Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGTTCACTACCTCAAGAAAAAAACAGCTTCTGCTCCTCTTCCGGTAGCCATAATCGCCGAGGTTGATCTCTACAAGTTCGATCCATGGGAGCTACCCGgtatgttcttcaattaatttcatccaacgaatcaaaagattcaaacttcacgttcaaaactcaaatgggtctgctttgttttttttatttattattattatgatttttctttatattttgtttgtggttaacag

Basic information

species Glycine max
transcript GLYMA12G34990.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G34990.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os07g37920.1 (Oryza sativa), 5'ss of exon 1
GTGGTTCACTACCTCAAGAAAAAAACAGCTTCTGCTCCTCTTCCGGTAGCCATAATCGCCGAGGTTGATCTCTACAAGTTCGATCCATGGGAGCTACCCGgtatgttcttcaattaatttcatcca-acgaatcaaaagattcaaacttcacgttcaaaactcaaatgggtctgctttgttttttttatttattattattatgatttttctttatattttgtttgtggttaacag
||||| |||||||||||||| ||  | || || | ||| || || ||  |||| ||||||||||| |||||||||||||||||||| ||||| || ||||||| ||  || ||| | || || ||| || ||||| || ||| | | || |   | | | || | ||         || |  |   | | ||||||    |  |                               
GTGGTGCACTACCTCAAGAAGAAGGCCGCCTCCGTTCCGCTCCCCGTCACCATCATCGCCGAGGTCGATCTCTACAAGTTCGATCCCTGGGATCTCCCCGgtacgtaatttaatcacttacacccataccaatcataa-attaagaatttattattacagcttatatatacta---ttatcatgcatgtatattatctaaaaaa-------------------------------

upper sequence: GLYMA12G34990.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G179885_T04 (Zea mays), 5'ss of exon 2
GTGGTTCACTACCTCAAGAAAAAAACAGCTTCTGCTCCTCTTCCGGTAGCCATAATCGCCGAGGTTGATCTCTACAAGTTCGATCCATGGGAGCTACCCGgtatgttcttcaattaatttcatccaacgaatcaaaagattcaaacttcacgttcaaaactcaaatgggtctgctttgttttttttatttattattattatgatttttctttat--attttgtttgtggttaacag
         ||||||||||| ||  | || || |  || || || || ||||| ||||| ||||| || ||||||||||||||||| ||||||||||| |||| ||     |        |||   |     |   | || || |       ||   |||   | ||         ||  | |  ||||||||   ||  |||| |    |||   ||| || |            
---------TACCTCAAGAAGAAGGCCGCGTCCGTGCCACTCCCCGTCGCCATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGGTACGTAAGgtagcgcgcgccat---atatgccgccatatacatatcc----tttccaacgtgattga--------tgaatataatatttattggcatggtgatctcatcttactcattctgct------------

upper sequence: GLYMA12G34990.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G179885_T02 (Zea mays), 5'ss of exon 1
GTGGTTCACTACCTCAAGAAAAAAACAGCTTCTGCTCCTCTTCCGGTAGCCATAATCGCCGAGGTTGATCTCTACAAGTTCGATCCATGGGAGCTACCCGgtatgttcttcaattaatttcatccaacgaatcaaaagattcaaacttcacgttcaaaactcaaatgggtctgctttgttttttttatttattattattatgatttttctttatattttgtttgtggttaacag
|| || |||||||||||||| ||  | || || |  || || || || ||||| ||||| ||||| || ||||||||||||||||| ||||||||||| |||| ||     |        |||   |     |   | || || |       ||   |||   | ||         ||  | |  ||||||||   ||  |||| |    |||                     
GTCGTCCACTACCTCAAGAAGAAGGCCGCGTCCGTGCCACTCCCCGTCGCCATCATCGCGGAGGTCGACCTCTACAAGTTCGATCCGTGGGAGCTACCTGgtacgtaaggtagcgcgcgccat---atatgccgccatatacatatcc----tttccaacgtgattga--------tgaatataatatttattggcatggtgatctcatcttact-------------------

upper sequence: GLYMA12G34990.1 (Glycine max), 5'ss of exon 1
lower sequence: AT3G15510.1 (Arabidopsis thaliana), 5'ss of exon 1
GTGGTTCACTACCTCAAGAAAAAAACAGCTTCTGCTCCTCTTCCGGTAGCCATAATCGCCGAGGTTGATCTCTACAAGTTCGATCCATGGGAGCTACCCGgtatgttc--ttcaattaatttcatccaacgaatcaaaagattcaaacttcacgtt-caaaactcaaatgggtctgctttgttttttttatttattattattatgat----------ttttctttatattttgtttgtggttaacag---------------
|| ||||||||||||||    ||| |||| ||||||||| | || || ||||| |||||||| || |||||||| || || ||||||||||| || ||||||| || |      || |   |||||      | | |    || | |  |    ||     | | | |||  | ||     ||||||||  |||| || ||    ||          |||| | |||| ||| ||| |||||    |               
GTTGTTCACTACCTCAAACGCAAAGCAGCCTCTGCTCCTTTACCTGTCGCCATCATCGCCGAAGTCGATCTCTATAAATTTGATCCATGGGAACTTCCCGgtacgtacgacctcatcatcatcatcatcaacaactacttttttatatatagtattatttgatttatatgaatttgtgaccttttttttggttatgatgatctaaatctttttcttcttttttctataatttttttttggtttgtggattcgtttgttgcag

upper sequence: GLYMA12G34990.1 (Glycine max), 5'ss of exon 1
lower sequence: AT1G52880.1 (Arabidopsis thaliana), 5'ss of exon 1
GTGGTTCACTACCTCAAGAAAAAAACAGCTTCTGCTCCTCTTCCGGTAGCCATAATCGCCGAGGTTGATCTCTACAAGTTCGATCCATGGGAGCTACCCGgtatgttcttcaattaatttcatccaacgaatcaaaagattcaaacttcacgttcaaaactcaaatgggtctgctttgttttttttatttattattattatgatttttctttatatt-ttgtttgtggttaacag
||  |||| ||||||||    ||| ||| ||||| |||| | || || || || |||||||| |||||||| ||||| || ||||||||||| || ||||||| |||                     ||| ||| |           || | ||| ||  | |   | |||| ||  |||||||| |||| |   ||| |  ||||| ||| | || ||| |||||        
GTAATTCATTACCTCAAACGCAAAGCAGATTCTGTTCCTTTACCAGTCGCGATCATCGCCGACGTTGATCTTTACAAATTTGATCCATGGGAACTTCCCGgtaagtt---------------------gaaacaaga----------ccaagatcataatccgatcagatctgtttcatttttttt-tttactg--atttttgtttttttttgtgttcttgattgtgacag----

upper sequence: GLYMA12G34990.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv19s0014g03300.t01 (Vitis vinifera), 5'ss of exon 1
GTGGTTCACTACCTCAAGAAAAAAACAGCTTCTGCTCCTCTTCCGGTAGCCATAATCGCCGAGGTTGATCTCTACAAGTTCGATCCATGGGAGCTACCCGgtatgttcttcaattaatttcatccaacgaatcaaaagattcaaacttcacgttcaa-aactcaaatgggtctgctttgttttttttatttattattattatgatttttctttatattttgtttgtggttaacag
|| |||||||| || ||||| ||  |  | ||||||||||||||||| ||||||||||| |||||||||||||| ||||| ||||| ||||| || |||||||     | ||   ||   || | ||  |     ||||||      | | ||   |  | |   |||     | || |           |  |  |||| ||||   |  | |                     
GTAGTTCACTATCTGAAGAAGAAGGCCTCATCTGCTCCTCTTCCGGTCGCCATAATCGCAGAGGTTGATCTCTATAAGTTTGATCCCTGGGAACTCCCCGgta--acttacatcaaaccccagctaattatgattaagattatgtgattatgtatgatgaattgtatgtaaaaggttagaaagaaagccatgctgatatt-tgatcaattctcag--------------------

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|254347165|gb|GR856835.1|GR856835
EST:     CATAATCGCCGAGGTTGATCTCTACAAGTTCGATCCATGGGAGCTACCCG                         CTAAGGCCGCGTTTGGGGAGCAGGAGTGGTATTTCTTTACACCGAGGGACA
genomic: CATAATCGCCGAGGTTGATCTCTACAAGTTCGATCCATGGGAGCTACCCGgtatgttctt ... tggttaacagCTAAGGCCGCGTTTGGGGAGCAGGAGTGGTATTTCTTTACACCGAGGGACA
EST: gi|213604451|gb|DB970627.1|DB970627
EST:     CATAATCGCCGAGGTTGATCTCTACAAGTTCGATCCATGGGAGCTACCCG                         CTAAGGCCGCGTTTGGGGAGCAGGAGTGGTATTTCTTTACACCGAGGGACA
genomic: CATAATCGCCGAGGTTGATCTCTACAAGTTCGATCCATGGGAGCTACCCGgtatgttctt ... tggttaacagCTAAGGCCGCGTTTGGGGAGCAGGAGTGGTATTTCTTTACACCGAGGGACA
EST: gi|207746596|gb|GD721583.1|GD721583
EST:     CCATGGGAGCTACCCG                         CTAAGGCCGCGTTTGGGGAGCAGGAGTGGTATTTCTTTACACCGAGGGACA
genomic: CCATGGGAGCTACCCGgtatgttctt ... tggttaacagCTAAGGCCGCGTTTGGGGAGCAGGAGTGGTATTTCTTTACACCGAGGGACA
EST: gi|298189148|gb|HO037551.1|HO037551
EST:     CATAATCGCCGAGGTTGATCTCTACAAGTTCGATCCATGGGAGCTACCCG                         CTAAGGCCGCGTTTGGGGAGCAGGAGTGGTATTTCTTTACACCGAGGGACA
genomic: CATAATCGCCGAGGTTGATCTCTACAAGTTCGATCCATGGGAGCTACCCGgtatgttctt ... tggttaacagCTAAGGCCGCGTTTGGGGAGCAGGAGTGGTATTTCTTTACACCGAGGGACA
EST: gi|298163153|gb|HO011886.1|HO011886
EST:     CATAATCGCCGAGGTTGATCTCTACAAGTTCGATCCATGGGAGCTACCCG                         CTAAGGCCGCGTTTGGGGAGCAGGAGTGGTATTTCTTTACACCGAGGGACA
genomic: CATAATCGCCGAGGTTGATCTCTACAAGTTCGATCCATGGGAGCTACCCGgtatgttctt ... tggttaacagCTAAGGCCGCGTTTGGGGAGCAGGAGTGGTATTTCTTTACACCGAGGGACA
EST: gi|120491768|gb|EH219935.1|EH219935
EST:     CATAATCGCCGAGGTTGATCTCTACAAGTTCGATCCATGGGAGCTACCCG                         CTAAGGCCGCGTTTGGGGAGCAGGAGTGGTATTTCTTTACACCGAGGGACA
genomic: CATAATCGCCGAGGTTGATCTCTACAAGTTCGATCCATGGGAGCTACCCGgtatgttctt ... tggttaacagCTAAGGCCGCGTTTGGGGAGCAGGAGTGGTATTTCTTTACACCGAGGGACA
EST: gi|298172573|gb|HO019613.1|HO019613
EST:     CATAATCGCCGAGGTTGATCTCTACAAGTTCGATCCATGGGAGCTACCCG                         CTAAGGCCGCGTTTGGGGAGCAGGAGTGGTATTTCTTTACACCGAGGGACA
genomic: CATAATCGCCGAGGTTGATCTCTACAAGTTCGATCCATGGGAGCTACCCGgtatgttctt ... tggttaacagCTAAGGCCGCGTTTGGGGAGCAGGAGTGGTATTTCTTTACACCGAGGGACA
EST: gi|298168656|gb|HO009586.1|HO009586
EST:     CATAATCGCCGAGGTTGATCTCTACAAGTTCGATCCATGGGAGCTACCCG                         CTAAGGCCGCGTTTGGGGAGCAGGAGTGGTATTTCTTTACACCGAGGGACA
genomic: CATAATCGCCGAGGTTGATCTCTACAAGTTCGATCCATGGGAGCTACCCGgtatgttctt ... tggttaacagCTAAGGCCGCGTTTGGGGAGCAGGAGTGGTATTTCTTTACACCGAGGGACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGTTCACTACCTCAAGAAAAAAACAGCTTCTGCTCCTCTTCCGGTAGCCATAATCGCCGAGGTTGATCTCTACAAGTTCGATCCATGGGAGCTACCCGgtatgttcttcaattaatttcatccaacgaatcaaaagattcaaacttcacgttcaaaactcaaatgggtctgctttgttttttttatttattattattatgatttttctttatattttgtttgtggttaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT