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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttttctctttctttgttgcgttatctgttaattgcgtttttatttttttttcattttctgagatcaaagtctaataatatacgaacactgtatgagtagGTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAG

Basic information

species Glycine max
transcript GLYMA02G10640.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G10640.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G02840.2 (Arabidopsis thaliana), 3'ss of exon 1
----------------gtttttctctttctttgttgcgttatctgttaattgcgt-----tttt---atttttttttcattttctgagat-caaagtctaataatatacgaacactgtatgagtagGTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAG
                | || ||| | | | | | |  |||  ||  | |||| |     ||||   |||| | |||  |||  ||   | | | || | ||    ||     | | | |  | |||||||| ||||| |||||||| ||||| || ||||| ||||| ||||| || || ||||||||||| |||||||| |
gtatggtttctactcggattctctttatttct-tcggtttaattggaatttgcttcgaaattttgagatttctctttgttttcatgctcttcgatgtttgatttcgtatctggatt-ttttcgcagGTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTG

upper sequence: GLYMA02G10640.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv19s0015g01330.t01 (Vitis vinifera), 3'ss of exon 1
gtttttctctttctttgttgcgttatctgttaattgcgtttttattttt-ttttcattttctgagatcaaagtctaataatatacgaacactgtatgagtagGTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAG
                ||    |||| | | | ||    | || ||||  || |||||  ||    |  |   |||     |||||||   |        |||||||| |||||| | ||||| || || |||||||||||||||||||| || ||  |||||||||||||||| ||||
----------------gtctgcttatttttcagtttttctcttgttttcattctcattaactattgttga--cctagcttgatacgaaattt-------cagGTTTTTGATGAAGCTCAACAACGAGACTGTGTCAATTGAGCTCAAGAACGGTACCGTTGTTCATGGCACCATCACAG

upper sequence: GLYMA02G10640.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0104g00160.t01 (Vitis vinifera), 3'ss of exon 3
gtttttctctttctttgttgcgttatctgttaattgcgtttttatttttttttcattttctgagatcaaagtctaataatatacgaacactgtatgagtagGTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAG
||||     |   ||  || |  |||   |  | |   | |  |||| ||| |  | || ||   | ||| ||| ||||| ||       | ||  |  |||||| | |||||||||||||| ||||||||||| || |||||||||||||| ||  | |||||||||||||| ||||
gtttgatcttcaattaattaccatatacatatacta-atctcgatttatttattttgttttg---ttaaattcttataattta------gtctaaaaacagGTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAG

upper sequence: GLYMA02G10640.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S726_1V6.1 (Physcomitrella patens), 3'ss of exon 1
gtttttctctttctttgttgcgttatctgttaattgcgtttttatttttttttcattttctgagatcaaagtctaataatatacgaacactg-tatgagtagGTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAG
|||          ||       |||  | ||    | ||||||||||  ||||   |||    | | | |      || | |  |  |   | |  | |||| ||||| |||||  |||||||||| || || ||||| || ||||||||||| ||||| || || ||||| |||||||
gttggggagcggtttatggattttaatttttttgggtgtttttatttacttttgggtttt--ggctgagaagtggttattttttgggcgtgggtgggcgtagATTTTTGATGAAACTGAACAATGAGACGGTATCAATAGAACTCAAGAATGGTACTATCGTGCACGGCACTATTACAG

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|120496339|gb|EH224506.1|EH224506
EST:     AGAGAGCGCAATCGAGTCTTCATCTTCGACTCACCATGGAAGCTCGTCAG                         GTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
genomic: AGAGAGCGCAATCGAGTCTTCATCTTCGACTCACCAT-GAAGCTCGTCAGgtttttctct ... gtatgagtagGTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
EST: gi|208121198|gb|GD920307.1|GD920307
EST:     TAGAGAGCGCAATCGAGTCTTCATCTTCGACTCACCATGAAGCTCGTCAG                         GTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
genomic: TAGAGAGCGCAATCGAGTCTTCATCTTCGACTCACCATGAAGCTCGTCAGgtttttctct ... gtatgagtagGTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
EST: gi|23727600|gb|BU761836.1|BU761836
EST:     TAGAGAGCGCAATCGAGTCTTCATCTTCGACTCACCATGAAGCTCGTCAG                         GTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
genomic: TAGAGAGCGCAATCGAGTCTTCATCTTCGACTCACCATGAAGCTCGTCAGgtttttctct ... gtatgagtagGTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
EST: gi|19052973|gb|BM731640.1|BM731640
EST:     TAGAGAGCGCAATCGAGTCTTCATCTTCGACTCACCATGAAGCTCGTCAG                         GTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
genomic: TAGAGAGCGCAATCGAGTCTTCATCTTCGACTCACCATGAAGCTCGTCAGgtttttctct ... gtatgagtagGTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
EST: gi|192315263|gb|FK007721.1|FK007721
EST:     TAGAGAGCGCAATCGAGTCTTCATCTTCGACTCACCATGAAGCTCGTCAG                         GTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
genomic: TAGAGAGCGCAATCGAGTCTTCATCTTCGACTCACCATGAAGCTCGTCAGgtttttctct ... gtatgagtagGTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
EST: gi|193570947|gb|FK529966.1|FK529966
EST:     TAGAGAGCGCAATCGAGTCTTCATCTTCGACTCACCATGAAGCTCGTCAG                         GTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
genomic: TAGAGAGCGCAATCGAGTCTTCATCTTCGACTCACCATGAAGCTCGTCAGgtttttctct ... gtatgagtagGTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
EST: gi|298192845|gb|HO033279.1|HO033279
EST:     TAGAGAGCGCAATCGAGTCTTCATCTTCGACTCACCATGAAGCTCGTCAG                         GTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
genomic: TAGAGAGCGCAATCGAGTCTTCATCTTCGACTCACCATGAAGCTCGTCAGgtttttctct ... gtatgagtagGTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
EST: gi|58015388|gb|CX702130.1|CX702130
EST:     TAGAGAGCGCAATCGAGTCTTCATCTTCGACTCACCATGAAGCTCGTCAG                         GTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
genomic: TAGAGAGCGCAATCGAGTCTTCATCTTCGACTCACCATGAAGCTCGTCAGgtttttctct ... gtatgagtagGTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
EST: gi|7284502|gb|AW597091.1|AW597091
EST:     TTCGACTCACCATGAAGCTCGTCAG                         GTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
genomic: TTCGACTCACCATGAAGCTCGTCAGgtttttctct ... gtatgagtagGTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
EST: gi|13791520|gb|BG654111.1|BG654111
EST:     TAGAGAGCGCAATCGAGTCTTCATCTTCGACTCACCATGAAGCTCGTCAG                         GTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
genomic: TAGAGAGCGCAATCGAGTCTTCATCTTCGACTCACCATGAAGCTCGTCAGgtttttctct ... gtatgagtagGTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
EST: gi|10847035|gb|BF069805.1|BF069805
EST:     TAGAGAGCGCAATCGAGTCTTCATCTTCGACTCACCATGAAGCTCGTCAG                         GTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
genomic: TAGAGAGCGCAATCGAGTCTTCATCTTCGACTCACCATGAAGCTCGTCAGgtttttctct ... gtatgagtagGTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
EST: gi|58025133|gb|CX711874.1|CX711874
EST:     TAGAGAGCGCAATCGAGTCTTCATCTTCGACTCACCATGAAGCTCGTCAG                         GTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
genomic: TAGAGAGCGCAATCGAGTCTTCATCTTCGACTCACCATGAAGCTCGTCAGgtttttctct ... gtatgagtagGTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
EST: gi|58018364|gb|CX705106.1|CX705106
EST:     TAGAGAGCGCAATCGAGTCTTCATCTTCGACTCACCATGAAGCTCGTCAG                         GTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
genomic: TAGAGAGCGCAATCGAGTCTTCATCTTCGACTCACCATGAAGCTCGTCAGgtttttctct ... gtatgagtagGTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
EST: gi|22541357|gb|BU091200.1|BU091200
EST:     TAGAGAGCGCAATCGAGTCTTCATCTTCGACTCACCATGAAGCTCGTCAG                         GTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
genomic: TAGAGAGCGCAATCGAGTCTTCATCTTCGACTCACCATGAAGCTCGTCAGgtttttctct ... gtatgagtagGTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
EST: gi|19268713|gb|BM884969.1|BM884969
EST:     TAGAGAGCGCAATCGAGTCTTCATCTTCGACTCACCATGAAGCTCGTCAG                         GTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
genomic: TAGAGAGCGCAATCGAGTCTTCATCTTCGACTCACCATGAAGCTCGTCAGgtttttctct ... gtatgagtagGTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
EST: gi|192301564|gb|FG994776.1|FG994776
EST:     TAGAGAGCGCAATCGAGTCTTCATCTTCGACTCACCATGAAGCTCGTCAG                         GTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
genomic: TAGAGAGCGCAATCGAGTCTTCATCTTCGACTCACCATGAAGCTCGTCAGgtttttctct ... gtatgagtagGTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
EST: gi|58015707|gb|CX702449.1|CX702449
EST:     TAGAGAGCGCAATCGAGTCTTCATTTTCGACTCACCATGAAGCTCGTCAG                         GTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
genomic: TAGAGAGCGCAATCGAGTCTTCATCTTCGACTCACCATGAAGCTCGTCAGgtttttctct ... gtatgagtagGTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
EST: gi|9902219|gb|BE611187.1|BE611187
EST:     TAGAGAGCGCAATCGAGTCTTCATCTTCGACTCACCATGAAGCTCGTCAG                         GTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
genomic: TAGAGAGCGCAATCGAGTCTTCATCTTCGACTCACCATGAAGCTCGTCAGgtttttctct ... gtatgagtagGTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
EST: gi|14991002|gb|BI316675.1|BI316675
EST:     GAAGCTCGTCAG                         GTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
genomic: GAAGCTCGTCAGgtttttctct ... gtatgagtagGTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
EST: gi|298187789|gb|HO031746.1|HO031746
EST:     TAGAGAGCGCAATCGAGTCTTCATCTTCGACTCACCATGAAGCTCGTCAT                         GTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG
genomic: TAGAGAGCGCAATCGAGTCTTCATCTTCGACTCACCATGAAGCTCGTCAGgtttttctct ... gtatgagtagGTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttttcattttctgagatcaaagtctaataatatacgaacactgtatgagtagGTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAG
                        gtctaat  putative branch site (score: 3)
                     aaagtctaataatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttttctctttctttgttgcgttatctgttaattgcgtttttatttttttttcattttctgagatcaaagtctaataatatacgaacactgtatgagtagGTTTTTAATGAAGTTGAACAATGAAACCGTGTCAATTGAGCTCAAGAATGGCACTATTGTTCATGGCACCATTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA