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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtgggataagattttgttgttgttgttgtagagaagtttgcttcttttaaggggtgtgtgtgtgtttacatagatttaatgtgggaaaattccttgcagGCATTTTGGATTGAATTGGGCATTTGTTGATCCGAAGACACCAGTCCAACAAGGAGTGAAGTTCTGTGTTTGTGTCAAGGAGTTCTTCCCGTGGCTCATG

Basic information

species Glycine max
transcript GLYMA16G22910.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G22910.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G17695.1 (Arabidopsis thaliana), 3'ss of exon 2
agtgggataagattttgttgttgttgttgtagagaagtttgcttcttttaaggggtgtgtgtgtgtttacatagatttaatgtgggaaaattccttgcagGCATTTTGGATTGAATTGGGCATTTGTTGATCCGAAGACACCAGTCCAACAAGGAGTGAAGTTCTGTGTTTGTGTCAAGGAGTTCTTCCCGTGGCTCATG
       || | |||  || || |  |   | |  | |         | ||  |||     | ||||  ||| |||||             |  |||||||||||||||  || |||||||||||||||||||    ||||| ||  ||   ||   |||||| ||  |||| || || ||  |  | || ||| | |||
------gtatgttttgctttttatcatctcaaatcaatggaac---atcaatcggt-----tctgttctcattgattt------------ctaattgcagGCATTTTGGTATGGATTGGGCATTTGTTGATCCTGCAACACCTGTTGAAACCGGTAAGAAGTTTTGCATTTGCGTGAAAGAAGTTCTTCCATGGGTGATG
















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|298198079|gb|HO039618.1|HO039618
EST:     TCTGGTATTGAGACCTTTGAAAAGGGCAAGAGTGCTCTTAGAAGTTGGAG                         GCATTTTGGATTGAATTGGGCATTTGTTGATCCGAAGACACCAGTCCAACA
genomic: TCTGGTATTGAGACCTTTGAAAAGGGCAAGAGTGCTCTTAGAAGTTGGAGgtatgttaat ... ttccttgcagGCATTTTGGATTGAATTGGGCATTTGTTGATCCGAAGACACCAGTCCAACA
EST: gi|151407653|gb|EV277468.1|EV277468
EST:     TCTGGTATTGAGACCTTTGAAAAGGGCAAGAGTGCTCTTAGAAGTTGGAG                         GCACTTTGGATTGAATTGGGCATTTGTTGATCCGAAGACACCAGTCCAACA
genomic: TCTGGTATTGAGACCTTTGAAAAGGGCAAGAGTGCTCTTAGAAGTTGGAGgtatgttaat ... ttccttgcagGCATTTTGGATTGAATTGGGCATTTGTTGATCCGAAGACACCAGTCCAACA
EST: gi|213590342|gb|DB963877.1|DB963877
EST:     TCTGGTATTGAGACCTTTGAAAAGGGCAAGAGTGCTCTTAGAAGTTGGAG                         GCATTTTGGATTGAATTGGGCATTTGTTGATCCGAAGACACCAGTCCAACA
genomic: TCTGGTATTGAGACCTTTGAAAAGGGCAAGAGTGCTCTTAGAAGTTGGAGgtatgttaat ... ttccttgcagGCATTTTGGATTGAATTGGGCATTTGTTGATCCGAAGACACCAGTCCAACA
EST: gi|15000576|gb|BI321390.1|BI321390
EST:     TCTGGTATTGAGACCTTTGAAAAGGGCAAGAGTGCTCTTAGAAGTTGGAG                         GCATTTTGGATTGAATTGGGCCTTTGTTGATCCGAAGACACCAGTCCAACA
genomic: TCTGGTATTGAGACCTTTGAAAAGGGCAAGAGTGCTCTTAGAAGTTGGAGgtatgttaat ... ttccttgcagGCATTTTGGATTGAATTGGGCATTTGTTGATCCGAAGACACCAGTCCAACA
EST: gi|151405142|gb|EV274956.1|EV274956
EST:     TCTGGTATTGAGACCTTTGAAAAGGGCAAGAGTGCTCTTAGAAGTTGGAG                         GCATTTTGGATTGAATTGGGCATTTGTTGATCCGAAGACACCAGTCCAACA
genomic: TCTGGTATTGAGACCTTTGAAAAGGGCAAGAGTGCTCTTAGAAGTTGGAGgtatgttaat ... ttccttgcagGCATTTTGGATTGAATTGGGCATTTGTTGATCCGAAGACACCAGTCCAACA
EST: gi|298194598|gb|HO043070.1|HO043070
EST:     TCTGGTATTGAGACCTTTGAAAAGGGCAAGAGTGCTCTTAGAAGTTGGAG                         GCATTTTGGATTGAATTGGGCATTTGTTGATCCGAAGACACCAGTCCAACA
genomic: TCTGGTATTGAGACCTTTGAAAAGGGCAAGAGTGCTCTTAGAAGTTGGAGgtatgttaat ... ttccttgcagGCATTTTGGATTGAATTGGGCATTTGTTGATCCGAAGACACCAGTCCAACA
EST: gi|298168986|gb|HO020290.1|HO020290
EST:     TCTGGTATTGAGACCTTTGAAAAGGGCAAGAGTGCTCTTAGAAGTTGGAG                         GCATTTTGGATTGAATTGGGCATTTGTTGATCCGAAGACACCAGTCCAACA
genomic: TCTGGTATTGAGACCTTTGAAAAGGGCAAGAGTGCTCTTAGAAGTTGGAGgtatgttaat ... ttccttgcagGCATTTTGGATTGAATTGGGCATTTGTTGATCCGAAGACACCAGTCCAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttaaggggtgtgtgtgtgtttacatagatttaatgtgggaaaattccttgcagGCATTTTGGATTGAATTGGGCATTTGTTGATCCGAAGACACCAGTCCAACAAGGAGTGAAGTTCTGTGTTTGTGTCAAGGAGTTCTTCCCGTGGCTCATG
                             atttaat  putative branch site (score: 4)
                                             ttccttgc  putative PPT
                    tttacatagatttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtgggataagattttgttgttgttgttgtagagaagtttgcttcttttaaggggtgtgtgtgtgtttacatagatttaatgtgggaaaattccttgcagGCATTTTGGATTGAATTGGGCATTTGTTGATCCGAAGACACCAGTCCAACAAGGAGTGAAGTTCTGTGTTTGTGTCAAGGAGTTCTTCCCGTGGCTCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - -tgttgtt
- - - - - - - - gttgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - gggtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtggga