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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggggtgtatgtgtaaaagcggtgatatctcatgctttttagtttaaatctatagcattatctgttgaatttgaagcctttttaattgcaagtatctgcagGATCTTCGGAGAAAGCTTCCTGTCACCCGCACGTTATTTCCATGGCATAATACTTTGCAGTTCAGCTTGACAAGAGACATCTCAAAAGAACTTGGCATTG

Basic information

species Glycine max
transcript GLYMA03G39530.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G39530.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv14s0060g02220.t01 (Vitis vinifera), 3'ss of exon 9
ggggtgtatgtgtaaaagcggtgatatctcatgctttttagtttaaatctatagcattatctgttgaatttgaagcctttttaattgcaagtatctgcagGATCTTCGGAGAAAGCTTCCTGTCACCCGCACGTTATTTCCATGGCATAATACTTTGCAGTTCAGCTTGACAAGAGACATCTCAAAAGAACTTGGCATTG
      ||| | | |||    | |  |   |   |||    |     | | | | |    ||  ||| |        ||| |         | | |||||||||||||||| |||||||| || || || ||| |||| |||||||| || ||| |||| || ||| || ||||||||||||||||||||||||| || |
ttttattatttatcaaattactcaacttcgaacatttaccttgctcgtttcttggacacacttatgattcattctattttctggaccattttttatgcagGATCTTCGGAGGAAGCTTCCAGTTACACGGACGCTATTCCCATGGCACAACACTATGCAATTTAGCCTGTCAAGAGACATCTCAAAAGAACTTGGAATCG
















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|19453054|gb|BM954464.1|BM954464
EST:     GCATCATATCTAAACCTTCCTGATTCTACTTTCAAG                         GATCTTCGGAGAAAGCTTCCTGTCACCCGCACGTTATTTCCATGGCATAAT
genomic: GCATCATATCTAAACCTTCCTGATTCTACTTTCAAGgtaaccattg ... gtatctgcagGATCTTCGGAGAAAGCTTCCTGTCACCCGCACGTTATTTCCATGGCATAAT
EST: gi|192303326|gb|FG995620.1|FG995620
EST:     GCATCATATCTAAACCTTCCTGATTCTACTTTCAAG                         GATCTTCGGAGAAAGCTTCCTGTCACCCGCACGTTATTTCCATGGCATAAT
genomic: GCATCATATCTAAACCTTCCTGATTCTACTTTCAAGgtaaccattg ... gtatctgcagGATCTTCGGAGAAAGCTTCCTGTCACCCGCACGTTATTTCCATGGCATAAT
EST: gi|37997277|gb|CF808866.1|CF808866
EST:     GCATCATATCTAAACCTTCCTGATTCTACTTTCAAG                         GATCTTCGGAGAAAGCTTCCTGTCACCCGCACGTTATTTCCATGGCATAAT
genomic: GCATCATATCTAAACCTTCCTGATTCTACTTTCAAGgtaaccattg ... gtatctgcagGATCTTCGGAGAAAGCTTCCTGTCACCCGCACGTTATTTCCATGGCATAAT
EST: gi|192299933|gb|FG992146.1|FG992146
EST:     AAACCTTCCTGATTCTACTTTCAAG                         GATCTTCGGAGAAAGCTTCCTGTCACCCGCACGTTATTTCCATGGCATAAT
genomic: AAACCTTCCTGATTCTACTTTCAAGgtaaccattg ... gtatctgcagGATCTTCGGAGAAAGCTTCCTGTCACCCGCACGTTATTTCCATGGCATAAT
EST: gi|31311467|gb|CD396670.1|CD396670
EST:     GCATCATATCTAAACCTTCCTGATTCTACTTTCAAG                         GATCTTCGGAGAAAGCTTCCTGTCACCCGCACGTTATTTCCATGGCATAAT
genomic: GCATCATATCTAAACCTTCCTGATTCTACTTTCAAGgtaaccattg ... gtatctgcagGATCTTCGGAGAAAGCTTCCTGTCACCCGCACGTTATTTCCATGGCATAAT
EST: gi|37996140|gb|CF807729.1|CF807729
EST:     GCATCATATCTAAACCTTCCTGANTTCTACTTTCAAG                         GATCTTCGGAGAAAGCTTCCTGTCACCCGCACGTTATTTCCATGGCATAAT
genomic: GCATCATATCTAAACCTTCCTGA-TTCTACTTTCAAGgtaaccattg ... gtatctgcagGATCTTCGGAGAAAGCTTCCTGTCACCCGCACGTTATTTCCATGGCATAAT
EST: gi|298184842|gb|HO030055.1|HO030055
EST:     GCATCATATCTAAACCTTCCTGATTCTACTTTCAAG                         GATCTTCGGAGAAAGCTTCCTGTCACCCGCACGTTATTTCCATGGCATAAT
genomic: GCATCATATCTAAACCTTCCTGATTCTACTTTCAAGgtaaccattg ... gtatctgcagGATCTTCGGAGAAAGCTTCCTGTCACCCGCACGTTATTTCCATGGCATAAT
EST: gi|19269660|gb|BM885916.1|BM885916
EST:     GCATCATATCTAAACCTTCCTGATTCTACTTTCAAG                         GATCTTCGGAGAAAGCTTCCTGTCACCCGCACGTTATTTCCATGGCATAAT
genomic: GCATCATATCTAAACCTTCCTGATTCTACTTTCAAGgtaaccattg ... gtatctgcagGATCTTCGGAGAAAGCTTCCTGTCACCCGCACGTTATTTCCATGGCATAAT
EST: gi|302141262|gb|HO212138.1|HO212138
EST:     GCATCATATCTAAACCTTCCTGATTCTACTTTCAAG                         GATCTTCGGAGAAAGCTTCCTGTCACCCGCACGTTATTTCCATGGCATAAT
genomic: GCATCATATCTAAACCTTCCTGATTCTACTTTCAAGgtaaccattg ... gtatctgcagGATCTTCGGAGAAAGCTTCCTGTCACCCGCACGTTATTTCCATGGCATAAT
EST: gi|9987385|gb|BE661493.1|BE661493
EST:     GCATCATATCTNAACCTTTCTGAATCTACTTTCAAG                         GATCTTCGGAGAAAAGCTTTCTGTCACCCCGCACCGTTANTTTCCATGG
genomic: GCATCATATCTAAACCTTCCTGATTCTACTTTCAAGgtaaccattg ... gtatctgcagGATCTTCGGAGAAA-GCTTCCTGTCACCC-GCAC-GTTA-TTTCCATGG
EST: gi|58022852|gb|CX709593.1|CX709593
EST:     GCATCATATCTAAACCTTCCTGATTCTACTTTCAAG                         GATCTTCGGAGAAAGCTTCCTGTCACCCGCACGTTATTTCCATGGCATAAT
genomic: GCATCATATCTAAACCTTCCTGATTCTACTTTCAAGgtaaccattg ... gtatctgcagGATCTTCGGAGAAAGCTTCCTGTCACCCGCACGTTATTTCCATGGCATAAT
EST: gi|58019780|gb|CX706522.1|CX706522
EST:     GCATCATATCTAAACCTTCCTGATTCTACTTTCAAG                         GATCTTCGGAGAAAGCTTCCTGTCACCCGCACGTTATTTCCATGGCATAAT
genomic: GCATCATATCTAAACCTTCCTGATTCTACTTTCAAGgtaaccattg ... gtatctgcagGATCTTCGGAGAAAGCTTCCTGTCACCCGCACGTTATTTCCATGGCATAAT
EST: gi|18711075|gb|BM522558.1|BM522558
EST:     GCATCATATCTAAACCTTCCTGATTCTACTTTCAAG                         GATCTTCGGAGAAAGCTTCCTGTCACCCGCACGTTATTTCCATGGCATAAT
genomic: GCATCATATCTAAACCTTCCTGATTCTACTTTCAAGgtaaccattg ... gtatctgcagGATCTTCGGAGAAAGCTTCCTGTCACCCGCACGTTATTTCCATGGCATAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatctatagcattatctgttgaatttgaagcctttttaattgcaagtatctgcagGATCTTCGGAGAAAGCTTCCTGTCACCCGCACGTTATTTCCATGGCATAATACTTTGCAGTTCAGCTTGACAAGAGACATCTCAAAAGAACTTGGCATTG
                                 ttttaat  putative branch site (score: 3)
                                tttttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggggtgtatgtgtaaaagcggtgatatctcatgctttttagtttaaatctatagcattatctgttgaatttgaagcctttttaattgcaagtatctgcagGATCTTCGGAGAAAGCTTCCTGTCACCCGCACGTTATTTCCATGGCATAATACTTTGCAGTTCAGCTTGACAAGAGACATCTCAAAAGAACTTGGCATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
ggggtgt
- - - - - - - - - - - - - - tcatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctgttg