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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctctactacttttctcttgggaattcttgtttgagtatggtgtgtttgtccttgaagtggtggtactaattaattttattctttttgatcaacagCTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGAGCTTACGATACACGCAATATCTTCCAGTCACTAGATCTTGCATGGACTT

Basic information

species Glycine max
transcript GLYMA09G38110.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G38110.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 14
gtctctactacttttctcttgggaattcttgtttgagtatggtgtgtttgtc-cttgaagtggtggtactaattaattttattctttttgatcaacagCTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGAGCTTACGATACACGCAATATCTTCCAGTCACTAGATCTTGCATGGACTT
           |||     |   || | |||    | |    ||    |||| |||  ||  ||     ||||  ||| |||  ||    |||  ||||| |||||||||||  | || || ||||||||||| |||||| | |||||||| || |||||| | || ||||| |||||||| || || |||||||| |
----------gtttgtcactaataactattgaaataatcccatgctgatgtctcttttagaagtaaatttaat--attctatcttt----atctgcagCTTTATTTGGAATTCCTTGACAAATTTGAGAGGAAATTTGTTACACAAGGAGCATATGATACAAGAAACATCTTTCAGTCACTTGACCTAGCATGGACAT

upper sequence: GLYMA09G38110.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G181151_T04 (Zea mays), 3'ss of exon 5
--------------------gtctctactacttttctct-----tgggaattcttgtttgagtatggtgt--gtttgtccttgaagtggtggtactaat-taattttattctttttgatcaacagCTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGAGCTTACGATACACGCAATATCTTCCAGTCACTAGATCTTGCATGGACTT
                     |  |||     ||  ||       | | |  | |    ||  | |   |  ||| || |||     | ||     ||  |||| || |  |  ||  |   ||||| || || || ||  | || ||||||||||||||||||||  | |||||||| ||||| ||||| || ||||||||||||||||||||||||||||| |
gtctgtttcgagtgaaataaattcctaagggcttgttcgggttgcgtgcagacgtaaccgaacaagccctaagttagttctttttcagatgtccaaaacctaatgttctgttacttcttgctcagCTTTACTTAGAGTTCCTTGACAAGTTTGAGAGGAAGTTTGTGACACAAGGAGCATACGACACACGGAACATCTTCCAGTCACTAGATCTTGCATGGACAT

upper sequence: GLYMA09G38110.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G094497_T02 (Zea mays), 3'ss of exon 13
gtctctactacttttctcttgggaattcttgtttgagtatggtgtgtttgtccttgaagtggtggt-actaattaattttattctttttgatcaacagCTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGAGCTTACGATACACGCAATATCTTCCAGTCACTAGATCTTGCATGGACTT
              ||| ||| || |       | | | | ||  ||| || |||     |      |  | ||||| || |  |  ||  |  |||||| || || || ||  | || ||||||||||||||||||||  | |||||||| || || ||||| || |||||||||||||| |||||||||||||| |
-------------gtctgttgcgagtg---aaataaat-tcgtaagttagttctttttcagacccccaaaacttaatgttctgttccttattgcacagCTTTACTTAGAGTTCCTTGACAAGTTTGAGAGGAAGTTTGTGACACAAGGAGCATATGACACACGGAACATCTTCCAGTCACTCGATCTTGCATGGACAT

upper sequence: GLYMA09G38110.1 (Glycine max), 3'ss of exon 14
lower sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 15
gtctctactacttttctcttgggaattcttgtttgagtatggtgtgtttgtccttgaagtggtggtactaattaattttattctttttgatcaacagCTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGAGCTTACGATACACGCAATATCTTCCAGTCACTAGATCTTGCATGGACTT
            | ||||||     || |  | | |  |  || |   ||   |     |  |    || |  | |||| || | |      ||||||| ||| | || || ||||| ||||| |||||||||||||| || || |||||||| ||||| || || |||||||||||||| || || ||||||||| 
-----------gtctctctt----cttttcttcttaccacagtctaaatgctttccgttttattcctcttaacactttttttatctgatgcaaacagCTATATCTTGAGTTCTTGGATAAGTTCGAGAGGAAGTTTGTGGCTCAGGGAGCTTATGATACCCGAAACATCTTCCAGTCACTCGACCTGGCATGGACTC

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|10253833|gb|BE821599.1|BE821599
EST:     AGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTG                         CTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGA
genomic: AGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTGgtctctacta ... tgatcaacagCTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGA
EST: gi|27426282|gb|CA937802.1|CA937802
EST:     AGGCAATGAAAGCCGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTG                         CTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGA
genomic: AGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTGgtctctacta ... tgatcaacagCTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGA
EST: gi|5752591|gb|AI959878.1|AI959878
EST:     AGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTG                         CTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGA
genomic: AGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTGgtctctacta ... tgatcaacagCTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGA
EST: gi|27426098|gb|CA937618.1|CA937618
EST:     AGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTG                         CTGTATTTGGAATTTTTGGAGAAGTT-GAAAAGAAGTTTGTTGCCC
genomic: AGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTGgtctctacta ... tgatcaacagCTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCC
EST: gi|207690144|gb|GD671529.1|GD671529
EST:     AGGCAATGAAAGCCGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTG                         CTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGA
genomic: AGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTGgtctctacta ... tgatcaacagCTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGA
EST: gi|9898667|gb|BE607635.1|BE607635
EST:     AGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTG                         CTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGA
genomic: AGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTGgtctctacta ... tgatcaacagCTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGA
EST: gi|19053919|gb|BM732586.1|BM732586
EST:     AGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTG                         CTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGA
genomic: AGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTGgtctctacta ... tgatcaacagCTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGA
EST: gi|20812032|gb|BQ296510.1|BQ296510
EST:     AGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTG                         CTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGA
genomic: AGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTGgtctctacta ... tgatcaacagCTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGA
EST: gi|16277795|gb|BI942566.1|BI942566
EST:     AGGCAATGAAAGCCGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTG                         CTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGA
genomic: AGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTGgtctctacta ... tgatcaacagCTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGA
EST: gi|21255992|gb|BQ452880.1|BQ452880
EST:     AGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTG                         CTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGA
genomic: AGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTGgtctctacta ... tgatcaacagCTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGA
EST: gi|7235272|gb|AW570601.1|AW570601
EST:     AGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTG                         CTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGGAGCCCAAGGA
genomic: AGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTGgtctctacta ... tgatcaacagCTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGA
EST: gi|193391746|gb|FK354237.1|FK354237
EST:     AGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTG                         CTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGA
genomic: AGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTGgtctctacta ... tgatcaacagCTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGA
EST: gi|16277730|gb|BI942533.1|BI942533
EST:     AGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTG                         CTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGA
genomic: AGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTGgtctctacta ... tgatcaacagCTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGA
EST: gi|9258589|gb|BE346736.1|BE346736
EST:     AGGCAATGAAAGCTGTGGTCGTAGAAGAAGCACTTTCATCTGAGGACCTG                         CTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGA
genomic: AGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTGgtctctacta ... tgatcaacagCTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGA
EST: gi|16284553|gb|BI946150.1|BI946150
EST:     AGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTG                         CTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGA
genomic: AGGCAATGAAAGCTGTGGTCGGAGAAGAAGCACTTTCATCTGAGGACCTGgtctctacta ... tgatcaacagCTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtttgtccttgaagtggtggtactaattaattttattctttttgatcaacagCTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGAGCTTACGATACACGCAATATCTTCCAGTCACTAGATCTTGCATGGACTT
                                 ttttattcttttt  CT-rich tract
                       tactaattaattttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctctactacttttctcttgggaattcttgtttgagtatggtgtgtttgtccttgaagtggtggtactaattaattttattctttttgatcaacagCTGTATTTGGAATTTTTGGAGAAGTTTGAGAGGAAGTTTGTTGCCCAAGGAGCTTACGATACACGCAATATCTTCCAGTCACTAGATCTTGCATGGACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA