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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtatgcatttgtaattatttatttaaatgtacttatatatatatatatatatatatatatatatatatatatattatcattgattctcattctaattacactattctttaaaagGCTGTTGACTTTGTTGACAAGTTATTACGCTATGATCACCAAGAACGTCCCACAGCAAAAGAAGCCATG

Basic information

species Glycine max
transcript GLYMA05G22320.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G22320.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv07s0129g00270.t01 (Vitis vinifera), 3'ss of exon 8
gtagtatgcatttgtaattatttatttaaatgtacttatatatatatatatatatatatatatatatatatatatattatcattgattctcattctaattacactattctttaaaagGCTGTTGACTTTGTTGACAAGTTATTACGCTATGATCACCAAGAACGTCCCACAGCAAAAGAAGCCATG
                          || |  |  ||    || | ||  |  |  | |   |  ||  |  | |  |    ||  |  ||||  | |||    | || | |  ||| |  |||||||| ||||||||||  | || ||||||||||||||| | || || ||||||||||| |||
-------------------------gtagac-tgttttgtcatttctacttgaaattttgattccattaactttttgtggtgttagtaatcatg-tgatt----tcttttctccaagTCAATTGACTTTCTTGACAAGTTGCTGCGATATGATCACCAAGAAAGGCCAACCGCAAAAGAAGCAATG
















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|31470201|gb|CD412349.1|CD412349
EST:     CATGGGCAAAGTTCATTAATGTAGAAAATCATCACATGGCTGTTCCTGAG                         GCTGTTGACTTTGTTGACAAGTTATTACGCTATGATCACCAAGAACGTCCC
genomic: CATGGGCAAAGTTCATTAATGTAGAAAATCATCACATGGCTGTTCCTGAGgtagtatgca ... tctttaaaagGCTGTTGACTTTGTTGACAAGTTATTACGCTATGATCACCAAGAACGTCCC
EST: gi|15815566|gb|BI787841.1|BI787841
EST:     CATGGGCAAAGTTCATTAATGTAGAAAATCATCACATGGCTGTTCCTGAG                         GCTGCTGACTTT
genomic: CATGGGCAAAGTTCATTAATGTAGAAAATCATCACATGGCTGTTCCTGAGgtagtatgca ... tctttaaaagGCTGTTGACTTT
EST: gi|16279966|gb|BI943709.1|BI943709
EST:     CATGGGCAAAGTTCATTAATGTAGAAAATCATCACATGGCTGTTCCTGAG                         GCTGTTGACTTTGTTGACAAGTTATTACGCTATGATCACCAAGAACGTCCC
genomic: CATGGGCAAAGTTCATTAATGTAGAAAATCATCACATGGCTGTTCCTGAGgtagtatgca ... tctttaaaagGCTGTTGACTTTGTTGACAAGTTATTACGCTATGATCACCAAGAACGTCCC
EST: gi|17153984|gb|BM143917.1|BM143917
EST:     CATGGGCAAAGTTCATTAATGTAGAAAATCATCACATGGCTGTTCCTGAG                         GCTGTTGACTTTGTTGACAAGTTATTACGCTATGATCACCAAGAACGTCCC
genomic: CATGGGCAAAGTTCATTAATGTAGAAAATCATCACATGGCTGTTCCTGAGgtagtatgca ... tctttaaaagGCTGTTGACTTTGTTGACAAGTTATTACGCTATGATCACCAAGAACGTCCC
EST: gi|17518848|gb|BM187890.1|BM187890
EST:     CATGGGCAAAGTTCATTAATGTAGAAAATCATCACATGGCTGTTCCTGAG                         GCTGTTGACTTTGTTGACAAGTTATTACGCTATGATCACCAAGAACGTCCC
genomic: CATGGGCAAAGTTCATTAATGTAGAAAATCATCACATGGCTGTTCCTGAGgtagtatgca ... tctttaaaagGCTGTTGACTTTGTTGACAAGTTATTACGCTATGATCACCAAGAACGTCCC
EST: gi|20814462|gb|BQ298940.1|BQ298940
EST:     CATGGGCAAAGTTCATTAATGTAGAAAATCATCACATGGCTGTTCCTGAG                         GCTGTTGACTTTGTTGACAAGTTATTACGCTATGATCACCAAGAACGTCCC
genomic: CATGGGCAAAGTTCATTAATGTAGAAAATCATCACATGGCTGTTCCTGAGgtagtatgca ... tctttaaaagGCTGTTGACTTTGTTGACAAGTTATTACGCTATGATCACCAAGAACGTCCC
EST: gi|192303250|gb|FG995586.1|FG995586
EST:     CATGGGCAAAGTTCATTAATGTAGAAAATCATCACATGGCTGTTCCTGAG                         GCTGTTGACTTTGTTAACAAGTTATTACGCTATGATCACCAAGAACGTCCC
genomic: CATGGGCAAAGTTCATTAATGTAGAAAATCATCACATGGCTGTTCCTGAGgtagtatgca ... tctttaaaagGCTGTTGACTTTGTTGACAAGTTATTACGCTATGATCACCAAGAACGTCCC
EST: gi|31465610|gb|CD407638.1|CD407638
EST:     CATGGGCAAAGTTCATTAATGTAGAAAATCATCACATGGCTGTTCCTGAG                         GCTGTTGACTTTGTTGACAAGTTATTACGCTATGATCACCAAGAACGTCCC
genomic: CATGGGCAAAGTTCATTAATGTAGAAAATCATCACATGGCTGTTCCTGAGgtagtatgca ... tctttaaaagGCTGTTGACTTTGTTGACAAGTTATTACGCTATGATCACCAAGAACGTCCC
EST: gi|16343159|gb|BI968754.1|BI968754
EST:     CATGGGCAAAGTTCATTAATGTAAAAAATCATCACATGGCTGTTCCTGAG                         GCTGTTGACTTTGTTGACAAGTTATTACGCTATGATCACCAAGAACGTCCC
genomic: CATGGGCAAAGTTCATTAATGTAGAAAATCATCACATGGCTGTTCCTGAGgtagtatgca ... tctttaaaagGCTGTTGACTTTGTTGACAAGTTATTACGCTATGATCACCAAGAACGTCCC
EST: gi|22927857|gb|BU544996.1|BU544996
EST:     CATGGGCAAAGTTCATTAATGTAGAAAATCATCACATGGCTGTTCCTGAG                         GCTGTTGACTTTGTTGACAAGTTATTACGCTATGATCACCAAGAACGTCCC
genomic: CATGGGCAAAGTTCATTAATGTAGAAAATCATCACATGGCTGTTCCTGAGgtagtatgca ... tctttaaaagGCTGTTGACTTTGTTGACAAGTTATTACGCTATGATCACCAAGAACGTCCC
EST: gi|4299430|gb|AI442903.1|AI442903
EST:     CATGGGCANAGTTCATTAATGTAGAAAATCATCACATGGCTGTTCCTGAG                         GCTGTTGACTTTGTTGACAAGTTATTACGCTATGATCACCAAGAACGTCCC
genomic: CATGGGCAAAGTTCATTAATGTAGAAAATCATCACATGGCTGTTCCTGAGgtagtatgca ... tctttaaaagGCTGTTGACTTTGTTGACAAGTTATTACGCTATGATCACCAAGAACGTCCC
EST: gi|7327072|gb|AW620870.1|AW620870
EST:     CATGGGCAAAGTTCATTAATGTAGAAAATCATCACATGGCTGTTCCTGAG                         GCTGTTGACTTTGTTGACAAGTTATTACGCTATGATCACCAAGAACGTCCC
genomic: CATGGGCAAAGTTCATTAATGTAGAAAATCATCACATGGCTGTTCCTGAGgtagtatgca ... tctttaaaagGCTGTTGACTTTGTTGACAAGTTATTACGCTATGATCACCAAGAACGTCCC
EST: gi|17401154|gb|BM177936.1|BM177936
EST:     CATGGGCAAAGTTCATTAATGTAGAAAATCATCACATGGCTGTTCCTGAG                         GCTGTTGACTTTGTTGACAAGTTATTACGCTATGATCACCAAGAACGTCCC
genomic: CATGGGCAAAGTTCATTAATGTAGAAAATCATCACATGGCTGTTCCTGAGgtagtatgca ... tctttaaaagGCTGTTGACTTTGTTGACAAGTTATTACGCTATGATCACCAAGAACGTCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatatatatatattatcattgattctcattctaattacactattctttaaaagGCTGTTGACTTTGTTGACAAGTTATTACGCTATGATCACCAAGAACGTCCCACAGCAAAAGAAGCCATG
                              ttctaat  putative branch site (score: 2)
                                         ctattcttt  putative PPT
     atatatatattatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtatgcatttgtaattatttatttaaatgtacttatatatatatatatatatatatatatatatatatatatattatcattgattctcattctaattacactattctttaaaagGCTGTTGACTTTGTTGACAAGTTATTACGCTATGATCACCAAGAACGTCCCACAGCAAAAGAAGCCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC