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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccgaacgaacttggtcctcttagctgtttcataggtaataatggtggaatcagcttatgcaaatcctaatttgatttgttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG

Basic information

species Glycine max
transcript GLYMA11G02410.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G02410.3 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g34460.1 (Oryza sativa), 3'ss of exon 1
----gtatccgaac--gaacttggtcctcttagctgtttcataggtaataatggtggaatcagcttatgcaaatcctaatttgatttgttttgtgc-agATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
    | ||| || |   || |   |       |  | ||||    |  |  ||||| |  | |    || |  |  |  | |  ||| |||| ||  ||||||| ||| |||||||||| || ||||||||||| |||||||||||||
gtacgcatctgagcccaaaatcaatgtgtcccgtcggttca--attcgt--tggtgaatactggcgctg-atgttgtggtgtttttttttttctgttagATCATCCCCAAGAAGAACCGGAATGAGATCTGCAAGTACCTCTTCCAAG

upper sequence: GLYMA11G02410.3 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os04g35090.1 (Oryza sativa), 3'ss of exon 1
------------gtatccgaacgaacttggtcctcttagctgtttcataggta-ataatggtgga-atcagcttatgcaaatcct--------aatttgatttgtt--ttgt-gcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
               || |||   |     |  || | || || ||    |       || ||       | | |||| ||||            |||    ||||  |||| ||||||||| ||  |||||||||| || ||||||||||| |||||||||||||
gtaaacgcgcgaagctctgaatccatcctctgttcctcgcggtctcgcgtgcgtgccgtgctgcttgctggttgatgctaatctcctcactcgcgtttcgcctgtttgttgttgcagATCATCCCGAAGAAGAACCGCAATGAGATCTGCAAGTACCTCTTCCAAG

upper sequence: GLYMA11G02410.3 (Glycine max), 3'ss of exon 1
lower sequence: AC209215.4_FGT006 (Zea mays), 3'ss of exon 1
------------gtatccgaacgaacttggtcctcttagctgtttcataggtaata-atggtggaatcagcttatgcaaatcctaatttgatttgttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
              | |      |   |    |||   |||| | ||    |     ||| |    |  |||  ||  ||| ||      ||||| |   |||||||||| ||| |||||||||| || ||||||||||| ||||||||| | |
ctcgaccgccgctcaccatggtaaggattacgctcgaggctgctccacgattttcgtatgttcccttttgctggtgttaatactgt----atttgctac-tgcagATCATCCCCAAGAAGAACCGCAATGAGATCTGCAAGTACCTCTTCAAGG

upper sequence: GLYMA11G02410.3 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G050925_T01 (Zea mays), 3'ss of exon 1
gtatccga--acgaacttggtcctcttagctgtt--tcataggtaataatggtggaatcagcttatgcaaat-cctaatttgatttgttttg--tgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
|||  |||  |||  |  ||  |  |  |||| |  || | ||   |           | ||   ||  |||  |  |  || |||  ||     ||||||||| ||| |||||||||| || ||||||||||| ||||||||| | |
gtaagcgagtacgcgcgaggctcaatacgctgctgctcctcggctttcgcctgttctgctgccggtgttaatatcgcacctgtttttcttcaaccgcagATCATCCCCAAGAAGAACCGCAATGAGATCTGCAAGTACCTCTTCAAGG

upper sequence: GLYMA11G02410.3 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G043737_T02 (Zea mays), 3'ss of exon 1
gtatccgaacgaacttggtcctcttagctgtttcataggtaataatggtggaatcagcttatgcaaatcctaat-ttgatttgttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG---------------------------------------------------
           |   |    |||   |||| | ||    |       ||     |  ||| ||| | |  ||||  ||  ||   |   ||||||||| ||| |||||||||| || ||||||||||| ||||||||| | |                                                   
--------gtaaggattacgctcgaggctgctccacgattttcgtctgt-----ccccttttgccagtgttaatactgtatttgctaccgcagATCATCCCCAAGAAGAACCGCAATGAGATCTGCAAGTACCTCTTCAAGGGTATGTGGTTCTTGGTCCACTAGACTCGCAGTAGGGTAACCTGGGCTGATT

upper sequence: GLYMA11G02410.3 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G043737_T01 (Zea mays), 3'ss of exon 1
gtatccgaacgaacttggtcctcttagctgtttcataggtaataatggtggaatcagcttatgcaaatcctaat-ttgatttgttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
           |   |    |||   |||| | ||    |       ||     |  ||| ||| | |  ||||  ||  ||   |   ||||||||| ||| |||||||||| || ||||||||||| ||||||||| | |
--------gtaaggattacgctcgaggctgctccacgattttcgtctgt-----ccccttttgccagtgttaatactgtatttgctaccgcagATCATCCCCAAGAAGAACCGCAATGAGATCTGCAAGTACCTCTTCAAGG

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|8404306|gb|BE059940.1|BE059940
EST:     AGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATG                         ATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
genomic: AGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATGgtatccgaac ... ttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
EST: gi|14990519|gb|BI316192.1|BI316192
EST:     GAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGC-ACCATG                         ATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
genomic: GAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATGgtatccgaac ... ttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
EST: gi|15204011|gb|BI426708.1|BI426708
EST:     GAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATG                         ATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
genomic: GAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATGgtatccgaac ... ttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
EST: gi|4301666|gb|AI443223.1|AI443223
EST:     AGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATG                         ATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
genomic: AGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATGgtatccgaac ... ttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
EST: gi|18734269|gb|BM528086.1|BM528086
EST:     CAGCAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATG                         ATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
genomic: CAGCAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATGgtatccgaac ... ttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
EST: gi|21676898|gb|BQ629249.1|BQ629249
EST:     CAGCAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATG                         ATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
genomic: CAGCAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATGgtatccgaac ... ttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
EST: gi|22541467|gb|BU091310.1|BU091310
EST:     GCAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATG                         ATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
genomic: GCAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATGgtatccgaac ... ttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
EST: gi|193419203|gb|FK384855.1|FK384855
EST:     GCTTCA-CCACCGTAGCAACCATG                         ATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
genomic: GCTTCACCCACCGTAGCAACCATGgtatccgaac ... ttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
EST: gi|10844274|gb|BF067584.1|BF067584
EST:     AGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATG                         ATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
genomic: AGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATGgtatccgaac ... ttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
EST: gi|298189969|gb|HO031634.1|HO031634
EST:     CAGCAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATG                         ATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
genomic: CAGCAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATGgtatccgaac ... ttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
EST: gi|15338023|gb|BI498679.1|BI498679
EST:     CAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATG                         ATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
genomic: CAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATGgtatccgaac ... ttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
EST: gi|298163410|gb|HO012143.1|HO012143
EST:     CAGCAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATG                         ATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
genomic: CAGCAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATGgtatccgaac ... ttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
EST: gi|298198100|gb|HO039639.1|HO039639
EST:     CAGCAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATG                         ATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
genomic: CAGCAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATGgtatccgaac ... ttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
EST: gi|20448412|gb|BQ252536.1|BQ252536
EST:     GCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATG                         ATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
genomic: GCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATGgtatccgaac ... ttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
EST: gi|7146276|gb|AW508130.1|AW508130
EST:     GCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATG                         ATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
genomic: GCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATGgtatccgaac ... ttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
EST: gi|5606370|gb|AI900524.1|AI900524
EST:     GCCGCTTCACCCACCGTAGCAACCATG                         ATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
genomic: GCCGCTTCACCCACCGTAGCAACCATGgtatccgaac ... ttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
EST: gi|13252336|gb|BG363239.1|BG363239
EST:     CAGCAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATG                         ATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
genomic: CAGCAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATGgtatccgaac ... ttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
EST: gi|4314073|gb|AI461192.1|AI461192
EST:     CACCGTAGCAACCATG                         ATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
genomic: CACCGTAGCAACCATGgtatccgaac ... ttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
EST: gi|10845562|gb|BF068656.1|BF068656
EST:     CAGCAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATG                         ATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
genomic: CAGCAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATGgtatccgaac ... ttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
EST: gi|20207847|gb|BQ133936.1|BQ133936
EST:     CAGCAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATG                         ATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
genomic: CAGCAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATGgtatccgaac ... ttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
EST: gi|19052687|gb|BM731354.1|BM731354
EST:     CAGCAGCTGAGCTTGTTTCCGTCGACGCTTCACCCACCGTAGCAACCATG                         ATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
genomic: CAGCAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATGgtatccgaac ... ttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
EST: gi|207782357|gb|GD752864.1|GD752864
EST:     CAGCAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATG                         ATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
genomic: CAGCAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATGgtatccgaac ... ttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
EST: gi|298180908|gb|HO022347.1|HO022347
EST:     CAGCAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATG                         ATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
genomic: CAGCAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATGgtatccgaac ... ttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
EST: gi|27424478|gb|CA935998.1|CA935998
EST:     CTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATG                         ATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
genomic: CTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATGgtatccgaac ... ttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
EST: gi|14259594|gb|BG882502.1|BG882502
EST:     CAGCAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATG                         ATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
genomic: CAGCAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATGgtatccgaac ... ttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
EST: gi|8284522|gb|BE022090.1|BE022090
EST:     GCAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATG                         ATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
genomic: GCAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATGgtatccgaac ... ttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
EST: gi|8827009|gb|BE210739.1|BE210739
EST:     CAGCAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATG                         ATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
genomic: CAGCAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATGgtatccgaac ... ttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
EST: gi|15338149|gb|BI498805.1|BI498805
EST:     CAGCAGCTGAGCTTGTTTCCGTCGCCGATTCACCCACCGTAGCAACCATG                         ATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
genomic: CAGCAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATGgtatccgaac ... ttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
EST: gi|298183411|gb|HO028624.1|HO028624
EST:     CAGCAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATG                         ATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
genomic: CAGCAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATGgtatccgaac ... ttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
EST: gi|9900485|gb|BE609453.1|BE609453
EST:     AGCAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATG                         ATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
genomic: AGCAGCTGAGCTTGTTTCCGTCGCCGCTTCACCCACCGTAGCAACCATGgtatccgaac ... ttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtaataatggtggaatcagcttatgcaaatcctaatttgatttgttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG
                                         tttgtttt  CT-rich tract
                                 taatttgatttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatccgaacgaacttggtcctcttagctgtttcataggtaataatggtggaatcagcttatgcaaatcctaatttgatttgttttgtgcagATCATTCCCGAGAAGAACCGTAAAGAGATCTGCAAATACCTCTTCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC