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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcttttatattgtaacattttcatttgtcattgttttgttaaaaatctgccccattatatgtagggaatattcacctccattttttctctgtccccagCATTCCTGTGGCAGCTGATGAGGTTTACTATGCTTCAACTTCTGAGAAATTTGAGATCACACTCACAAGGTAAAGAGATTACTGATGCTGATATTCTAAA

Basic information

species Glycine max
transcript GLYMA02G47800.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G47800.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G35700.1 (Arabidopsis thaliana), 3'ss of exon 11
---------------------------------------------------------------------------tttcttttatattgtaacattttcatttgtcattgttttgttaaaaatctgccccattatat-gtagggaatattcacctccattttttctctgtccccagCATTCCTGTGGCAGCTGATGAGGTTTACTATGCTTCAACTTCTGAGAAATTTGAGATCACACTCACAAGGTAAAGAGATTACTGATGCTGATATTCTAAA
                                                                           ||| || | | || |  | | || |    |   | |  | |   || |     | | |   | | ||   ||| |  | |  |   |   |   ||  |||||||  ||||||| || ||||| | ||| ||||| ||||||||||| || |||||||||||||| ||||||||||| ||||| ||||| |||||||| ||
gtgagttctcctaaaagtcacactgataagattatgcaatttcatataacagactcacataactgttagtattgttttgttctgtcttttctcttcttgaaagatgcatctgctatagtaagttcattctaattggtagcagtatataatttcttgtaccatcattgattctgcagCATTTTTGTGGCAACTAATGAGATATACAATGCTCCAACTTCTGAGGAACTTGAGATCACACTCGCAAGGTAAAGAAATTACAGATGCAGATATTCTTAA
















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|51336658|gb|CO980524.1|CO980524
EST:     GAATGTTGCTGGTAATGATATTGTACAAGGGAATAAGAAGNNNNTATTGG                         CATTCCTGTGGCAGCTGATGAGGTTTACTATGCTTCAACTTCTGAGAAATT
genomic: GAATGTTGCTGGTAATGATATTGTACAAGGGAATAAGAAGCTCTTATTGGgtgagtttca ... ctgtccccagCATTCCTGTGGCAGCTGATGAGGTTTACTATGCTTCAACTTCTGAGAAATT
EST: gi|22521801|gb|BU080612.1|BU080612
EST:     GAATGTTGCTGGTAATGATATTGTACAAGGGAATAAGAAGCTCTTATTGG                         CATTCCTGTGGCAGCTGATGAGGTTTACTATGCTTCAACTTCTGAGAAATT
genomic: GAATGTTGCTGGTAATGATATTGTACAAGGGAATAAGAAGCTCTTATTGGgtgagtttca ... ctgtccccagCATTCCTGTGGCAGCTGATGAGGTTTACTATGCTTCAACTTCTGAGAAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatctgccccattatatgtagggaatattcacctccattttttctctgtccccagCATTCCTGTGGCAGCTGATGAGGTTTACTATGCTTCAACTTCTGAGAAATTTGAGATCACACTCACAAGGTAAAGAGATTACTGATGCTGATATTCTAAA
                         tattcacctccatttt  CT-rich tract
          attatatgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcttttatattgtaacattttcatttgtcattgttttgttaaaaatctgccccattatatgtagggaatattcacctccattttttctctgtccccagCATTCCTGTGGCAGCTGATGAGGTTTACTATGCTTCAACTTCTGAGAAATTTGAGATCACACTCACAAGGTAAAGAGATTACTGATGCTGATATTCTAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - -tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - ctgcccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgtag