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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattaattttatgcacatgaatatgtcctttctgaaattttctcactttcctatataattaatttcccttttcttttaacttcctgcttcttggtgatagACAGATGCAGTTGATCCTAAGAGCAGACACAAGGGAAAGCTTGAGACAGAGAGTTTGCTGCAAGCAAGGGGTGTTAATTGGACTTCTATAAGGCCAGTCT

Basic information

species Glycine max
transcript GLYMA19G41540.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G41540.2 (Glycine max), 3'ss of exon 6
lower sequence: AT1G09340.1 (Arabidopsis thaliana), 3'ss of exon 6
---------------------------------------------------------cattaattttatgc--acatgaatatgtcctttc-tgaaattttctcac-------tttcctatataat-taatttcccttttcttttaacttcctgcttcttggtgatagACAGATGCAGTTGATCCTAAGAGCAGACACAAGGGAAAGCTTGAGACAGAGAGTTTGCTGCAAGCAAGGGGTGTTAATTGGACTTCTATAAGGCCAGTCT
                                                          ||||    ||       |||| |||||  |||  | | ||  | ||||       |||  ||| |||    ||||    |  ||||| | ||    | |    |    ||   |||||||||||||| |||||||| |||||||| ||||| ||||| ||||| || |||||| |||  ||||| || |||||||||||| | || ||||
gtatgtaaaagatatcttattcttattcctggaagatatgagcttgtacttttcttgaattagccatagaatagtatgattatgtaatttgatcatatgatgtcacccagaagtttattatctaaggccatttgtaataactttttatttgggacataactgatgcagGAGGATGCAGTTGATCCGAAGAGCAGGCACAAGGGGAAGCTGGAGACTGAGAGCTTACTGCAATCAAAAGGTGTAAACTGGACTTCTATACGTCCTGTCT

upper sequence: GLYMA19G41540.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv14s0060g00820.t01 (Vitis vinifera), 3'ss of exon 6
-cattaattttatgcacatgaatatgtcctttctgaaattttctcactttcctatataattaatttccct---tttcttttaacttcctgcttcttggtgatagACAGATGCAGTTGATCCTAAGAGCAGACACAAGGGAAAGCTTGAGACAGAGAGTTTGCTGCAAGCAAGGGGTGTTAATTGGACTTCTATAAGGCCAGTCT
     || |||   ||  |   | | |||| ||  | | | | |      ||| |      |||||  |    || ||  | || |  || |   | ||| ||||| ||||||||||| || |||||||| |||||||| ||||| ||||||||||| |||||| |  ||||||||||||| ||||||||||||||||| ||||
ctgcaaacttt---catgttcttttttcctctccaatactatgttttccccctttgcctagaatttttcgatattactgctgacctgttggtggcttgtg-tagACCGATGCAGTTGACCCAAAGAGCAGGCACAAGGGGAAGCTCGAGACAGAGAGCTTGCTGGATTCAAGGGGTGTTAACTGGACTTCTATAAGGCCTGTCT
















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|8670400|gb|BE191507.1|BE191507
EST:     GCTCTTCTGCTGGTGTCTATCTCAAATCTGATCTATTACCTCATGCAGAG                         ACAGATGCAGTTGATCCTAAGAGCAGACACAAGGGAAAGCTTGAGACAGAG
genomic: GCTCTTCTGCTGGTGTCTATCTCAAATCTGATCTATTACCTCATGCAGAGgtcagtttac ... ttggtgatagACAGATGCAGTTGATCCTAAGAGCAGACACAAGGGAAAGCTTGAGACAGAG
EST: gi|209702885|gb|BW655995.1|BW655995
EST:     GCTCTTCTGCTGGTGTCTATCTCAAATCTGATCTATTACCTCATGCAGAG                         ACAGATGCAGTTGATCCTAAGAGCAGACACAAGGGAAAGCTTGAGACAGAG
genomic: GCTCTTCTGCTGGTGTCTATCTCAAATCTGATCTATTACCTCATGCAGAGgtcagtttac ... ttggtgatagACAGATGCAGTTGATCCTAAGAGCAGACACAAGGGAAAGCTTGAGACAGAG
EST: gi|105632122|gb|DW246321.1|DW246321
EST:     GCTCTTCTGCTGGTGTCTATCTCAAATCTGATCTATTACCTCATGCAGAG                         ACAGATGCAGTTGATCCTAAGAGCAGACACAAGGGAAAGCTTGAGACAGAG
genomic: GCTCTTCTGCTGGTGTCTATCTCAAATCTGATCTATTACCTCATGCAGAGgtcagtttac ... ttggtgatagACAGATGCAGTTGATCCTAAGAGCAGACACAAGGGAAAGCTTGAGACAGAG
EST: gi|213595578|gb|DB962434.1|DB962434
EST:     GCTCTTCTGCTGGTGTCTATCTCAAATCTGATCTATTACCTCATGCAGAG                         ACAGATGCAGTTGATCCTAAGAGCAGACACAAGGGAA
genomic: GCTCTTCTGCTGGTGTCTATCTCAAATCTGATCTATTACCTCATGCAGAGgtcagtttac ... ttggtgatagACAGATGCAGTTGATCCTAAGAGCAGACACAAGGGAA
EST: gi|9903043|gb|BE612011.1|BE612011
EST:     GCTCTTCTGCTGGTGTCTATCTCAAATCTGATCTATTACCTCATGCAGAG                         ACAGATGCAGTTGATCCTAAGAGCAGACACAAGGGAAAGCTTGAGACAGAG
genomic: GCTCTTCTGCTGGTGTCTATCTCAAATCTGATCTATTACCTCATGCAGAGgtcagtttac ... ttggtgatagACAGATGCAGTTGATCCTAAGAGCAGACACAAGGGAAAGCTTGAGACAGAG
EST: gi|120530586|gb|EH258719.1|EH258719
EST:     GCTCTTCTGCTGGTGTCTATCTCAAATCTGATCTATTACCTCATGCAGAG                         ACAGATGCAGTTGATCCTAAGAGCAGACACAAGGGAAAGCTTGAGACAGAG
genomic: GCTCTTCTGCTGGTGTCTATCTCAAATCTGATCTATTACCTCATGCAGAGgtcagtttac ... ttggtgatagACAGATGCAGTTGATCCTAAGAGCAGACACAAGGGAAAGCTTGAGACAGAG
EST: gi|9258516|gb|BE346663.1|BE346663
EST:     GCTCTTCTGCTGGTGTCTATCTCAAATCTGATCTATTACCTCATGCAGAG                         ACAGATGCAGTTGATCCTAAGAGCAGACACAAGGGAAAGCTTGAGACAGAG
genomic: GCTCTTCTGCTGGTGTCTATCTCAAATCTGATCTATTACCTCATGCAGAGgtcagtttac ... ttggtgatagACAGATGCAGTTGATCCTAAGAGCAGACACAAGGGAAAGCTTGAGACAGAG
EST: gi|16348529|gb|BI974124.1|BI974124
EST:     GCTCTTCTGCTGGTGTCTATCTCAAATCTGATCTATTACCTCATGCAGAG                         ACAGATGCAGTTGATCCTAAGAGCAGA
genomic: GCTCTTCTGCTGGTGTCTATCTCAAATCTGATCTATTACCTCATGCAGAGgtcagtttac ... ttggtgatagACAGATGCAGTTGATCCTAAGAGCAGA
EST: gi|7284172|gb|AW596769.1|AW596769
EST:     GCTCTTCTGCTGGTGTCTATCTCAAATCTGATCTATTACCTCATGCAGAG                         ACAGATGCAGTTGATTCTAAGAGCAGAC
genomic: GCTCTTCTGCTGGTGTCTATCTCAAATCTGATCTATTACCTCATGCAGAGgtcagtttac ... ttggtgatagACAGATGCAGTTGATCCTAAGAGCAGAC
EST: gi|23064426|gb|BU579199.1|BU579199
EST:     GCTCTTCTGCTGGTGTCTATCTCAAATCTGATCTATTACCTCATGCAGAG                         ACAGATGCAGTTGATCCTAAGAGCAGACACAAGGGAAAGCTTGAGACAGAG
genomic: GCTCTTCTGCTGGTGTCTATCTCAAATCTGATCTATTACCTCATGCAGAGgtcagtttac ... ttggtgatagACAGATGCAGTTGATCCTAAGAGCAGACACAAGGGAAAGCTTGAGACAGAG
EST: gi|120533740|gb|EH261873.1|EH261873
EST:     GCTCTTCTGCTGGTGTCTATCTCAAATCTGATCTATTACCTCATGCAGAG                         ACAGATGCAGTTGATCCTAAGAGCAGACACAAGGGAAAGCTTGAGACAGAG
genomic: GCTCTTCTGCTGGTGTCTATCTCAAATCTGATCTATTACCTCATGCAGAGgtcagtttac ... ttggtgatagACAGATGCAGTTGATCCTAAGAGCAGACACAAGGGAAAGCTTGAGACAGAG
EST: gi|209707067|gb|BW653204.1|BW653204
EST:     GCTCTTCTGCTGGTGTCTATCTCAAATCTGATCTATTACCTCATGCAGAG                         ACAGATGCAGTTGATCCTAAGAGCAGACACAAGGGAAAGCTTGAGACAGAG
genomic: GCTCTTCTGCTGGTGTCTATCTCAAATCTGATCTATTACCTCATGCAGAGgtcagtttac ... ttggtgatagACAGATGCAGTTGATCCTAAGAGCAGACACAAGGGAAAGCTTGAGACAGAG
EST: gi|209719660|gb|BW669219.1|BW669219
EST:     GCTCTTCTGCTGGTGTCTATCTCAAATCTGATCTATTACCTCATGCAGAG                         ACAGATGCAGTTGATCCTAAG
genomic: GCTCTTCTGCTGGTGTCTATCTCAAATCTGATCTATTACCTCATGCAGAGgtcagtttac ... ttggtgatagACAGATGCAGTTGATCCTAAG
EST: gi|15286291|gb|BI470182.1|BI470182
EST:     GCTCTTCTGCTGGTGTCTATCTCAAATCTGATCTATTACCTCATGCAGAG                         ACAGATGCAGTTGAT
genomic: GCTCTTCTGCTGGTGTCTATCTCAAATCTGATCTATTACCTCATGCAGAGgtcagtttac ... ttggtgatagACAGATGCAGTTGAT
EST: gi|7925259|gb|AW831285.1|AW831285
EST:     GCTCTTCTGCTGGTGTCTATCTCAAATCTGATCTATTACCTCATGCAGAG                         ACAGATGCAGTTGATCCTAAGAGCAGACACAAGGGAAAGCTTGAGACAGAG
genomic: GCTCTTCTGCTGGTGTCTATCTCAAATCTGATCTATTACCTCATGCAGAGgtcagtttac ... ttggtgatagACAGATGCAGTTGATCCTAAGAGCAGACACAAGGGAAAGCTTGAGACAGAG
EST: gi|22523298|gb|BU082109.1|BU082109
EST:     GCTCTTCTGCTGGTGTCTATCTCAAATCTGATCTATTACCTCATGCAGAG                         ACAGATGCAGTTGATCCTAAGAGC
genomic: GCTCTTCTGCTGGTGTCTATCTCAAATCTGATCTATTACCTCATGCAGAGgtcagtttac ... ttggtgatagACAGATGCAGTTGATCCTAAGAGC
EST: gi|120533723|gb|EH261856.1|EH261856
EST:     GCTCTTCTGCTGGTGTCTATCTCAAATCTGATCTATTACCTCATGCAGAG                         ACAGATGCAGTTGATCCTAAGAGCAGACACAAGGGAAAGCTTGAGACAGAG
genomic: GCTCTTCTGCTGGTGTCTATCTCAAATCTGATCTATTACCTCATGCAGAGgtcagtttac ... ttggtgatagACAGATGCAGTTGATCCTAAGAGCAGACACAAGGGAAAGCTTGAGACAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttcctatataattaatttcccttttcttttaacttcctgcttcttggtgatagACAGATGCAGTTGATCCTAAGAGCAGACACAAGGGAAAGCTTGAGACAGAGAGTTTGCTGCAAGCAAGGGGTGTTAATTGGACTTCTATAAGGCCAGTCT
                            ttttaac  putative branch site (score: 2)
             ttaatttcccttttct  CT-rich tract
      tatataattaatttcc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattaattttatgcacatgaatatgtcctttctgaaattttctcactttcctatataattaatttcccttttcttttaacttcctgcttcttggtgatagACAGATGCAGTTGATCCTAAGAGCAGACACAAGGGAAAGCTTGAGACAGAGAGTTTGCTGCAAGCAAGGGGTGTTAATTGGACTTCTATAAGGCCAGTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - -tatgcac
- - - - - - - - - - - - - -ctttctg
- - - - - - - - - - - - - - - - - - - - - -cactttc