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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgaaaattatgcatagcacacaccaaagtagccataaacacagatcgtgcttaactatatgggatacattgtcttatattcctgttgcttcccaaacagAATTTCTTTTCAGAGCTCCAAGATAGAGAAGAAGAATTTGGCATATCTGATATCCAGCTTGGTCTAACAACGCTCGAAGAAGTTTTCTTGAATATTGCTA

Basic information

species Glycine max
transcript GLYMA06G20360.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G20360.2 (Glycine max), 3'ss of exon 13
lower sequence: AT3G47730.1 (Arabidopsis thaliana), 3'ss of exon 14
gtgaaaattatgcatagcacacaccaaagtagccataaacacagatcgtgcttaactatatgggatacattgtcttatattcctgttgcttcccaaacagAATTTCTTTTCAGAGCTCCAAGATAGAGAAGAAGAATTTGGCATATCTGATATCCAGCTTGGTCTAACAACGCTCGAAGAAGTTTTCTTGAATATTGCTA
                | |  ||   |   | || ||   | | || |   || ||||  |    || |       |||       ||      |||||||  || ||  | ||||| ||||| ||||||||||||||||| || || |||||||| ||||||||  | || || |||||||| || ||||| || || |
----------------gtaagcatttacacaaccttatg-atatatag-atttcactacctaccttaaaactaagcata-----agtgacaatgaaacagAGCTTTTTCGCTGAGCTTCAAGACAGAGAAGAAGAATTTGGAATCTCAGATATCCAACTTGGTCTTGCTACTCTTGAAGAAGTCTTTTTGAACATAGCAA

upper sequence: GLYMA06G20360.2 (Glycine max), 3'ss of exon 13
lower sequence: Vv17s0000g05850.t01 (Vitis vinifera), 3'ss of exon 14
-------------------------------------------------gtgaaaattatgcat-agcacacaccaaagtagccataaacacagatcgtgcttaactatatgggatacattgtcttatattcct--gttgctt-------cccaaacagAATTTCTTTTCAGAGCTCCAAGATAGAGAAGAAGAATTTGGCATATCTGATATCCAGCTTGGTCTAACAACGCTCGAAGAAGTTTTCTTGAATATTGCTA
                                                    ||  | ||  || || |      |     || |  ||   ||||  ||  ||   || |||  |   ||    | |  ||||  || ||||       ||  || |||| ||||||   ||||||||||||||||||  ||||||||| ||| | || || || || || || ||||| || ||||||||||||||||||||||| |
gtagacgactctctcattttttgccttgtttaattatatacttactctgaacaacctaatttatcaggattttttactacggctaccaatgaagattttgagtaga-atttggtgtttgtttctcttttctccttcgtggcttttatattcctcaatagAAATTCTTTGGGGAGCTCCAAGATAGAGAAACAGAATTTGGAATAGCAGACATTCAACTGGGGCTTACAACTCTTGAAGAAGTTTTCTTGAATATTGCAA
















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|208089754|gb|GD889143.1|GD889143
EST:     TTTTAGTGATTCCTCATGACGGAGAGGCGCTCATGACG                         AATTTCTTTTCAGAGCTCCAAGATAGAGAAGAAGAATTTGGCATATCTGAT
genomic: TTTT-GTGATTCCTCATGACAGAGAGGCGCTCATGACGgtaagctttc ... tcccaaacagAATTTCTTTTCAGAGCTCCAAGATAGAGAAGAAGAATTTGGCATATCTGAT
EST: gi|193427222|gb|FK394802.1|FK394802
EST:     TAAACTTCCTAACTTTTGTGATTCCTCATGACAGAGAGGCGCTCATGACG                         AATTTCTTTTCAGAGCTCCAAGATAGAGAAGAAGAATTTGGCATATCTGAT
genomic: T-AACTTCCTAACTTTTGTGATTCCTCATGACAGAGAGGCGCTCATGACGgtaagctttc ... tcccaaacagAATTTCTTTTCAGAGCTCCAAGATAGAGAAGAAGAATTTGGCATATCTGAT
EST: gi|120494823|gb|EH222990.1|EH222990
EST:     ATAACTTCCTAACTTTTGTGATTCCTCATGACAGAGAGGCGCTCATGACG                         AATTTCTTTTCAGAGCTCCAAGATAGAGAAGAAGAATTTGGCATATCTGAT
genomic: ATAACTTCCTAACTTTTGTGATTCCTCATGACAGAGAGGCGCTCATGACGgtaagctttc ... tcccaaacagAATTTCTTTTCAGAGCTCCAAGATAGAGAAGAAGAATTTGGCATATCTGAT
EST: gi|37996900|gb|CF808489.1|CF808489
EST:     ATAACTTCCTAACTTTTGTGATTCCTCATGACAGAGAGGCGCTCATGACG                         AATTTCTTTTCAGAGCTCCAAGATAGAGAAGAAGAATTTGGCATATCTGAT
genomic: ATAACTTCCTAACTTTTGTGATTCCTCATGACAGAGAGGCGCTCATGACGgtaagctttc ... tcccaaacagAATTTCTTTTCAGAGCTCCAAGATAGAGAAGAAGAATTTGGCATATCTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgtgcttaactatatgggatacattgtcttatattcctgttgcttcccaaacagAATTTCTTTTCAGAGCTCCAAGATAGAGAAGAAGAATTTGGCATATCTGATATCCAGCTTGGTCTAACAACGCTCGAAGAAGTTTTCTTGAATATTGCTA
    gcttaac  putative branch site (score: 3)
                                  ttcctgttgcttccc  putative PPT
      ttaactatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaaaattatgcatagcacacaccaaagtagccataaacacagatcgtgcttaactatatgggatacattgtcttatattcctgttgcttcccaaacagAATTTCTTTTCAGAGCTCCAAGATAGAGAAGAAGAATTTGGCATATCTGATATCCAGCTTGGTCTAACAACGCTCGAAGAAGTTTTCTTGAATATTGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - tatgcat
- - - - - - - - - acacacc
- - - - - - - - - - - - - - - - - - aaacaca
- - - - - - - - - - - - - - - - - - - - - - - -gtgctta