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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcataatttcctgcctatgatatagcatcatgatcccttagcctgatgttctccaacttgataaattctgagaataactattttttcccctcctgccaaactgtttttctccacagCTGATGCATATAACCACACCGACTCTGAATTTCTGAAATCTGAAAATAATCAAAACAGAGATGCTGGATCAACTGCTTCCACTGCCATTCTTGTTGGTGA

Basic information

species Glycine max
transcript GLYMA17G33690.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G33690.2 (Glycine max), 3'ss of exon 4
lower sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgcataatttcctgcctatgatatagcatcatgatcccttagcctgatgttctccaacttgataaattctg-agaataactattttttcccctcctgccaaactgtttttctccacagCTGATGCATATAACCACACCGACTCTGAATTTCTGAAATCTGAAAATAATCAAAACAGAGATGCTGGATCAACTGCTTCCACTGCCATTCTTGTTGGTGA
     |  ||| |  ||| | |||| |            |||||| |||| |     | |  ||| |    | |   |  ||| || |  |  |         ||| |  ||  | ||||||||||||| ||||| || ||||| || ||||| ||||| ||||||| ||| |||||||||||||| ||||| || || || |||||  | ||||||||
----gtgcttttc-acctttaatattg------------ttagccagatgattc---aataaatagacctagcaaggtgcctaattctgactttttcatttgcctgctcctcatctcagCTGATGCATACAACCAAACAGACTCAGAGTTTCTTAAATCAGAAAATAGTCAGAACAGAGATGCTGGTTCAACGGCGTCAACAGCCATCTTAGTTGGTGA

upper sequence: GLYMA17G33690.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0008g07320.t01 (Vitis vinifera), 3'ss of exon 4
gtgcataatttcctgcctatgata-tagcatcatgatcccttagcctgatgttctccaacttgataaattctgagaataactattttttcccctcctgccaaactgtttttctccacagCTGATGCATATAACCACACCGACTCTGAATTTCTGAAATCTGAAAATAATCAAAACAGAGATGCTGGATCAACTGCTTCCACTGCCATTCTTGTTGGTGA
     |  ||||||| || ||  | ||   |||   | |  |||||||      |   |  || |  | ||| |  |  ||| | ||      ||||      ||||   |     ||||||||||||| || ||||| ||||| |||||||||||||| ||||||||||| || |||||||||||||||||||| ||||| || || |||||||||||
---gtttgtttcctgactgtgccagtaatgtcact-ttctatagcctg------tatgaagtg-ttcactctaaatactactgtcttaaattatcct------ctgtacat----gcagCTGATGCATACAAGCACACAGACTCAGAATTTCTGAAATCAGAAAATAATCAGAATAGAGATGCTGGATCAACTGCCTCCACCGCTATCCTTGTTGGTGA
















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|308098639|gb|HO760380.1|HO760380
EST:     CAATTTGATCAGTCATCCAAAATTCATTTCTGACACCAAATCTGCAATAG                         CTGATGCATATAACCATACCGACTCTGAATTTCTGAAATCTGAAAATAATC
genomic: CAATTTGATCAGTCATCCTAAATTCATTTCTGACACCAAATCTGCAATAGgtgcataatt ... ttctccacagCTGATGCATATAACCACACCGACTCTGAATTTCTGAAATCTGAAAATAATC
EST: gi|298177029|gb|HO023390.1|HO023390
EST:     CAATTTGATCAGTCATCCTAAATCCATTTCTGACACCAAATCTGCAATAG                         CTGATGCATATAACCACACCGACTCTGAATTTCTGAAACCTGAAAATAATC
genomic: CAATTTGATCAGTCATCCTAAATTCATTTCTGACACCAAATCTGCAATAGgtgcataatt ... ttctccacagCTGATGCATATAACCACACCGACTCTGAATTTCTGAAATCTGAAAATAATC
EST: gi|27427212|gb|CA938732.1|CA938732
EST:     CAATTTGATCAGTCATCCAAAATTCATTTCTGACACCAAATCTGCAATAG                         CTGATGCATATAACCATACCGACTCTGAATTTCTGAAATCTGAAAATAATC
genomic: CAATTTGATCAGTCATCCTAAATTCATTTCTGACACCAAATCTGCAATAGgtgcataatt ... ttctccacagCTGATGCATATAACCACACCGACTCTGAATTTCTGAAATCTGAAAATAATC
EST: gi|151406983|gb|EV276798.1|EV276798
EST:     CAATTTGATCAGTCATCCTAAATTCATTTCTGACACCAAATCTGCAATAA                         CTGATGCATATAACCACACCGACTCTGAATTTCTGAAATCTGAAAATAATC
genomic: CAATTTGATCAGTCATCCTAAATTCATTTCTGACACCAAATCTGCAATAGgtgcataatt ... ttctccacagCTGATGCATATAACCACACCGACTCTGAATTTCTGAAATCTGAAAATAATC
EST: gi|15662272|gb|BI699643.1|BI699643
EST:     CAATTTGATCAGTCATCCAAAATTCATTTCTGACACCAAATCTGCAATAG                         CTGATGCATATAACCATACCGACTCTGAATTTCTGAAATCTGAAAATAATC
genomic: CAATTTGATCAGTCATCCTAAATTCATTTCTGACACCAAATCTGCAATAGgtgcataatt ... ttctccacagCTGATGCATATAACCACACCGACTCTGAATTTCTGAAATCTGAAAATAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaattctgagaataactattttttcccctcctgccaaactgtttttctccacagCTGATGCATATAACCACACCGACTCTGAATTTCTGAAATCTGAAAATAATCAAAACAGAGATGCTGGATCAACTGCTTCCACTGCCATTCTTGTTGGTGA
          gaataac  putative branch site (score: 2)
                                       ctgtttttctccac  putative PPT
         agaataactatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcataatttcctgcctatgatatagcatcatgatcccttagcctgatgttctccaacttgataaattctgagaataactattttttcccctcctgccaaactgtttttctccacagCTGATGCATATAACCACACCGACTCTGAATTTCTGAAATCTGAAAATAATCAAAACAGAGATGCTGGATCAACTGCTTCCACTGCCATTCTTGTTGGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA