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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatctgggaaatatgatctgatgttcagttattcttatattctctattatttatgtctgtattttgttgttgatagttatttttgtcattttgatgcagCTCCTGAAGTGGTTGAGAAGCCTGGGGATAACTCATTGGCAAGGCTGAAATTTTTGTATACTCAAGCAAAAGAACTTTCAGAAAGTGAAGCAAG

Basic information

species Glycine max
transcript GLYMA19G08050.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G08050.2 (Glycine max), 3'ss of exon 1
lower sequence: AT5G40550.2 (Arabidopsis thaliana), 3'ss of exon 1
----atatctgggaaatatgatctgatgttcagttattcttatattctctattatttatgtctgtattttgttgttgatagttatttttgtcattttgatgcagCTCCTGAAGTGGTTGAGAAGCCTGGGGATAACTCATTGGCAAGGCTGAAATTTTTGTATACTCAAGCAAAAGAACTTTCAGAAAGTGAAGCAAG
     |   |  | |  ||||  | |  || |   |   | || |    || |  |||  | |  ||  || |     ||    || |||| || ||||||||||||||||  | |||||||||||||| ||||  ||||| |||| ||| ||   |||||| | |||||| ||||| || ||||||| ||||| || 
agttttgattttggatcatgaagtaa--ttaaagaaaattaatctagattagtgatta-atttagatactgctaa-attaagctttgttgtaatgttgatgcagCTCCTGAGATAGTTGAGAAGCCTGGTGATATTTCATTAGCAAAGCTTAAGAATTTGTACATTCAAGCGAAAGAGCTCTCAGAAAATGAAGTAAC

upper sequence: GLYMA19G08050.2 (Glycine max), 3'ss of exon 1
lower sequence: AT3G27460.2 (Arabidopsis thaliana), 3'ss of exon 1
--atatctgg-gaaatatgatctgatgttcagttattcttatattctctattatttatgtctgtattttgttgttgatagttatttttgtcattttgatgcagCTCCTGAAGTGGTTGAGAAGCCTGGGGATAACTCATTGGCAAGGCTGAAATTTTTGTATACTCAAGCAAAAGAACTTTCAGAAAGTGAAGCAAG
    || ||| |  ||  ||| | |   | | | |  ||   || ||    || ||     || ||| | | | |||   || | | |||  |    ||||||| || ||  | |||||||||||||| ||||  |||||| ||| ||| |||  |||||| | |||||||||||| |||||||||||||||| || 
cctcatttggtggtatcagatataagtattattgagcctctaatacttatctacttg---gtgaattatctggctgactcttgtgtatgtgttgaaaatgcagCGCCGGAGATAGTTGAGAAGCCTGGTGATATTTCATTGTCAAAGCTTAAAAATTTGTACATTCAAGCAAAAGAGCTTTCAGAAAGTGAAGTAAC
















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|193319176|gb|FK286348.1|FK286348
EST:     GAGGATTATTCTGTCGGAGATCAACAAGCTTCACAAGAAGCTTCAAGCAA                         CTCCTGAAGTGGTTGAGAAGCCTGGGGATAACTCATTGGCAAGGCTGAAAT
genomic: GAGGA-TATTCTGTCGGAGATCAACAAGCTTCACAAGAAGCTTCAAGCAAgtaagtttct ... tttgatgcagCTCCTGAAGTGGTTGAGAAGCCTGGGGATAACTCATTGGCAAGGCTGAAAT
EST: gi|151403633|gb|EV273443.1|EV273443
EST:     GGAGGATATTCTGTCGGAGATCAACAAGCTTCACAAGAAGCTTCAAGCAA                         CTCCTGAAGTGGTTGAGAAGCCTGGGGATAACTCATTGGCAAGGCTGAAAT
genomic: GGAGGATATTCTGTCGGAGATCAACAAGCTTCACAAGAAGCTTCAAGCAAgtaagtttct ... tttgatgcagCTCCTGAAGTGGTTGAGAAGCCTGGGGATAACTCATTGGCAAGGCTGAAAT
EST: gi|207760530|gb|GD731417.1|GD731417
EST:     GGAGGATATTCTGTCGGAGATCAACAAGCTTCACAAGAAGCTTCAAGCAA                         CTCCTGAAGTGGTTGAGAAGCCTGGGGATAA
genomic: GGAGGATATTCTGTCGGAGATCAACAAGCTTCACAAGAAGCTTCAAGCAAgtaagtttct ... tttgatgcagCTCCTGAAGTGGTTGAGAAGCCTGGGGATAA
EST: gi|193439189|gb|FK404874.1|FK404874
EST:     GGAGGATATTCTGTCGGAGATCAACAAGCTTCACAAGAAGCTTCAAGCAA                         CTCCTGAAGTGGTTGAGAAGCCTGGGGATAACTCATTGGCAAGGCTGAAAT
genomic: GGAGGATATTCTGTCGGAGATCAACAAGCTTCACAAGAAGCTTCAAGCAAgtaagtttct ... tttgatgcagCTCCTGAAGTGGTTGAGAAGCCTGGGGATAACTCATTGGCAAGGCTGAAAT
EST: gi|193339594|gb|FK302785.1|FK302785
EST:     GGAGGATATTCTGTCGGAGATCAACAAGCTTCACAAGAAGCTTCAAGCAA                         CTCCTGAAGTGGTTGAGAAGCCTGGGGATAACTCATTGGCAAGGCTGAAAT
genomic: GGAGGATATTCTGTCGGAGATCAACAAGCTTCACAAGAAGCTTCAAGCAAgtaagtttct ... tttgatgcagCTCCTGAAGTGGTTGAGAAGCCTGGGGATAACTCATTGGCAAGGCTGAAAT
EST: gi|207822826|gb|GD793627.1|GD793627
EST:     ATATTCTGTCGGAGATCAACAAGCTCCACAAGAAGCTTCAAGCAA                         CTCCTGAAGTGGTTGAGAAGCCTGGGGATAACTCATTGGCAAGGCTGAAAT
genomic: ATATTCTGTCGGAGATCAACAAGCTTCACAAGAAGCTTCAAGCAAgtaagtttct ... tttgatgcagCTCCTGAAGTGGTTGAGAAGCCTGGGGATAACTCATTGGCAAGGCTGAAAT
EST: gi|208110483|gb|GD913101.1|GD913101
EST:     GGAGGATATTCTGTCGGAGATCAACAAGCTTCACAAGAAGCTTCAAGCAA                         CTCCTGAAGTGGTTGAGAAGCCTGGGGATAACTCATTGGCAAGGCTGAAAT
genomic: GGAGGATATTCTGTCGGAGATCAACAAGCTTCACAAGAAGCTTCAAGCAAgtaagtttct ... tttgatgcagCTCCTGAAGTGGTTGAGAAGCCTGGGGATAACTCATTGGCAAGGCTGAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattatttatgtctgtattttgttgttgatagttatttttgtcattttgatgcagCTCCTGAAGTGGTTGAGAAGCCTGGGGATAACTCATTGGCAAGGCTGAAATTTTTGTATACTCAAGCAAAAGAACTTTCAGAAAGTGAAGCAAG
                                            ttttgat  putative branch site (score: 4)
                                         tcatttt  CT-rich tract
                                ttatttttgtcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatctgggaaatatgatctgatgttcagttattcttatattctctattatttatgtctgtattttgttgttgatagttatttttgtcattttgatgcagCTCCTGAAGTGGTTGAGAAGCCTGGGGATAACTCATTGGCAAGGCTGAAATTTTTGTATACTCAAGCAAAAGAACTTTCAGAAAGTGAAGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - -tctgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - -atgtctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttgttg