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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacgctctttctttctctcgtttttctccttttttgcttcccgattttactgttttgccactgattggtgcggttgatgcttgttttctcgctgatcgcagCAAATCGAAGCTTTACCGGTTCGACAAGGACGGGAACCAGTGGAAGGAGCGTGGCGCCGGCACTGTGAAGTTCCTGAAGCATAAGGCTTCCGGCAAGGTT

Basic information

species Glycine max
transcript GLYMA10G36500.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G36500.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g18180.1 (Oryza sativa), 3'ss of exon 1
gtaa-cgctctttctttctctcgtttttctccttttttgcttcccgattttactgttttgccactgattggtgcggttgatgcttgttttctcgctgatcgcagCAAATCGAAGCTTTACCGGTTCGACAAGGACGGGAACCAGTGGAAGGAGCGTGGCGCCGGCACTGTGAAGTTCCTGAAGCATAAGGCTTCCGGCAAGGTT
|||| |   ||  |  || |||| |     ||   |  | |  ||        || | ||   ||||  |   || ||        ||||     |   ||||| || |||||||| ||||| ||||||||||| |||||||| ||||||||| | ||| ||||||| |||||| | |||||||| ||||   |||||||||| 
gtaagccgcctccccctccctcgatccagccccgatccgatctcccccggctttgatctgagcctgac-gactcgttt--------tttttggatttcccgcagGAAGTCGAAGCTGTACCGCTTCGACAAGGAGGGGAACCAATGGAAGGAGAGAGGCACCGGCACGGTGAAGCTGCTGAAGCACAAGGAGACCGGCAAGGTC

upper sequence: GLYMA10G36500.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g28290.1 (Oryza sativa), 3'ss of exon 1
-----------gtaacgctctttctttctctcgtttttctccttttttgcttcccgattttactgttttgccactgattggtgcggttgatgcttgttttctcg-ctgatcgcagCAAATCGAAGCTTTACCGGTTCGACAAGGACGGGAACCAGTGGAAGGAGCGTGGCGCCGGCACTGTGAAGTTCCTGAAGCATAAGGCTTCCGGCAAGGTT
               |||     ||| |||||  |  ||| ||    |   |      |    || |||    | | | | |  ||| |  |||  |   | ||  || | |||| ||  |||||||||||||||| |||||||| |||||||||||||||||||| ||  | ||||| || ||| |||| ||||| ||||    ||||||||| 
gtgagccccccccgccgccgccgcttgctctctctcctcttctcccctctcttgtagctcgtgtgctttttttcggttcgatctggt-ggcgctgatccgcgcgattgtttgcagGAAGGCGAAGCTTTACCGGTTTGACAAGGAGGGGAACCAGTGGAAGGAGCGGGGGACGGGCACCGTCAAGCTCCTCAAGCACAAGGAGAACGGCAAGGTC

upper sequence: GLYMA10G36500.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G094388_T01 (Zea mays), 3'ss of exon 1
gtaacgctctttctttctctcgtttttctccttttttgcttcccgattttactgttttgccactgattggtgcggttgatgcttgttttctcgctgatcgcagCAAATCGAAGCTTTACCGGTTCGACAAGGACGGGAACCAGTGGAAGGAGCGTGGCGCCGGCACTGTGAAGTTCCTGAAGCATAAGGCTTCCGGCAAGGTT
|| | ||     |   | ||    || | ||       || ||||||    | | ||||||  ||  | ||     |||||   |       ||||   |||| ||  ||||||| ||||||||||||||||| |||||||||||||| ||||| ||| | |||||||||||| | || ||||| || |   ||| |||||| 
gtgaggcatccgcggccgcttcgattccccccc-----ctccccgat----ccgatttgcccatgtcttgttgatctgatgtgcggcg----gctg--tgcagGAAGGCGAAGCTCTACCGGTTCGACAAGGAGGGGAACCAGTGGAAAGAGCGCGGCACAGGCACTGTGAAGCTGCTCAAGCACAAAGACACCGCCAAGGTC

upper sequence: GLYMA10G36500.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G078933_T01 (Zea mays), 3'ss of exon 1
gtaacgc-tctttctttctctcgtttttctccttttttgcttcccgattttactgttttgccactgattggtgcggttgatgcttgttttctcgctgatcgcagCAAATCGAAGCTTTACCGGTTCGACAAGGACGGGAACCAGTGGAAGGAGCGTGGCGCCGGCACTGTGAAGTTCCTGAAGCATAAGGCTTCCGGCAAGGTT
|| | || || |        ||| || || ||       |  ||||||   | |    |     |  ||| | |   ||| |  ||      || | || |||| ||  ||||||| ||||||||||||||||| | |||||||||||| || |||||| | |||||||||||| | || ||||| ||||   ||| |||||| 
gtgatgcatcctcggccgcttcgattctccccaccccaac--cccgatccgattcggctaggttttgttgat-catctgacgtgtgg-----cggttat-gcagGAAGGCGAAGCTCTACCGGTTCGACAAGGAGGCGAACCAGTGGAAAGAACGTGGCACAGGCACTGTGAAGCTGCTTAAGCACAAGGAGACCGCCAAGGTC

upper sequence: GLYMA10G36500.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G07140.1 (Arabidopsis thaliana), 3'ss of exon 1
gtaacgctctttctt--------tctctcgtttttctccttttttgcttcccgattttactg---ttttgccactga----ttggtgcggttga-tgcttgttttctcgctgatc-gcagCAAATCGAAGCTTTACCGGTTCGACAAGGACGGGAACCAGTGGAAGGAGCGTGGCGCCGGCACTGTGAAGTTCCTGAAGCATAAGGCTTCCGGCAAGGTT
||||   | ||||||        | | | ||||||||  | |    |  |  ||| | |  |   || |     | |    |||||| | |||| ||  | |||  | |   |||   || |||||||||||||| || ||||| ||||| | ||| |||||||||||| | || || || |||||||||||| | |||||||||    | || ||| ||
gtaagtgtttttcttaattggtgtttatagtttttctgatctaggtcaactggatctgatcgaatttataaggtttagcttttggtgtgtttgactgaatttttgtttgtgaatctaaagGAAATCGAAGCTTTATCGATTCGATAAGGATGCGAATCAGTGGAAGGAGAGAGGAGCTGGTACTGTGAAGTTCTTAAAGCATAAGAACACTGGGAAGATT

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|16105079|gb|BI892819.1|BI892819
EST:     GAGGTTGCTGTCACCACCGGCGAGGAGGATTATTATGCAATCCTGGATCT                         CAAATCGAAGCTTTACCGGTTCGACAAGGACGGGAACCAGTGGAAGGAGCG
genomic: GAGGTTGCTGTCACCACCGGCGAGGAGGACGAAGATGCAATCCTGGATCTgtaacgctct ... ctgatcgcagCAAATCGAAGCTTTACCGGTTCGACAAGGACGGGAACCAGTGGAAGGAGCG
EST: gi|213598628|gb|DB964250.1|DB964250
EST:     GAGGTTGCTGTCACCACCGGCGAGGAGGACGAAGATGCAATCCTGGATCT                         CAAATCGAAGCTTTACCGGTTCGACAAGGACGGGAACCAGTGGAAGGAGCG
genomic: GAGGTTGCTGTCACCACCGGCGAGGAGGACGAAGATGCAATCCTGGATCTgtaacgctct ... ctgatcgcagCAAATCGAAGCTTTACCGGTTCGACAAGGACGGGAACCAGTGGAAGGAGCG
EST: gi|26045879|gb|CA783312.1|CA783312
EST:     GAGGTTGCTGTCACCACCGGCGAGGAGGACGAAGATGCAATCCTGGATCT                         CAAATCGAAGCTTTACCGGTTCGACAAGGACGGGAACCAGTGGAAGGAGCG
genomic: GAGGTTGCTGTCACCACCGGCGAGGAGGACGAAGATGCAATCCTGGATCTgtaacgctct ... ctgatcgcagCAAATCGAAGCTTTACCGGTTCGACAAGGACGGGAACCAGTGGAAGGAGCG
EST: gi|9985899|gb|BE659905.1|BE659905
EST:     GAGGTTGCTGTCACCACCGGCGAGGAGGACGAAGATGCAATCCTGGATCT                         CAAATCGAAGCTTTACCGGTTCGACAAGGACGGGAACCAGTGGAAGGAGCG
genomic: GAGGTTGCTGTCACCACCGGCGAGGAGGACGAAGATGCAATCCTGGATCTgtaacgctct ... ctgatcgcagCAAATCGAAGCTTTACCGGTTCGACAAGGACGGGAACCAGTGGAAGGAGCG
EST: gi|18040952|gb|BM309246.1|BM309246
EST:     GAGGTTGCTGTCACCACCGGCGAGGAGGACGAAGATGCAATCCTGGATCT                         CAAATCGAAGCTTTACCGGTTCGACAAGGACGGGAACCAGTGGAAGGAGCG
genomic: GAGGTTGCTGTCACCACCGGCGAGGAGGACGAAGATGCAATCCTGGATCTgtaacgctct ... ctgatcgcagCAAATCGAAGCTTTACCGGTTCGACAAGGACGGGAACCAGTGGAAGGAGCG
EST: gi|7042320|gb|AW472214.1|AW472214
EST:     GAGGTTGCTGTCACCACCGGCGAGGAGGACGAAGATGCAATCCTGGATCT                         CAAATCGAAGCTTTACCGGTTCGACAAGGACGGGAACCAGTGGAAGGAGCG
genomic: GAGGTTGCTGTCACCACCGGCGAGGAGGACGAAGATGCAATCCTGGATCTgtaacgctct ... ctgatcgcagCAAATCGAAGCTTTACCGGTTCGACAAGGACGGGAACCAGTGGAAGGAGCG
EST: gi|254322064|gb|GR837478.1|GR837478
EST:     GAGGTTGCTGTCACCACCGGCGAGGAGGACGAAGATGCAATCCTGGATCT                         CAAATCGAAGCTTTACCGGTTCGACAAGGACGGGAACCAGTGGAAGGAGCG
genomic: GAGGTTGCTGTCACCACCGGCGAGGAGGACGAAGATGCAATCCTGGATCTgtaacgctct ... ctgatcgcagCAAATCGAAGCTTTACCGGTTCGACAAGGACGGGAACCAGTGGAAGGAGCG
EST: gi|9985900|gb|BE659906.1|BE659906
EST:     GAGGTTGCTGTCACCACCGGCGAGGAGGACGAAGATGCAATCCTGGATCT                         CAAATCGAAGCTTTACCGGTTCGACAAGGACGGGAACCAGTGGAAGGAGCG
genomic: GAGGTTGCTGTCACCACCGGCGAGGAGGACGAAGATGCAATCCTGGATCTgtaacgctct ... ctgatcgcagCAAATCGAAGCTTTACCGGTTCGACAAGGACGGGAACCAGTGGAAGGAGCG
EST: gi|6567189|gb|AW234804.1|AW234804
EST:     GAGGTTGCTGTCACCACCGGCGAGGAGGACGAAGATGCAATCCTGGATCT                         CAAATCGAAGCTTTACCGGTTCGACAAGGACGGGAACCAGTGGAAGGAGCG
genomic: GAGGTTGCTGTCACCACCGGCGAGGAGGACGAAGATGCAATCCTGGATCTgtaacgctct ... ctgatcgcagCAAATCGAAGCTTTACCGGTTCGACAAGGACGGGAACCAGTGGAAGGAGCG
EST: gi|9565033|gb|BE474542.1|BE474542
EST:     GAGGTTGCTGTCACCACCGGCGAGGAGGACGAAGATGCAATCCTGGATCT                         CAAATCGAAGCTTTACCGGTTCGACAAGGACGGGAACCAGTGGAAGGAGCG
genomic: GAGGTTGCTGTCACCACCGGCGAGGAGGACGAAGATGCAATCCTGGATCTgtaacgctct ... ctgatcgcagCAAATCGAAGCTTTACCGGTTCGACAAGGACGGGAACCAGTGGAAGGAGCG
EST: gi|24205315|gb|BU964568.1|BU964568
EST:     GAGGTTGCTGTCACCACCGGCGAGGAGGACGAAGATGCAATCCTGGATCT                         CAAATCGAAGCTTTACCGGTTCGACAAGGACGGGAACCAGTGGAAGGAGCG
genomic: GAGGTTGCTGTCACCACCGGCGAGGAGGACGAAGATGCAATCCTGGATCTgtaacgctct ... ctgatcgcagCAAATCGAAGCTTTACCGGTTCGACAAGGACGGGAACCAGTGGAAGGAGCG
EST: gi|192330808|gb|FK021595.1|FK021595
EST:     GAGGTTGCTGTCACCACCGGCGAGGAGGACGAAGATGCAATCCTGGATCT                         CAAATCGAAGCTTTACCGGTTCGACAAGGACGGGAACCAGTGGAAGGAGCG
genomic: GAGGTTGCTGTCACCACCGGCGAGGAGGACGAAGATGCAATCCTGGATCTgtaacgctct ... ctgatcgcagCAAATCGAAGCTTTACCGGTTCGACAAGGACGGGAACCAGTGGAAGGAGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttactgttttgccactgattggtgcggttgatgcttgttttctcgctgatcgcagCAAATCGAAGCTTTACCGGTTCGACAAGGACGGGAACCAGTGGAAGGAGCGTGGCGCCGGCACTGTGAAGTTCCTGAAGCATAAGGCTTCCGGCAAGGTT
                                 cttgttttctcgct  CT-rich tract
                                  ttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacgctctttctttctctcgtttttctccttttttgcttcccgattttactgttttgccactgattggtgcggttgatgcttgttttctcgctgatcgcagCAAATCGAAGCTTTACCGGTTCGACAAGGACGGGAACCAGTGGAAGGAGCGTGGCGCCGGCACTGTGAAGTTCCTGAAGCATAAGGCTTCCGGCAAGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC