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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atagttggatatttagttagactagtatactgtgtttttgtcattccctattgttcagttaactatgatggaaactaatatatcattgttaactttttagCAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGAGGTGAAACTTAAGGAAATGAAGTCTTCTTTAACAGCACAGATAACAGAG

Basic information

species Glycine max
transcript GLYMA18G47780.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G47780.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os11g21990.1 (Oryza sativa), 3'ss of exon 5
atagttggatatttagttagactagtatactgtgtttttgtcattccctattgttcagttaactatgatggaaactaatatatcattgttaactttttagCAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGAGGTGAAACTTAAGGAAATGAAGTCTTCTTTAACAGCACAGATAACAGAG
                 ||   |  |||  ||  ||||||     |   | |  | |  | | |||  ||    ||| | | ||||| |   || || || || |||||  ||       | || ||||| ||||||||||| || |||||||| ||||||||||| || ||||   |  | ||| ||  ||| |  || 
----------------gtaagttgttatcatgattttttgctgaacagaagtagttaaatga-tattctgagttctagtgtttcattatgctctcttcagTAAAGAAGGTCTGACAAGTCTTGTTGAGTACAATGAAAAGAAGATGTTTGAGGTTAAACTTAAGGAGATAAAGTTAACACTGACAACAATGATCAATGAA

upper sequence: GLYMA18G47780.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G65220.1 (Arabidopsis thaliana), 3'ss of exon 5
--atagttggatatttagttagactagtatactgtgtttttgtcattccctattgttcagttaactatgatggaaactaatatatcattgttaac--tttttagCAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGAGGTGAAACTTAAGGAAATGAAGTCTTCTTTAACAGCACAGATAACAGAG
   |  ||   ||||   |||  |   | |  | | | | ||   || | ||||||  |  |||   ||||  |  ||  ||||   ||  |     |||| || |||| |||||||   ||  |||| ||||| ||||||| |||||| ||||||||||| || |||||||| ||  |     | ||    ||  | ||||||
ttctgattctgtattcgattat-cacttgtcttttatctctgc--tttcttattgtatatgtaaaattgatatat-ctgctatacttttccttctgattttaagTAAGGCAGGATTGACAGCTCTGGTAGAGTACAATGAAAGGAAAATATTTGAGGTGAAGCTGAAGGAAATCAAAGCGGTCCTTACGAGCCAAGTGACAGAG

upper sequence: GLYMA18G47780.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0023g00670.t01 (Vitis vinifera), 3'ss of exon 6
-----atagttggatatttagttagactagtatactgt-gtttttgtcattccctattgttcagttaactatgatggaaactaatatatcattgttaactttttagCAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGAGGTGAAACTTAAGGAAATGAAGTCTTCTTTAACAGCACAGATAACAGAG
     | | | | || |  ||||     | ||   | | |||| | | || |   | |||    || | | |      | ||     || ||| | || |||| ||||| |||||  ||||  ||||||| || || ||||||||||| || |||||||||||||| ||||||||||| ||| | |||||| | |||||  |||| 
tgtgaacaatagcatgtggagttt--tcaatactttatagtttctttgatgcgtcactgtaagtttgaatttat----atctgtctgattattttcaatttttcagCAAAGAAGGGCTGGTCCCCTTGGTTGAATACAATGAAAAGAAGATCTTTGAGGTGAAACTGAAGGAAATGAAATCTGCATTAACAACCCAGATTGCAGAT

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|7147137|gb|AW509059.1|AW509059
EST:     ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCAC                         CAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGA
genomic: ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCACgtaagtattg ... aactttttagCAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGA
EST: gi|19347148|gb|BM892028.1|BM892028
EST:     ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCAC                         CAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGA
genomic: ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCACgtaagtattg ... aactttttagCAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGA
EST: gi|15204267|gb|BI427035.1|BI427035
EST:     ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCAC                         CAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGA
genomic: ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCACgtaagtattg ... aactttttagCAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGA
EST: gi|10845794|gb|BF068838.1|BF068838
EST:     ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCAC                         CAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATCTTTGA
genomic: ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCACgtaagtattg ... aactttttagCAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGA
EST: gi|18723976|gb|BM523507.1|BM523507
EST:     ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCAC                         CAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGA
genomic: ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCACgtaagtattg ... aactttttagCAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGA
EST: gi|24135580|gb|BU926090.1|BU926090
EST:     ATTTTCCCCCCTACAAAAAGATCCATTGGAGCTTTCTCTGAGCATTTCAC                         CAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGA
genomic: ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCACgtaagtattg ... aactttttagCAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGA
EST: gi|9819737|gb|BE555250.1|BE555250
EST:     ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATNTCAC                         CAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAA
genomic: ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCACgtaagtattg ... aactttttagCAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAA
EST: gi|9903108|gb|BE612076.1|BE612076
EST:     ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCAC                         CAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGA
genomic: ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCACgtaagtattg ... aactttttagCAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGA
EST: gi|5606675|gb|AI900773.1|AI900773
EST:     ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCAC                         CAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGA
genomic: ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCACgtaagtattg ... aactttttagCAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGA
EST: gi|4313805|gb|AI460924.1|AI460924
EST:     ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCAC                         CAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGA
genomic: ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCACgtaagtattg ... aactttttagCAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGA
EST: gi|192327753|gb|FK022382.1|FK022382
EST:     ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCAC                         CAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGA
genomic: ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCACgtaagtattg ... aactttttagCAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGA
EST: gi|17401556|gb|BM178338.1|BM178338
EST:     ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCAC                         CAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGA
genomic: ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCACgtaagtattg ... aactttttagCAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGA
EST: gi|298186006|gb|HO031167.1|HO031167
EST:     ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCAC                         CAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGA
genomic: ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCACgtaagtattg ... aactttttagCAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGA
EST: gi|14990964|gb|BI316637.1|BI316637
EST:     ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCAC                         CAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGA
genomic: ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCACgtaagtattg ... aactttttagCAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGA
EST: gi|27426659|gb|CA938179.1|CA938179
EST:     ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCAC                         CAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAANATTTTTGA
genomic: ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCACgtaagtattg ... aactttttagCAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGA
EST: gi|18734822|gb|BM528406.1|BM528406
EST:     ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCAC                         CAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGA
genomic: ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCACgtaagtattg ... aactttttagCAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGA
EST: gi|27808981|gb|CB063403.1|CB063403
EST:     ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCAC                         CAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGA
genomic: ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCACgtaagtattg ... aactttttagCAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGA
EST: gi|6134569|gb|AW132962.1|AW132962
EST:     ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCAC                         CAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGA
genomic: ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCACgtaagtattg ... aactttttagCAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGA
EST: gi|17518869|gb|BM187911.1|BM187911
EST:     ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCAC                         CAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGA
genomic: ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCACgtaagtattg ... aactttttagCAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGA
EST: gi|16345992|gb|BI971578.1|BI971578
EST:     ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCAC                         CAAGGAAAGATTGGTGGCCTTG
genomic: ATTTTCCCCCCTACAAAAAGATCCATTGAAGCTTTCTCTGAGCATTTCACgtaagtattg ... aactttttagCAAGGAAGGATTGGTGGCCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctattgttcagttaactatgatggaaactaatatatcattgttaactttttagCAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGAGGTGAAACTTAAGGAAATGAAGTCTTCTTTAACAGCACAGATAACAGAG
                                         tgttaac  putative branch site (score: 2)
                                               cttttt  CT-rich tract
                          aaactaatatatcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atagttggatatttagttagactagtatactgtgtttttgtcattccctattgttcagttaactatgatggaaactaatatatcattgttaactttttagCAAGGAAGGATTGGTGGCCTTGGTGGAGTATAATGAAAAGAAAATTTTTGAGGTGAAACTTAAGGAAATGAAGTCTTCTTTAACAGCACAGATAACAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - -tactgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgatgg