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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttcttgaattattcttcaacttgaatgcctgttacttaagacatgccgtagctaattgattaatttaatctcaatcacagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAGGATGTAACAGCTGGTTTGCCTTCCACCAAAAACCTCGTCAGAGAGGTGA

Basic information

species Glycine max
transcript GLYMA03G38520.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G38520.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os05g24550.4 (Oryza sativa), 3'ss of exon 11
gtatgtttcttg-aatta------ttcttcaacttgaatgcctgttacttaagacatgccg--tagctaattg-attaatttaatctcaatcacagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAGGATGTAACAGCTGGTTTGCCTTCCACCAAAAACCTCGTCAGAGAG-GTGA
||| ||   | | || ||      |||   || |  ||||     || ||   |  |   |      ||||    ||   |   |   | |   ||||||| ||||||||||||  ||| || |||||||||||||| || ||||| |||||    |||||| |||| || || || ||| | || ||  |   || 
gtaagtccttggcaaatatataagttcaataagtgaaatgttgcataatttgtattttttgagctattaataatgtttggtcggtgatactggtagGATGGGTACTTCAAGATCATAAGGGGCACAAACGAATGTGGCATCGAAGAAGATGTTGTTGCTGGTATGCCCTCGACGAAGAACATGGTGAGGAACTATG-

upper sequence: GLYMA03G38520.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G02305.1 (Arabidopsis thaliana), 3'ss of exon 10
gtatgtttcttgaattattcttcaa-cttgaatgcctgttacttaagacatgccgtagctaattgattaatttaatctcaa--tcacagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAGGATGTAACAGCTGGTTTGCCTTCCACCAAAAACCTCGTCAGAGAGGTGA
||| |||  |    |      |||| |||  |     |    |  | | |  ||  ||    ||   || |  ||||| ||  |  |||||||| |||||||||||| | ||||| |||||||||||||| |||||| | | |||   ||||||||| |||||   ||  ||| | || | ||   | |
gtaagttcttcttctctccaatcaaacttttactttcgaccttccaaagaaaccacagaaccttagata-tagaatctgaaaatttcagGATGGGTACTTCAAGATCAGGAGAGGAACAAACGAATGTGGCATTGAACATGGTGTTGTAGCTGGTTTACCTTCAGACAGGAACGTAGTTAAAGGTATTA

upper sequence: GLYMA03G38520.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G02300.1 (Arabidopsis thaliana), 3'ss of exon 9
-------gtatgtttcttgaattat--tcttcaacttgaatgcctgttacttaagacatgccgtagctaattgattaatttaatctcaatcacagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAGGATGTAACAGCTGGTTTGCCTTCCACCAAAAACCTCGTCAGAGAGGTGA
        |   |||||  ||| |     || || ||  |  | |   | | || | | ||           |||  |     |   |||| ||||||||||||||||||||| | ||||| || ||||||||||| |||||| ||  |||   ||||||||| |||||    || ||| |  | | ||   | |
gtaagttcttcttttctccaatcaaaacttttaaattagac-cttccaagtaaacaaaagcacagaacctgagatagaaaatgtgaaaatctcagGATGGTTACTTCAAGATCAGGAGAGGAACGAACGAATGTGGCATTGAACAGAGTGTTGTAGCTGGTTTACCTTCAGAGAAGAACGTATTTAAAGGTATTA

upper sequence: GLYMA03G38520.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv07s0005g02820.t01 (Vitis vinifera), 3'ss of exon 9
gtatgtttcttgaattattcttcaacttgaatgcctgttacttaagacatgccgtagctaattg-attaatttaatctcaatcacagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAGGATGTAACAGCTGGTTTGCCTTCCACCAAAAACCTCGTCAGAGAGGTGA
||| | ||||   |  ||||  |  |||||||  |||| ||   |    || |    ||  |   | ||  | | | | |||  |||||||||||||||| ||||||||||||   ||| || ||||| || |||||||  ||    ||||||||||||||  |||||||| |  | |  |  |   
gtaagattct-atacaattcccc--cttgaattactgtcacaagaagtttgtctcgactcttaacactacatcattttgaatggcagGATGGTTACTTCATGATCCGAAGAGGAGTAAATGAGTGTGGCATCGAAGAGGGCGTGGTTGCTGGTTTGCCTTCTTCCAAAAACTTGATGATTGGAGACT

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|193635003|gb|FK579752.1|FK579752
EST:     CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTCAAGATCCGAAGAGG-ACAAACGAATGT
genomic: CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... tcaatcacagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGT
EST: gi|13252459|gb|BG363370.1|BG363370
EST:     CTTCTTGCAAATCAGTGGAACAGAGAATGGG-AGAT                         GATGGTTACTTCAAGATCCGAAGAGGGA
genomic: CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... tcaatcacagGATGGTTACTTCAAGATCCGAAGAGGGA
EST: gi|31312156|gb|CD397359.1|CD397359
EST:     CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
genomic: CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... tcaatcacagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
EST: gi|11273992|gb|BF324368.1|BF324368
EST:     CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
genomic: CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... tcaatcacagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
EST: gi|18716048|gb|BM522863.1|BM522863
EST:     CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
genomic: CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... tcaatcacagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
EST: gi|9899704|gb|BE608672.1|BE608672
EST:     CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
genomic: CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... tcaatcacagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
EST: gi|41145378|gb|CK605589.1|CK605589
EST:     CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
genomic: CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... tcaatcacagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
EST: gi|58018606|gb|CX705348.1|CX705348
EST:     CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
genomic: CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... tcaatcacagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
EST: gi|298182905|gb|HO028118.1|HO028118
EST:     CTTCTTGCAAATCGGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
genomic: CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... tcaatcacagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
EST: gi|208272210|gb|GE067452.1|GE067452
EST:     CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
genomic: CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... tcaatcacagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
EST: gi|208270229|gb|GE070859.1|GE070859
EST:     GCAAATCAGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
genomic: GCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... tcaatcacagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
EST: gi|151400974|gb|EV270788.1|EV270788
EST:     CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT                         GACGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
genomic: CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... tcaatcacagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
EST: gi|18719713|gb|BM523220.1|BM523220
EST:     CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
genomic: CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... tcaatcacagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
EST: gi|17402160|gb|BM178942.1|BM178942
EST:     CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
genomic: CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... tcaatcacagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
EST: gi|193619181|gb|FK569425.1|FK569425
EST:     CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
genomic: CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... tcaatcacagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
EST: gi|10235663|gb|BE804551.1|BE804551
EST:     CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
genomic: CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... tcaatcacagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
EST: gi|10235891|gb|BE804779.1|BE804779
EST:     CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
genomic: CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... tcaatcacagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
EST: gi|8670417|gb|BE191524.1|BE191524
EST:     CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTTCA-GATCCGAAGAAGGACAAACGAATGTTGGATTGA
genomic: CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... tcaatcacagGATGGTTACTT-CAAGATCCGAAGAGGGACAAACGAATGTGGGATTGA
EST: gi|208279152|gb|GE077559.1|GE077559
EST:     GCTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
genomic: GCTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... tcaatcacagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
EST: gi|208287345|gb|GE085709.1|GE085709
EST:     GCAAATCAGTGGTAACAGAGAATGGGGAGAT                         GATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
genomic: GCAAATCAGTGG-AACAGAGAATGGGGAGATgtatgtttct ... tcaatcacagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
EST: gi|254336334|gb|GR842513.1|GR842513
EST:     CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
genomic: CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... tcaatcacagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcctgttacttaagacatgccgtagctaattgattaatttaatctcaatcacagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAGGATGTAACAGCTGGTTTGCCTTCCACCAAAAACCTCGTCAGAGAGGTGA
                           taattgattaatttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttcttgaattattcttcaacttgaatgcctgttacttaagacatgccgtagctaattgattaatttaatctcaatcacagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAGGATGTAACAGCTGGTTTGCCTTCCACCAAAAACCTCGTCAGAGAGGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG