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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttagtccttcaaatttgaaaaaataagttattacttgtttgacaaatgaagtgatgaggtgtttggactcacttgtacttgtatttgattaatactcagTCTAGCCACAGCTGGATATGGTACTGCTCTGGGTGTCATCCGTGCACTTCATAGTGCCGGAGTTCTAAAAAGGGCTTATTGCACAGAAACACGCCCATTT

Basic information

species Glycine max
transcript GLYMA09G08190.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G08190.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G05830.3 (Arabidopsis thaliana), 3'ss of exon 5
----------------------------------------------------------------------------------tttagtccttcaaatttgaaaaaataagttat-tacttgtttgacaaatgaagtg-atgaggtg----tttggactcacttgtact-tgtatttgattaatact-cagTCTAGCCACAGCTGGATATGGTACTGCTCTGGGTGTCATCCGTGCACTTCATAGTGCCGGAGTTCTAAAAAGGGCTTATTGCACAGAAACACGCCCATTT
                                                                                  | |     | ||  ||  |  ||   |||| | || | ||||      | | ||  ||| |||       | |     | |  |||  |  ||  ||| |   |  || || || || || |||||||||||||| || ||||||||||||||||| |||| |   ||| |  || |||| || || ||||||||||| || ||||||
gtattgatttagctagattttctgaattgcatagataccgtctgcataagttactcaagttgagtaatagcatgttaccacatatgtgtatgcagcttcaaccaatagagttgtgtaatggtttttggtgttatgtttatgtggtagattcctagtaaggcattaactacgagttctattgactttgtagCCTTGCTACCGCCGGATATGGTACTGCCCTCGGTGTCATCCGTGCACTCCATACTCAAGGAATCTTAGAAAGAGCATACTGCACAGAAACTCGTCCATTT

upper sequence: GLYMA09G08190.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv11s0016g00830.t01 (Vitis vinifera), 3'ss of exon 6
tttagtccttcaaatttgaaaaaataagttattacttgtttgacaaatgaa------gtgatgaggtgtttggactcacttgtacttgtatttgattaatactcagTCTAGCCACAGCTGGATATGGTACTGCTCTGGGTGTCATCCGTGCACTTCATAGTGCCGGAGTTCTAAAAAGGGCTTATTGCACAGAAACACGCCCATTT
  |  | |   |  |    || ||   |||    ||    |||    |||        ||   |  ||||   | |   || |  |  ||||   | ||    |||||| || ||||||||||||||||||||||| ||||| |||||| |  |||||  ||  ||| || ||   ||||| ||||||||||| ||||| ||||| 
--tgattcactagctggtgaagaaagtgttcaagctgaggtgaagcctgagctttccatgtaaaattgttctaatttttttcttttcatattgtttcaa----cagTCTTGCAACAGCTGGATATGGTACTGCTCTCGGTGTAATCCGTTCCGTTCATGCTGAAGGAATTTTACTGAGGGCCTATTGCACAGAGACACGTCCATTC
















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|151411952|gb|EV281763.1|EV281763
EST:     CAAACAGAGAAACAAAAGCTTTCTGTTTTGACTCATTGCAACACTGGAAG                         TCTAGCCACAGCTGGATATGGTACTGCTCTGGGTGTCATCCGTGCACTTCA
genomic: CAAACAGAGAAACAAAAGCTTTCTGTTTTGACTCATTGCAACACTGGAAGgtgcctgtta ... taatactcagTCTAGCCACAGCTGGATATGGTACTGCTCTGGGTGTCATCCGTGCACTTCA
EST: gi|151406212|gb|EV276027.1|EV276027
EST:     CAAACAGAGAAACAAAAGCTTTCTGTTTTGACTCATTGCAACACTGGAAG                         TCTAGCCACAGCTGGATATGGTACTGCTCTGGGTGTCATCCGTGCACTTCA
genomic: CAAACAGAGAAACAAAAGCTTTCTGTTTTGACTCATTGCAACACTGGAAGgtgcctgtta ... taatactcagTCTAGCCACAGCTGGATATGGTACTGCTCTGGGTGTCATCCGTGCACTTCA
EST: gi|192316660|gb|FK008253.1|FK008253
EST:     CAAACAGAGAAACAAAAGCTTTCTGTTTTGACTCATTGCAACACTGGAAG                         TCTAGCCACAGCTGGATATGGTACTGCTCTGGGTGTCATCCGTGCACTTCA
genomic: CAAACAGAGAAACAAAAGCTTTCTGTTTTGACTCATTGCAACACTGGAAGgtgcctgtta ... taatactcagTCTAGCCACAGCTGGATATGGTACTGCTCTGGGTGTCATCCGTGCACTTCA
EST: gi|151409355|gb|EV279163.1|EV279163
EST:     CAAACAGAGAAACAAAAGCTTTCTGTTTTGACTCATTGCAACACTGGAAG                         TCTAGCCACAGCTGGATATGGTACTGCTCTGGGTGTCATCCGTGCACTTCA
genomic: CAAACAGAGAAACAAAAGCTTTCTGTTTTGACTCATTGCAACACTGGAAGgtgcctgtta ... taatactcagTCTAGCCACAGCTGGATATGGTACTGCTCTGGGTGTCATCCGTGCACTTCA
EST: gi|192325814|gb|FK018036.1|FK018036
EST:     CAAACAGAGAAACAAAAGCTTTCTGTTTTGACTCATTGCAACACTGGAAG                         TCTAGCCACAGCTGGATATGGTACTGCTCTGGGTGTCATCCGTGCACTTCA
genomic: CAAACAGAGAAACAAAAGCTTTCTGTTTTGACTCATTGCAACACTGGAAGgtgcctgtta ... taatactcagTCTAGCCACAGCTGGATATGGTACTGCTCTGGGTGTCATCCGTGCACTTCA
EST: gi|192316659|gb|FK008252.1|FK008252
EST:     CAAACAGAGAAACAAAAGCTTTCTGTTTTGACTCATTGCAACACTGGAAG                         TCTAGCCACAGCTGGATATGGTACTGCTCTGGGTGTCATCCGTG
genomic: CAAACAGAGAAACAAAAGCTTTCTGTTTTGACTCATTGCAACACTGGAAGgtgcctgtta ... taatactcagTCTAGCCACAGCTGGATATGGTACTGCTCTGGGTGTCATCCGTG
EST: gi|192308219|gb|FK000855.1|FK000855
EST:     CAAACAGAGAAACAAAAGCTTTCTGTTTTGACTCATTGCAACACTGGAAG                         TCTAGCCACAGCTGGATATGGTACTGCTCTGGGTGTCATCCGTGCACTTCA
genomic: CAAACAGAGAAACAAAAGCTTTCTGTTTTGACTCATTGCAACACTGGAAGgtgcctgtta ... taatactcagTCTAGCCACAGCTGGATATGGTACTGCTCTGGGTGTCATCCGTGCACTTCA
EST: gi|192321693|gb|FK014037.1|FK014037
EST:     CAAACAGAGAAACAAAAGCTTTCTGTTTTGACTCATTGCAACACTGGAAG                         TCTAGCCACAGCTGGATATGGTACTGCTCTGGGTGTCATCCGTGCACTTCA
genomic: CAAACAGAGAAACAAAAGCTTTCTGTTTTGACTCATTGCAACACTGGAAGgtgcctgtta ... taatactcagTCTAGCCACAGCTGGATATGGTACTGCTCTGGGTGTCATCCGTGCACTTCA
EST: gi|21600546|gb|BQ610877.1|BQ610877
EST:     AAAGCTTTCTGTTTTGACTCATTGCAACACTGGAAG                         TCTAGCCACAGCTGGATATGGTACTGCTCTGGGTGTCATCCGTGCACTTCA
genomic: AAAGCTTTCTGTTTTGACTCATTGCAACACTGGAAGgtgcctgtta ... taatactcagTCTAGCCACAGCTGGATATGGTACTGCTCTGGGTGTCATCCGTGCACTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgaagtgatgaggtgtttggactcacttgtacttgtatttgattaatactcagTCTAGCCACAGCTGGATATGGTACTGCTCTGGGTGTCATCCGTGCACTTCATAGTGCCGGAGTTCTAAAAAGGGCTTATTGCACAGAAACACGCCCATTT
                                  ttgtatttgattaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttagtccttcaaatttgaaaaaataagttattacttgtttgacaaatgaagtgatgaggtgtttggactcacttgtacttgtatttgattaatactcagTCTAGCCACAGCTGGATATGGTACTGCTCTGGGTGTCATCCGTGCACTTCATAGTGCCGGAGTTCTAAAAAGGGCTTATTGCACAGAAACACGCCCATTT

- - -tccttca
- - - - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - -ttgtttg
- - - - - - - - - - - - - - - - - - - - - - - -tgaagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtacttg