAAGATATCGATTATTCCACGTGGCCAAGCTGGTGGGCTCACCTTTTT

upper sequence: GLYMA04G02100.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G50250.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgcattttttttattacccaagtttggtaagtgttggtttgtttttgggtattcaaccttttttttttctatgttgattttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCAGAATATGACCCTGTAGCCAAGATATCAATTATTCCTCGTGGCCAAGCTGGTGGTCTCACATTTTT
||  ||||||| | ||           |||     |  | |  | || | | | |   |||   |    |    | |  |||| |||||||||| |||||||||||||||||| | |||||||||||||| || || || ||||| || || ||||||||||||||||||||||| ||||| |||||
gttagcattttatctaactatatgtaatggagtacgcagctgggattcttgttttctgaccacctcaaatgaattttaaatttacagAGGCTGGTCATGCTCTAGTGGGTGCTCTTATGCCAGAATATGATCCGGTTGCAAAGATTTCTATCATTCCTCGTGGCCAAGCTGGTGGGCTCACTTTTTT

upper sequence: GLYMA04G02100.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g00190.t01 (Vitis vinifera), 3'ss of exon 2
----------gtatgcattttttttattacccaagtttggtaagtgttggtttgtttttgggtattcaaccttttttt---tttctatgttgattttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCAGAATATGACCCTGTAGCCAAGATATCAATTATTCCTCGTGGCCAAGCTGGTGGTCTCACATTTTT
          |    ||         ||   || || |  | |   ||| | |  |||||||| ||  | || ||| |   |||  |  |  |||| |||||||||| |||||  | || |||||  | ||||| |||||||||||||| ||||||||||| || ||||| ||||||||||| |||||||| || |||||
gtacataaaagagaacaacacaagctttgtacaggtctc-tgatgcttgttattgttttgggtgttttaactctttatgtgtttgcacttgaatttgcagAGGCTGGGCATGCATTGGTCGGTGCACTTATGCCTGAATATGACCCTGTGGCCAAGATATCCATCATTCCCCGTGGCCAAGCAGGTGGTCTTACCTTTTT

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|120494712|gb|EH222879.1|EH222879
EST:     GAAAAATGCTGTTGTCTCAGATGAGAAGAAGAAATTAGTAGCCTATCATG                         AGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCAGAATATGACCCTGTAG
genomic: GAAAAATGCTGTTGTCTCAGATGAGAAGAAGAAATTAGTAGCCTATCATGgtatgcattt ... tgattttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCAGAATATGACCCTGTAG
EST: gi|213613848|gb|DB971007.1|DB971007
EST:     GAAAAATGCTGTTGTCTCAGATGAGAAGAAGAAATTAGTAGCCTATCATG                         AGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCAGAATATGACCCTGTAG
genomic: GAAAAATGCTGTTGTCTCAGATGAGAAGAAGAAATTAGTAGCCTATCATGgtatgcattt ... tgattttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCAGAATATGACCCTGTAG
EST: gi|120494410|gb|EH222577.1|EH222577
EST:     GAAAAATGCTGTTGTCTCAGATGAGAAGAAGAAATTAGTAGCCTATCATG                         AGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCAGAATATGACCCTGTAG
genomic: GAAAAATGCTGTTGTCTCAGATGAGAAGAAGAAATTAGTAGCCTATCATGgtatgcattt ... tgattttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCAGAATATGACCCTGTAG
EST: gi|16279077|gb|BI943246.1|BI943246
EST:     GAAAAATGCTGTTGTCTCAGATGAGAAGAAGAAATTAGTAGCCTATCATG                         AGGCTGGCCATGCTCTAGTGGGTGCTNTAATGCCAGAATATGACCCTGTAG
genomic: GAAAAATGCTGTTGTCTCAGATGAGAAGAAGAAATTAGTAGCCTATCATGgtatgcattt ... tgattttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCAGAATATGACCCTGTAG
EST: gi|120494718|gb|EH222885.1|EH222885
EST:     GAAAAATGCTGTTGTCTCAGATGAGAAGAAGAAATTAGTAGCCTATCATG                         AGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCAGAATATGACCCTGTAG
genomic: GAAAAATGCTGTTGTCTCAGATGAGAAGAAGAAATTAGTAGCCTATCATGgtatgcattt ... tgattttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCAGAATATGACCCTGTAG
EST: gi|120495724|gb|EH223891.1|EH223891
EST:     GAAAAATGCTGTTGTCTCAGATGAGAAGAAGAAATTAGTAGCCTATCATG                         AGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCAGAATATGACCCTGTAG
genomic: GAAAAATGCTGTTGTCTCAGATGAGAAGAAGAAATTAGTAGCCTATCATGgtatgcattt ... tgattttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCAGAATATGACCCTGTAG
EST: gi|207737927|gb|GD717399.1|GD717399
EST:     GAAAAATGCTGTTGTCTCAGATGAGAAGAAGAAATTAGTAGCCTATCATG                         AGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCAGAAT
genomic: GAAAAATGCTGTTGTCTCAGATGAGAAGAAGAAATTAGTAGCCTATCATGgtatgcattt ... tgattttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCAGAAT
EST: gi|209727706|gb|BW658443.1|BW658443
EST:     GAAAAATGCTGTTGTCTCAGATGAGAAGAAGAAATTAGTAGCCTATCATG                         AGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCAGAATATGACCCTGTAG
genomic: GAAAAATGCTGTTGTCTCAGATGAGAAGAAGAAATTAGTAGCCTATCATGgtatgcattt ... tgattttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCAGAATATGACCCTGTAG
EST: gi|120494207|gb|EH222374.1|EH222374
EST:     GAAAAATGCTGTTGTCTCAGATGAGAAGAAGAAATTAGTAGCCTATCATG                         AGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCAGAATATGACCCTGTAG
genomic: GAAAAATGCTGTTGTCTCAGATGAGAAGAAGAAATTAGTAGCCTATCATGgtatgcattt ... tgattttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCAGAATATGACCCTGTAG
EST: gi|192306886|gb|FG999933.1|FG999933
EST:     GAGAAGAAGAAATTAGTAGCCTATCATG                         AGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCAGAATATGACCCTGTAG
genomic: GAGAAGAAGAAATTAGTAGCCTATCATGgtatgcattt ... tgattttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCAGAATATGACCCTGTAG
EST: gi|16282177|gb|BI944877.1|BI944877
EST:     GAAATTAGTAGCCTATCATG                         AGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCAGAATATGACCCTGTAG
genomic: GAAATTAGTAGCCTATCATGgtatgcattt ... tgattttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCAGAATATGACCCTGTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgttggtttgtttttgggtattcaaccttttttttttctatgttgattttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCAGAATATGACCCTGTAGCCAAGATATCAATTATTCCTCGTGGCCAAGCTGGTGGTCTCACATTTTT
                                          tgttgat  putative branch site (score: 4)
                           ccttttttttttctat  CT-rich tract
                             ttttttttttctatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcattttttttattacccaagtttggtaagtgttggtttgtttttgggtattcaaccttttttttttctatgttgattttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCAGAATATGACCCTGTAGCCAAGATATCAATTATTCCTCGTGGCCAAGCTGGTGGTCTCACATTTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG