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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgactcttagttggttttaaacaatattgaattgattgtggtttattaatttgtgaaaactgacatgacttgggatgatacaatacagttcactgatttagcattcacaaactcttttcattacataacagGTAAGCCTTGTTAAAATTGTGCCAGACTTTCCTCGAACATCTTCCAACAAAATACTGAGGAGAGTAATGAGGGATCAAATGAAGCTCCAGCTATCAGTTC

Basic information

species Glycine max
transcript GLYMA05G29030.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G29030.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv06s0004g00750.t01 (Vitis vinifera), 3'ss of exon 14
gtctgactcttagttggttttaaacaatattgaattgattgtggtttattaatttgtgaaaactgacatgacttgggatgatacaatacagttcactgatttagcattcacaaactcttttcattacataacagGTAAGCCTTGTTAAAATTGTGCCAGACTTTCCTCGAACATCTTCCAACAAAATACTGAGGAGAGTAATGAGGGATCAAATGAAGCTCCAGCTATCAGTTC
                       ||  || | || |||||       ||  |||| |  |   |    ||| |  | |||||    |  |||| |    | |        ||||||  ||  | |   | |||||| | | ||||||| ||||| || || |||||||||||  |||| ||||| ||||||||| ||||  ||||||| ||||| ||||   |||| |||||||
---------------------cgactgtaat-aagtgatta-aaaccatccatttctagatgtt----tgagt--gcatgatcattttgagttgatgagtatgat----gcaaactgattg-actgattgacagGTGAACTTTGTTAAGATTGTCCCCGAGTTTCCTCGAACTGCTTCTAACAAGATACTGAGGCGAGTTTTGAGGGACCAAATTAAGCATGAGCTTTCAGTTC

upper sequence: GLYMA05G29030.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv06s0004g00740.t01 (Vitis vinifera), 3'ss of exon 14
gtctgactcttagttggttttaaacaatattgaattgattgtggtttattaatttgtgaaaactgacatgacttgggatgatacaatacagttcactgatttagcattcacaaactcttttcattacataacagGTAAGCCTTGTTAAAATTGTGCCAGACTTTCCTCGAACATCTTCCAACAAAATACTGAGGAGAGTAATGAGGGATCAAATGAAGCTCCAGCTATCAGTTC
                           |  | || |||||          | ||   | |||      ||| |    ||| |    |  |||| |    | ||  ||   |||||| |||  | |   | |||||| ||| ||||||| |||||||| || |||||||||||  |||| ||||| ||||||||| ||||  ||||||| ||||| |||| | |||| |||||| 
--------------------------gtgat-aagtgattaaaaccatccagttctaggaaat--gtttgagt--acatgttcattttgagttgatgagtgtatgat--gcaaactgtttg-actgattgacagGTGAGCTTTGTTAAGATTGTGCCCGAGTTTCCTCGAACTGCTTCTAACAAGATACTGAGGCGAGTTTTGAGGGACCAAATTAAGCACGAGCTTTCAGTTT
















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|11689508|gb|BF597184.1|BF597184
EST:     ATTCACTCAAGCTATTCAAAGCATCCTTAACCCTTTGCTTAAG                         GTAAGCCTTGTTAAAATTGTGCCAGACTTTCCTCGAACATCTTCCAACAAA
genomic: ATTCACTAAAGCTATTCAAAGCAACCTTAACCCTTTGTTTAAGgtctgactct ... tacataacagGTAAGCCTTGTTAAAATTGTGCCAGACTTTCCTCGAACATCTTCCAACAAA
EST: gi|10254254|gb|BE822020.1|BE822020
EST:     AGATGAAATTCACTAAAGCTATTCAAAGCAACCTTAACCCTTTGTTTAAG                         GTAAGCCTTGTTAAAATTGTGCCAGACTTTCCTCGAACATCTTCCAACAAA
genomic: AGATGAAATTCACTAAAGCTATTCAAAGCAACCTTAACCCTTTGTTTAAGgtctgactct ... tacataacagGTAAGCCTTGTTAAAATTGTGCCAGACTTTCCTCGAACATCTTCCAACAAA
EST: gi|120532502|gb|EH260635.1|EH260635
EST:     AGATGAAATTCACTAAAGCTATTCAAAGCAACCTTAACCCTTTGTTTAAG                         GTAAGCCTTGTTAAAATTGTGCCAGACTTTCCTCGAACATCTTCCAACAAA
genomic: AGATGAAATTCACTAAAGCTATTCAAAGCAACCTTAACCCTTTGTTTAAGgtctgactct ... tacataacagGTAAGCCTTGTTAAAATTGTGCCAGACTTTCCTCGAACATCTTCCAACAAA
EST: gi|308098274|gb|HO760015.1|HO760015
EST:     AGATGAAATTCACTAAAGCTATTCTAAGCAACCTTAACCCTTTGTTTAAG                         GTAAGCCTTGTTAAAATTGTGCCAGACTTTCCTCGAACATCTTCCAACAAA
genomic: AGATGAAATTCACTAAAGCTATTCAAAGCAACCTTAACCCTTTGTTTAAGgtctgactct ... tacataacagGTAAGCCTTGTTAAAATTGTGCCAGACTTTCCTCGAACATCTTCCAACAAA
EST: gi|6455429|gb|AW186112.1|AW186112
EST:     AGATGAAATTCACTAAAGCTATTCAAAGCAACCTTAACCCTTTGTTTAAG                         GTAAGCCTTGTTAAAATTGTGCCAGACTTTCCTCGAACATCTTCCAACAAA
genomic: AGATGAAATTCACTAAAGCTATTCAAAGCAACCTTAACCCTTTGTTTAAGgtctgactct ... tacataacagGTAAGCCTTGTTAAAATTGTGCCAGACTTTCCTCGAACATCTTCCAACAAA
EST: gi|14011397|gb|BG726319.1|BG726319
EST:     AGATGAAATTCACTAAAGCTATTCAAAGCAACCTTAACCCTTTGTTTAAG                         GTAAGCCTTGTTAAAATTGTGCCAGACTTTCCTCGAACATCTTCCAACAAA
genomic: AGATGAAATTCACTAAAGCTATTCAAAGCAACCTTAACCCTTTGTTTAAGgtctgactct ... tacataacagGTAAGCCTTGTTAAAATTGTGCCAGACTTTCCTCGAACATCTTCCAACAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatacaatacagttcactgatttagcattcacaaactcttttcattacataacagGTAAGCCTTGTTAAAATTGTGCCAGACTTTCCTCGAACATCTTCCAACAAAATACTGAGGAGAGTAATGAGGGATCAAATGAAGCTCCAGCTATCAGTTC
              cactgat  putative branch site (score: 3)
                                   ctcttttcatt  putative PPT
                                      ttttcattacataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgactcttagttggttttaaacaatattgaattgattgtggtttattaatttgtgaaaactgacatgacttgggatgatacaatacagttcactgatttagcattcacaaactcttttcattacataacagGTAAGCCTTGTTAAAATTGTGCCAGACTTTCCTCGAACATCTTCCAACAAAATACTGAGGAGAGTAATGAGGGATCAAATGAAGCTCCAGCTATCAGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC