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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatagtaaaaaaaaattgtgatcataatcataatgatataaatatattgaagttcatttgaatgaccgtctaatatgtgagagatttatttacttttagATGATGGATTCCGCCTTACCTACCTTGGTTATGATTTTCTTGCCATTAAGACTATGGTGAACAAAGGAGTGTTTGTGGCTGTTGGACGTCAGATTGGCGT

Basic information

species Glycine max
transcript GLYMA11G33320.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G33320.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G51270.2 (Arabidopsis thaliana), 3'ss of exon 4
--------tcatagtaaaaaaaaattgtgatcataatcataatgatataaatatattgaa------gttcatttgaatgaccgt----ctaatatgtgagagatttatttacttttagATGATGGATTCCGCCTTACCTACCTTGGTTATGATTTTCTTGCCATTAAGACTATGGTGAACAAAGGAGTGTTTGTGGCTGTTGGACGTCAGATTGGCGT
        | ||    | |   | | || |   |  |    |||   |      |||| |      ||| | ||| |  | | |    ||| |  ||      ||||| |   | |||||||||||||||| || ||||| || |||||||| |||||||||||||| ||  |||| |||   ||  | |||   | ||| || ||||||||||| ||
gtgaggaattatctctataggcattagtaacttttcttgatatgtcttttgaggattggaagtcttgttaagttgcagaatcttatcgctattgcgttctttgtttatatctgtctagATGATGGATTCCGACTCACCTATCTGGGTTATGACTTTCTTGCCATTAAAACATTGGTCAACCGGGGTATATTTACCGGTGTCGGTCGTCAGATTGGTGT

upper sequence: GLYMA11G33320.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0094g01560.t01 (Vitis vinifera), 3'ss of exon 3
------------tcatagtaaaaa-aaaattgtgatcataatcat---aatgatataaatatattga-agttcatttgaatgaccgtctaatatgtgagagatttatt---tacttttagATGATGGATTCCGCCTTACCTACCTTGGTTATGATTTTCTTGCCATTAAGACTATGGTGAACAAAGGAGTGTTTGTGGCTGTTGGACGTCAGATTGGCGT
            | |||| ||  | ||||  || | | | ||  |   |   || | | |||||| | || | |||   |  |      |   |     |  ||| ||   | | | |||||||||| || || ||||| |||||||| |||||||||||||| || |||||| |||| ||    ||||| ||||| |||||||| ||||| ||||| ||
gtaaggaactattaatagaaactataaaacagtaaacctcatttttcgatccatttgattatatttatagcttattcacaaaaaaaaaaaggcttgatcatgtttgttctgtgcatctagATGATGGGTTTCGGCTTACTTACCTTGGATATGATTTTCTTGCAATAAAGACTCTGGTTAATCGTGGAGTATTTGTAGCTGTTGGTCGTCAAATTGGTGT
















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|7588583|gb|AW704375.1|AW704375
EST:     TTTGAAAAACTTGCTCAAGCATAAGTTGTTGCACCACGACTCCTCTAAAT                         ATGATGGATTCCGCCTTACCTACCTTGGTTATGATTTTCTTGCCATTAAGA
genomic: TTTGAAAAACTTGCTCAAGCATAAGTTGTTGCACCACGACTCCTCTAAATgttagtacct ... ttacttttagATGATGGATTCCGCCTTACCTACCTTGGTTATGATTTTCTTGCCATTAAGA
EST: gi|14260014|gb|BG882922.1|BG882922
EST:     TTTGAAAAACTTGCTCAAGCATAAGTTGTTGCACCACGACTCCTCTAAAT                         ATGATGGATTCCGCCTTACCTACCTTGGTTATGATTTTCTTGCCATTAAGA
genomic: TTTGAAAAACTTGCTCAAGCATAAGTTGTTGCACCACGACTCCTCTAAATgttagtacct ... ttacttttagATGATGGATTCCGCCTTACCTACCTTGGTTATGATTTTCTTGCCATTAAGA
EST: gi|6501956|gb|AW203329.1|AW203329
EST:     TTTGAAAAACTTGCTCAAGCATAAGTTGTTGCACCACGACTCCTCTAAAT                         ATGATGGATTCCGCCTTACCTACCTTGGTTATGATTTTCTTGCCATTAAGA
genomic: TTTGAAAAACTTGCTCAAGCATAAGTTGTTGCACCACGACTCCTCTAAATgttagtacct ... ttacttttagATGATGGATTCCGCCTTACCTACCTTGGTTATGATTTTCTTGCCATTAAGA
EST: gi|4293428|gb|AI442046.1|AI442046
EST:     TTTGAAAAACTTGCTCAAGCATAAGTTGTTGCACCACGACTCCTCTAAAT                         ATGATGGATTCCGCCTTACCTACCTTGGTTATGATTTTCTTGCCATTAAGA
genomic: TTTGAAAAACTTGCTCAAGCATAAGTTGTTGCACCACGACTCCTCTAAATgttagtacct ... ttacttttagATGATGGATTCCGCCTTACCTACCTTGGTTATGATTTTCTTGCCATTAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgaagttcatttgaatgaccgtctaatatgtgagagatttatttacttttagATGATGGATTCCGCCTTACCTACCTTGGTTATGATTTTCTTGCCATTAAGACTATGGTGAACAAAGGAGTGTTTGTGGCTGTTGGACGTCAGATTGGCGT
                       gtctaat  putative branch site (score: 3)
                                            tttactttt  putative PPT
                                     agatttatttactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcatagtaaaaaaaaattgtgatcataatcataatgatataaatatattgaagttcatttgaatgaccgtctaatatgtgagagatttatttacttttagATGATGGATTCCGCCTTACCTACCTTGGTTATGATTTTCTTGCCATTAAGACTATGGTGAACAAAGGAGTGTTTGTGGCTGTTGGACGTCAGATTGGCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - -aaaaaaa