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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattgatatacctttaagtagcataacagttttacttttacatgtacacactttcaaacattaatgggcacatgcatgattgttaaaacgttccttctacagCTCAAGGCCGAGGTCTGAGCAGGCGTTGGTTCGATGGGCAACACCTCAACTCCATGATATCGATGCTTTGGCTAAAATGGTTGATCCTGCATTGGAAGGA

Basic information

species Glycine max
transcript GLYMA16G01790.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G01790.1 (Glycine max), 3'ss of exon 14
lower sequence: AT3G14350.3 (Arabidopsis thaliana), 3'ss of exon 15
------gtaagattgatatacctttaagtagcataacagttttacttttacatgtacacactttcaaacattaatgggcacatgcatgattgttaaaacgttccttctacagCTCAAGGCCGAGGTCTGAGCAGGCGTTGGTTCGATGGGCAACACCTCAACTCCATGATATCGATGCTTTGGCTAAAATGGTTGATCCTGCATTGGAAGGA
       ||  ||  |||| |||     |   | || |  || |   | |  || | |    |||| | ||| | |          ||||||||          |   ||||| ||||| | || || || ||  | |||||  |||||||||||||||| || || || || ||||||||||  |||||||||||||| ||  |  |||| 
gtacttttacaatccatatccctcgccttcctaaaaaaacttaagagtga--tgcaaatgtgttcaga-attgaagtaagtcctggtgattgttgtg-------tgtgacagCACAAGGTCAAGATCGGAACAATCATTGGTAAGATGGGCAACACCTCAGCTTCACGACATTGATGCTTTGGGCAAAATGGTTGATCCAGCTCTCAAAGGG

upper sequence: GLYMA16G01790.1 (Glycine max), 3'ss of exon 14
lower sequence: AT1G53730.1 (Arabidopsis thaliana), 3'ss of exon 14
gtaagattgatatacctttaagtagcataacagttttacttttacatgtacacactttcaaacattaatgggcacatgcatgattgttaaaac-----gttccttctacagCTCAAGGCCGAGGTCTGAGCAGGCGTTGGTTCGATGGGCAACACCTCAACTCCATGATATCGATGCTTTGGCTAAAATGGTTGATCCTGCATTGGAAGGA
            ||   |  | ||  ||   |  |   |||    |||||   | ||   ||     ||| |    ||  ||| | ||| |||      |   ||   |||| ||||| | || ||||||||| |  ||||||||||||| ||||| ||||| || || || |||||||| || |||||||||||||| ||  |  |||| 
-----------gtaaactctattatgatccaaactaggctt---gatgtatgtagttgagaa-----atgtgtttctgtttgaatcttacaactggttataatttgagcagCACAAGGTCAAGATCTGAGCAGTCACTGGTTCGATGGGCGACACCACAACTTCACGACATTGATGCTTTAGCCAAAATGGTTGATCCAGCTCTTAAAGGG

upper sequence: GLYMA16G01790.1 (Glycine max), 3'ss of exon 14
lower sequence: AT1G53730.2 (Arabidopsis thaliana), 3'ss of exon 14
gtaagattgatatacctttaagtagcataacagttttacttttacatgtacacactttcaaacattaatgggcacatgcatgattgttaaaac-----gttccttctacagCTCAAGGCCGAGGTCTGAGCAGGCGTTGGTTCGATGGGCAACACCTCAACTCCATGATATCGATGCTTTGGCTAAAATGGTTGATCCTGCATTGGAAGGA
            ||   |  | ||  ||   |  |   |||    |||||   | ||   ||     ||| |    ||  ||| | ||| |||      |   ||   |||| ||||| | || ||||||||| |  ||||||||||||| ||||| ||||| || || || |||||||| || |||||||||||||| ||  |  ||   
-----------gtaaactctattatgatccaaactaggctt---gatgtatgtagttgagaa-----atgtgtttctgtttgaatcttacaactggttataatttgagCAGCACAAGGTCAAGATCTGAGCAGTCACTGGTTCGATGGGCGACACCACAACTTCACGACATTGATGCTTTAGCCAAAATGGTTGATCCAGCTCTTAAA---

upper sequence: GLYMA16G01790.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv09s0002g00150.t01 (Vitis vinifera), 3'ss of exon 14
gtaagattgatatacctttaagtagc--ataacagttttactttt----acatgtacacactttcaaacat--taatgggcacatgcatgattgttaa---aacgttccttctacagCTCAAGGCCGAGGTCTGAGCAGGCGTTGGTTCGATGGGCAACACCTCAACTCCATGATATCGATGCTTTGGCTAAAATGGTTGATCCTGCATTGGAAGGA
|||| | || |  ||   ||   | |  || |     |||| |||    |   | | |     | || |||   | |    || |   | | | |||    ||| ||  |   ||||||| ||| | || ||||||||  | |||||||||||||| || ||||| || ||||| ||||||||| ||||||||||||||||||| ||| |  |||| 
gtaaaaatgttgcactactagccatccaatgattccattaccttttttgaagagaaaaggacctgaatcataccattttctacttagctaactattatgttaacattt-tctgacagCTCCAGGTCCAGATCTGAGCAATCTTTGGTTCGATGGGCTACTCCTCAGCTTCATGACATCGATGCTCTGGCTAAAATGGTTGATCCGGCACTCAAAGGG

upper sequence: GLYMA16G01790.1 (Glycine max), 3'ss of exon 14
lower sequence: EFJ34030 (Selaginella moellendorffii), 3'ss of exon 4
gtaagattgatatacctttaagtagcataacagttttacttttacatgtacacactttcaaacattaatgggcacatgcatgattg--ttaaaacgttccttctacagCTCAAGGCCGAGGTCTGAGCAGGCGTTGGTTCGATGGGCAACACCTCAACTCCATGATATCGATGCTTTGGCTAAAATGGTTGATCCTGCATTGGAAGGA
                                               ||| |   || | |   || | ||  | |||    |||   | || | ||    | | ||| |||||  || | || |||||| || ||||  ||||||| |||||||||||||| ||||| |||||  || |||||||||| || ||||| ||| |||| 
-----------------------------------------------gta-aggtttcctagttttcaaggttatatgttccattagctaaagaggtgttctattcagTTCAAGAGCGCGCTCGGAGCAGTCGCTGGTGAGATGGGCCACACCTCAACTCCACGATATTGATGCGCTGTCTAAAATGGTGGACCCTGCGTTGAAAGGC

upper sequence: GLYMA16G01790.1 (Glycine max), 3'ss of exon 14
lower sequence: EFJ37538 (Selaginella moellendorffii), 3'ss of exon 13
gtaagattgatatacctttaagtagcataacagttttacttttacatgtacacactttcaaacattaatgggcacatgcatgattg--ttaaaacgttccttctacagCTCAAGGCCGAGGTCTGAGCAGGCGTTGGTTCGATGGGCAACACCTCAACTCCATGATATCGATGCTTTGGCTAAAATGGTTGATCCTGCATTGGAAGGA
                                               ||| |   || | |   || | ||  | |||    |||   | || | ||    | | ||| |||||  |  | || |||||| || ||||  ||||||| |||||||||||||| ||||| |||||  || |||||||||| || ||||| ||| |||| 
-----------------------------------------------gta-aggtttcctagttttcaaggttatatgttccattagctaaagaggtgttctattcagTTCAAGAGCACGCTCGGAGCAGTCGCTGGTGAGATGGGCCACACCTCAACTCCACGATATTGATGCGCTGTCTAAAATGGTGGACCCTGCGTTGAAAGGC

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|23732744|gb|BU764545.1|BU764545
EST:     TTCGGAGTTGTCATGTTGGAACTTCTTAGTGGACGGAAACCGTTTGATAG                         CTCAAGGCCGAGGTCTGAGCAGGCGTTGGTTCGATGGGCAACACCTCAACT
genomic: TTCGGAGTTGTCATGTTGGAACTTCTTAGTGGACGGAAACCGTTTGATAGgtaagattga ... ccttctacagCTCAAGGCCGAGGTCTGAGCAGGCGTTGGTTCGATGGGCAACACCTCAACT
EST: gi|4293506|gb|AI437915.1|AI437915
EST:     TTCGGAGTTGTCATGTTGGAACTTCTTAGTGGACGGAAACCGTTTGATAG                         CTCAAGGCCGAGGTCTGAGCAGGCGTTGGTTCGATGGGCAACACCTCAACT
genomic: TTCGGAGTTGTCATGTTGGAACTTCTTAGTGGACGGAAACCGTTTGATAGgtaagattga ... ccttctacagCTCAAGGCCGAGGTCTGAGCAGGCGTTGGTTCGATGGGCAACACCTCAACT
EST: gi|254326942|gb|GR836551.1|GR836551
EST:     TTCGGAGTTGTCATGTTGGAACTTCTTAGTGGACGGAAACCGTTTGATAG                         CTCAAGGCCGAGGTCTGAGCAGGCGTTGGTTCGATGGGCAACACCTCAACT
genomic: TTCGGAGTTGTCATGTTGGAACTTCTTAGTGGACGGAAACCGTTTGATAGgtaagattga ... ccttctacagCTCAAGGCCGAGGTCTGAGCAGGCGTTGGTTCGATGGGCAACACCTCAACT
EST: gi|15664525|gb|BI701896.1|BI701896
EST:     TTCGGAGTTGTCATGTTGGAACTTCTTAGTGGACGGAAACCGTTTGATAG                         CTCAAGGCCGAGGTCTGAGCAGGCGTTGGTTCGATGGGCAACACCTCAACT
genomic: TTCGGAGTTGTCATGTTGGAACTTCTTAGTGGACGGAAACCGTTTGATAGgtaagattga ... ccttctacagCTCAAGGCCGAGGTCTGAGCAGGCGTTGGTTCGATGGGCAACACCTCAACT
EST: gi|254326943|gb|GR836552.1|GR836552
EST:     TTCGGAGTTGTCATGTTGGAACTTCTTAGTGGACGGAAACCGTTTGATAG                         CTCAAGGCCGAGGTCTGAGCAGGCGTTGGTTCGATGGGCAACACCTCAACT
genomic: TTCGGAGTTGTCATGTTGGAACTTCTTAGTGGACGGAAACCGTTTGATAGgtaagattga ... ccttctacagCTCAAGGCCGAGGTCTGAGCAGGCGTTGGTTCGATGGGCAACACCTCAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acactttcaaacattaatgggcacatgcatgattgttaaaacgttccttctacagCTCAAGGCCGAGGTCTGAGCAGGCGTTGGTTCGATGGGCAACACCTCAACTCCATGATATCGATGCTTTGGCTAAAATGGTTGATCCTGCATTGGAAGGA
           cattaat  putative branch site (score: 3)
                                         cgttccttct  putative PPT
        aaacattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagattgatatacctttaagtagcataacagttttacttttacatgtacacactttcaaacattaatgggcacatgcatgattgttaaaacgttccttctacagCTCAAGGCCGAGGTCTGAGCAGGCGTTGGTTCGATGGGCAACACCTCAACTCCATGATATCGATGCTTTGGCTAAAATGGTTGATCCTGCATTGGAAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG