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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGGCATTCCGTGTTCCCACTGTGGATGTCTCTGTTGTTGACCTCACAGTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAAgtaatggcagaattctttgattctcctctaatgatattgtgtattattgggtcttatgcaaattttcacaacttgttattcaaaaatgctactccattttgggattggtccttctcaatttgtcttacataatgttgtctttctcag

Basic information

species Glycine max
transcript GLYMA04G36870.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G36870.1 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os08g03290.3 (Oryza sativa), 5'ss of exon 8
GTATGGCATTCCGTGTTCCCACTGTGGATGTCTCTGTTGTTGACCTCACAGTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAAgtaatggcagaattctttgattctcctctaatgatattgtgtattattgggtcttatgcaa-attttcacaacttgttattcaaaaatgctactccattttgggattggtccttctcaatttgtcttacataatgttgtctttctcag
| ||| | ||||||||||||||||| |||||||| |||||||| |||||||| ||  | |||||||  ||||| || ||||  || || | |||||||||||||    | |  |       ||      || |  | |||  ||       | ||  |||   ||   | ||||   | ||     | |  |  ||  |  | |||   |                                      
GAATGTCCTTCCGTGTTCCCACTGTCGATGTCTCAGTTGTTGATCTCACAGTTAGAATCGAGAAGGCTGCCTCATATGATGCTATCAAGAGTGCTATCAAgtaagtatatagct-------tccaacgcaaggggaatgtacatctc---attttgcgcactgttgctagaactgcatcttgtggcaggggataccgctcagtgatgtat--------------------------------------

upper sequence: GLYMA04G36870.1 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os04g40950.1 (Oryza sativa), 5'ss of exon 9
GTATGGCATTCCGTGTTCCCACTGTGGATGTCTCTGTTGTTGACCTCACAGTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAAgtaatggcagaattc-tttgattctcctctaatgatattgtgtattattgggtcttatgcaaattttcacaacttgttattcaaaaatgctactccattttgggattggtccttctcaatttgtcttacataatgttgtctttctcag
||||||| ||||||||||| || |||||||||||||| |||||  | || || ||||| ||||||  ||| ||||| ||| | |||||    ||||||||||||  | || ||   || || |  ||  ||  || | ||   |   |   || ||  | |      || |||  || ||  || | |   | |  | ||| |  |      || || |                             
GTATGGCTTTCCGTGTTCCAACCGTGGATGTCTCTGTCGTTGATTTGACTGTCAGGCTTGAGAAGCCAGCATCCTATGATCAGATTAAGGCAGCTATCAAgtaagtgtagcataaattagaattgcccttacagaaagtgaagaggctaaagtattgggta-----ccagaac--gtcatctaagactagcaattgacttttgtttgttctgttttctag----------------------------

upper sequence: GLYMA04G36870.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G046804_T04 (Zea mays), 5'ss of exon 8
GTATGGCATTCCGTGTTCCCACTGTGGATGTCTCTGTTGTTGACCTCACAGTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAAgtaatggcagaattctttgattctcctctaatgatattgtgtattattgg------gtcttatgcaaattttcacaacttgtt--attcaaaaatgctactccat-tttgggattggtccttctcaa--tttgtcttacataatgttgtctttctcag---------------------------------
||||| | ||||||||||| |||||||||||||| |||||||||||||| || ||  | |||||||  |||||||| || || || || || ||||| ||||||  |   ||   |||  |  |    |||  |     | ||||  |        |||| | |  |||   |||  ||||||  ||| |      ||||  ||| ||  |  |   |  ||| |    | | ||||     ||  |   | ||||                                   
GTATGTCCTTCCGTGTTCCTACTGTGGATGTCTCGGTTGTTGACCTCACCGTCAGAATCGAGAAGGGGGCCTCCTATGAGGATATCAAGAAAGCTATTAAgtaagtgatcaacaatttattcttttaataaccactcaatttatttctaaaccaatgtctgaaggtaataaacactccttgttggattaatcgccactaccacatgttcagtgtctatgtttcactgcgtctatcttgatctatagtagttctctccatatatgtttggtaatgcttgctgttgattacag

upper sequence: GLYMA04G36870.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G180625_T02 (Zea mays), 5'ss of exon 9
GTATGGCATTCCGTGTTCCCACTGTGGATGTCTCTGTTGTTGACCTCACAGTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAAgtaatggcagaattctttgattctcctctaatgatattgtgtattattgggtcttatgcaaattttcacaacttgttattcaaaaatgctactccattttgggattggtccttctcaatttgtcttacataatgttgtctttctcag
| ||| | ||||| |||||||| |||||||| || |||||||||||||| || ||  | |||||||  ||||| ||||| ||||| || || ||||| ||||||    | |  | ||| || |||        |  ||| || | |||   | || |     |||| | ||     | |  |  ||||| |   ||||    | | |                                        
GCATGTCCTTCCGGGTTCCCACCGTGGATGTGTCAGTTGTTGACCTCACTGTCAGAATCGAGAAGGGGGCCTCTTACGAGGAAATCAAGAAAGCTATTAAgtaagcttatacatttttaatactc--------agtttgagtgtcatttctttttttttttctttttataaaccaatgtctatgaatgcaataacattccttgttaga---------------------------------------

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|16281792|gb|BI944672.1|BI944672
EST:     GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAA                         GGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
genomic: GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAAgtaatggcag ... tctttctcagGGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
EST: gi|16284488|gb|BI946116.1|BI946116
EST:     GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAA                         GGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
genomic: GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAAgtaatggcag ... tctttctcagGGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
EST: gi|17401398|gb|BM178180.1|BM178180
EST:     GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAA                         GGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
genomic: GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAAgtaatggcag ... tctttctcagGGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
EST: gi|33387440|gb|CA850647.1|CA850647
EST:     GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAA                         GGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
genomic: GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAAgtaatggcag ... tctttctcagGGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
EST: gi|31459632|gb|CD401660.1|CD401660
EST:     TACGATGAAATTAAAAATGCTATCAA                         GGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
genomic: TACGATGAAATTAAAAATGCTATCAAgtaatggcag ... tctttctcagGGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
EST: gi|33388835|gb|CA852042.1|CA852042
EST:     GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAA                         GGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
genomic: GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAAgtaatggcag ... tctttctcagGGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
EST: gi|193693250|gb|FK633771.1|FK633771
EST:     GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAA                         GGAGGAACCAGAGGGCAAGTTGAAGGGAATTCTTTGGTTACACTGAAGATG
genomic: GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAAgtaatggcag ... tctttctcagGGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTT-GGTTACACTGAAGATG
EST: gi|16280046|gb|BI943754.1|BI943754
EST:     GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAA                         GGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
genomic: GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAAgtaatggcag ... tctttctcagGGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
EST: gi|254329019|gb|GR833391.1|GR833391
EST:     GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAA                         GGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
genomic: GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAAgtaatggcag ... tctttctcagGGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
EST: gi|254319963|gb|GR829259.1|GR829259
EST:     GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAA                         GGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
genomic: GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAAgtaatggcag ... tctttctcagGGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
EST: gi|16281224|gb|BI944377.1|BI944377
EST:     GTGAGGCTGGAGAAGGAAGCCTTCTACGATGAAATTAAAAATGCTATCAA                         GGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
genomic: GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAAgtaatggcag ... tctttctcagGGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
EST: gi|42722894|gb|CK768793.1|CK768793
EST:     GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAA                         GGAGGAATCAGA
genomic: GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAAgtaatggcag ... tctttctcagGGAGGAATCAGA
EST: gi|15813897|gb|BI786172.1|BI786172
EST:     GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAA                         GGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
genomic: GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAAgtaatggcag ... tctttctcagGGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
EST: gi|17519507|gb|BM188549.1|BM188549
EST:     GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAA                         GGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
genomic: GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAAgtaatggcag ... tctttctcagGGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
EST: gi|26047146|gb|CA784026.1|CA784026
EST:     GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAA                         GGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
genomic: GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAAgtaatggcag ... tctttctcagGGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
EST: gi|31312127|gb|CD397330.1|CD397330
EST:     GTGAGGCTGGAGAAGGAAGCCTCTTACGATGAAATTAAAAATGCTATCAA                         GGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTCGGTTACACTGAAGATGA
genomic: GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAAgtaatggcag ... tctttctcagGGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
EST: gi|16282130|gb|BI944853.1|BI944853
EST:     GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCCA                         GGAGGAATCAGAGGGCAAGCTGAAAGGAATTCTTGGTTACCCTGAAGATGA
genomic: GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAAgtaatggcag ... tctttctcagGGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
EST: gi|16276983|gb|BI942143.1|BI942143
EST:     GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAA                         GGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
genomic: GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAAgtaatggcag ... tctttctcagGGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
EST: gi|193619477|gb|FK570785.1|FK570785
EST:     GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAA                         GGAGGAACCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
genomic: GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAAgtaatggcag ... tctttctcagGGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
EST: gi|31308669|gb|CD393872.1|CD393872
EST:     GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAA                         GGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
genomic: GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAAgtaatggcag ... tctttctcagGGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
EST: gi|16276702|gb|BI941999.1|BI941999
EST:     AAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAA                         GGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
genomic: AAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAAgtaatggcag ... tctttctcagGGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
EST: gi|193686987|gb|FK630342.1|FK630342
EST:     TGAGGCTGGAGAAGGAAGCCTCCTACGATGAAAATTAAAAATGCTATCAA                         GGAGGAACCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
genomic: TGAGGCTGGAGAAGGAAGCCTCCTACGATGAAA-TTAAAAATGCTATCAAgtaatggcag ... tctttctcagGGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
EST: gi|31463425|gb|CD405453.1|CD405453
EST:     GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAA                         GGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
genomic: GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAAgtaatggcag ... tctttctcagGGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
EST: gi|16277862|gb|BI942602.1|BI942602
EST:     GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAA                         GGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
genomic: GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAAgtaatggcag ... tctttctcagGGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
EST: gi|26047478|gb|CA784257.1|CA784257
EST:     GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAA                         GGA--A-TCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA
genomic: GTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAAgtaatggcag ... tctttctcagGGAGGAATCAGAGGGCAAGTTGAAGGGAATTCTTGGTTACACTGAAGATGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATGGCATTCCGTGTTCCCACTGTGGATGTCTCTGTTGTTGACCTCACAGTGAGGCTGGAGAAGGAAGCCTCCTACGATGAAATTAAAAATGCTATCAAgtaatggcagaattctttgattctcctctaatgatattgtgtattattgggtcttatgcaaattttcacaacttgttattcaaaaatgctactccattttgggattggtccttctcaatttgtcttacataatgttgtctttctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA