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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atggtaatgcacatatttggtttctcttttaagtttcctttgatgtgctcaaaatttatgtctctttatgtctcctcttttctcctccacccattgccagCATTCACAGATAAAGGGAAGTTTCTGCTAGCAGCTAGGAGATATAGGTGTGGTACTCATACCGAGTATATAATTTCACTTGATGCTGATGATTTATCCCA

Basic information

species Glycine max
transcript GLYMA13G34470.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G34470.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G068586_T04 (Zea mays), 3'ss of exon 2
atggtaatgcac-atatttggtttctcttttaagtttcc----tttgatgtgctcaaaatttatgtctctttatgtctcctcttttctcctccacccattgccagCATTCACAGATAAAGGGAAGTTTCTGCTAGCAGCTAGGAGATATAGGTGTGGTACTCATACCGAGTATATAATTTCACTTGATGCTGATGATTTATCCCA
 |  |  | ||  | || |  ||| ||||     ||| |    |  ||| | ||  |   |||  |  ||||   ||||    | |||| |    |   || |||||      |||||||||||||||||  | || ||||| |||| |||| ||||| | ||||||||||| || || || |||||||| || || ||||| ||
-tttttgtacattagatgtattttttcttcagccttttcaccgtcagatatacttgatgatta-ataccttt---tctctctctctctctttgggcatctgacagCACCTGTGGATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTTAGGCGTGGTCCCCATACCGAGTACATTATATCTCTTGATGCAGAAGACTTATCACA

upper sequence: GLYMA13G34470.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv19s0014g01250.t01 (Vitis vinifera), 3'ss of exon 2
atggtaatgcacatatttggtttctcttttaagtttcctttgatgt--gctcaaaatttatgtctctttatgtctcctcttttct---cctccacccattgccagCATTCACAGATAAAGGGAAGTTTCTGCTAGCAGCTAGGAGATATAGGTGTGGTACTCATACCGAGTATATAATTTCACTTGATGCTGATGATTTATCCCA
    | ||| | |||| |  |   | ||||     |||||| ||||  |  ||    || |   | |||   ||    ||  |||     |||         |||||||||||||||| |||||||||||  |||| ||| | |||||||||  |||| |||| |||||||| ||||| |||||||||||||||||  |||| ||
-ctttgatgtatatatataatgcatatttt----ctcctttaatgttggtacatgtgttgtaaatgtttcaatcctggctcatctgagtgtcctttttccctcagCATTCACAGATAAGGGGAAGTTTCTCTTAGCTGCTCGAAGATATAGGCATGGTGCTCACACCGAGTACATAATATCACTTGATGCTGATGACATATCTCA
















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|18848480|gb|BM567698.1|BM567698
EST:     GCGGAACAAGAAAACTTCAACTTTTTATTTATATCTTGCCCTTACACCAT                         CATTCACAGATAAAGGGAAGTTTCTGCTAGCAGCTAGGAGATATAGGTGTG
genomic: GCGGAACAAGAAAACTTCAACTTTTTATTTATATCTTGCCCTTACACCATgtaagtaagt ... ccattgccagCATTCACAGATAAAGGGAAGTTTCTGCTAGCAGCTAGGAGATATAGGTGTG
EST: gi|15813642|gb|BI785917.1|BI785917
EST:     GCGGAACAAGAAAACTTCAACTTTTTATTTATATCTTGCCCTTACACCAT                         CATTCACAGATAAAGGGAAGTTTCTGCTAGCAGCTANGAGATATAGG
genomic: GCGGAACAAGAAAACTTCAACTTTTTATTTATATCTTGCCCTTACACCATgtaagtaagt ... ccattgccagCATTCACAGATAAAGGGAAGTTTCTGCTAGCAGCTAGGAGATATAGG
EST: gi|27425370|gb|CA936890.1|CA936890
EST:     GCGGAACAAGAAAACTTCAACTTTTTATTTATATCTTGCCCTTACACCAT                         CATTCACAGATAAAGGGAAGTTTCTGCTAGCAGCTAGGAGATATAGGTGTG
genomic: GCGGAACAAGAAAACTTCAACTTTTTATTTATATCTTGCCCTTACACCATgtaagtaagt ... ccattgccagCATTCACAGATAAAGGGAAGTTTCTGCTAGCAGCTAGGAGATATAGGTGTG
EST: gi|14125194|gb|BG789632.1|BG789632
EST:     GCGGAACAAGAAAACTTCAACTTTTTATTTATATCTTGCCCTTACACCAT                         CATTCACAGATAAAGGGAAGTTTCTGCTAGCAGCTAGGAGATATAGGTGTG
genomic: GCGGAACAAGAAAACTTCAACTTTTTATTTATATCTTGCCCTTACACCATgtaagtaagt ... ccattgccagCATTCACAGATAAAGGGAAGTTTCTGCTAGCAGCTAGGAGATATAGGTGTG
EST: gi|19271158|gb|BM887414.1|BM887414
EST:     CTTTTTATTTATATCTTGCCCTTACACCAT                         CATTCACAGATAAAGGGAAGTTTCTGCTAGCAGCTAGGAGATATAGGTGTG
genomic: CTTTTTATTTATATCTTGCCCTTACACCATgtaagtaagt ... ccattgccagCATTCACAGATAAAGGGAAGTTTCTGCTAGCAGCTAGGAGATATAGGTGTG
EST: gi|16996623|gb|BM085995.1|BM085995
EST:     GCGGAACAAGAAAACTTCAACTTTTTATTTATATCTTGCCCTTACACCAT                         CATTCACAGATAAAGGGAAGTTTCTGCTAGCAGCTAGGAGATATAGGTGTG
genomic: GCGGAACAAGAAAACTTCAACTTTTTATTTATATCTTGCCCTTACACCATgtaagtaagt ... ccattgccagCATTCACAGATAAAGGGAAGTTTCTGCTAGCAGCTAGGAGATATAGGTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctcaaaatttatgtctctttatgtctcctcttttctcctccacccattgccagCATTCACAGATAAAGGGAAGTTTCTGCTAGCAGCTAGGAGATATAGGTGTGGTACTCATACCGAGTATATAATTTCACTTGATGCTGATGATTTATCCCA
         tttatgtctctttatg  CT-rich tract
     aaaatttatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atggtaatgcacatatttggtttctcttttaagtttcctttgatgtgctcaaaatttatgtctctttatgtctcctcttttctcctccacccattgccagCATTCACAGATAAAGGGAAGTTTCTGCTAGCAGCTAGGAGATATAGGTGTGGTACTCATACCGAGTATATAATTTCACTTGATGCTGATGATTTATCCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - -aatgcac
- - - - - - - - - - - - - - - - - - - - tgatgtg