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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttattgcttctccaattttatattggtggtttgtattttcccaagatcaaaattgtccttcacaattgagaatttatcttcaaattttgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCAAGACTCCTTTCTTCAACCAACCAGCCTAGCTTTTTGAGCCCCAAAGATT

Basic information

species Glycine max
transcript GLYMA04G09180.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G09180.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os06g05860.1 (Oryza sativa), 3'ss of exon 13
tttttattgcttctccaattttatattggtggtttgtattttcccaagatcaaaattgtccttcacaattg----------agaat-ttatcttcaaattttgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCAAGACTCCTTTCTTCAACCAACCAGCCTAGCTTTTTGAGCCCCAAAGATT
    ||   | |   | ||     | |     ||| | ||    ||| |  ||||     || | | | ||           || |  | ||||   | |   ||   ||||| ||||  |||| ||||||||| |||   |||||||| || |||||||||||||| || || |||||||||||||| || ||  | |||   |||||| 
---gtaagtcattcgctatagggcagttaaactttctgttaatacaaaaaaaaaaaaactctgctccactgctctccatactgattactgtcttatcactaaaattttcagAGGATCACAGAGAAGCAGAACAAAGTTTCAATTACTGATAGGATGTGGGCAAGACTTCTCTCCTCAACCAACCAGCCAAGTTTCCTCAGCAAGAAAGATG

upper sequence: GLYMA04G09180.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os01g09570.1 (Oryza sativa), 3'ss of exon 10
------------------tttttattgct---tctccaattttatatt--ggtggtttgtattttcccaagatcaaaattgtccttcacaattgagaatttatcttcaaattttgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCAAGACTCCTTTCTTCAACCAACCAGCCTAGCTTTTTGAGCCCCAAAGATT
                  |||| | || |   |||  | | ||   ||  | |   || |     ||  | |||||   | ||||    |  ||   | | |   ||      |  |   ||||||||||  |||| |||||||||||| ||||| || ||||| |||||||| ||  | || |  || || ||||||||  ||||  |||||| | | ||  
gtaagtccagaacactctttttcaatgatcaatctttagtgttcagttcagttcagttcttcacaccagacatcaaccatatcctgataatctggacactgaaactccggcgatt-tctacagAGAATCACGGAGAAGCAGAACAAGGTGGTGATCACGGACAGGATGTGGGCGAGGGTGCTGTGCTCGACGAACCAGCCATGCTTCCTGAGCCACGAGGACG

upper sequence: GLYMA04G09180.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 12
---tttttattgcttctccaattttatattggtggtttgtattttcccaagatcaaaattgtccttcacaattgagaatttatcttcaaattttgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCAAGACTCCTTTCTTCAACCAACCAGCCTAGCTTTTTGAGCCCCAAAGATT
     || || |  ||  |  | ||  ||   || ||| |  | |       | | |     |  |     ||   ||  | |  |       ||||   ||| | ||||||||||| | ||||||||||||||| || ||||| ||||||||||| |||||||| ||||| |||||||| |||||   || |||||||||| 
aagaattcatggtgtcctc--tcttgaatgaatgattt-tgctcttaggttttgacacagaacagttgaggttacaaaacttttgtatttgactgatgtgcagCGCATCAATGAGAGTCGGAACAAGGTTGTGATAACCGACAGGATGTGGGCAAGGCTCCTTTCGTCAACAAACCAGCCAAGCTTCCAGAACCCCAAAGATG

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|193473086|gb|FK436675.1|FK436675
EST:     GATTTACAGTTGGACTGGTCAACGGCAGACATACTTATATTCCATTCAAT                         AGAATCAATGAGAGGCA
genomic: GATTTACAGTTGGACTGGTCAACGGCAGACATACTTATATTCCATTCAATgtaagtttct ... tgatacccagAGAATCAATGAGAGGCA
EST: gi|193532952|gb|FK488530.1|FK488530
EST:     GATTTACAGTTGGACTGGTCAATGGCAGACAGACTTATATTCCATTCATT                         AGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
genomic: GATTTACAGTTGGACTGGTCAACGGCAGACATACTTATATTCCATTCAATgtaagtttct ... tgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
EST: gi|207767243|gb|GD739655.1|GD739655
EST:     GATTTACAGTTGGACTGGTCAACGGCAGACATACTTATATTCCATTCAAT                         AGAATCAATGAGAGGCAG
genomic: GATTTACAGTTGGACTGGTCAACGGCAGACATACTTATATTCCATTCAATgtaagtttct ... tgatacccagAGAATCAATGAGAGGCAG
EST: gi|193437677|gb|FK403516.1|FK403516
EST:     ATTTACAGTTGGACTGGTCAACGGCAGACATTACTTATATTCCATTCAAT                         AGAATCAATGAGAGGCAGAACAAGGTTGTGATTACT
genomic: ATTTACAGTTGGACTGGTCAACGGCAGACAT-ACTTATATTCCATTCAATgtaagtttct ... tgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACT
EST: gi|193698617|gb|FK634956.1|FK634956
EST:     ATACTTATATTCCATTCAAT                         AGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
genomic: ATACTTATATTCCATTCAATgtaagtttct ... tgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
EST: gi|208279344|gb|GE080831.1|GE080831
EST:     GATTTACAGTTGGACTGGTCAATGGCAGACAGACTTATATTCCATTCATT                         AGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
genomic: GATTTACAGTTGGACTGGTCAACGGCAGACATACTTATATTCCATTCAATgtaagtttct ... tgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
EST: gi|193389545|gb|FK357160.1|FK357160
EST:     GATTTACAGTTGGACTGGTCAACGGCAGACATACTTATATTCCATTCAAT                         AGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
genomic: GATTTACAGTTGGACTGGTCAACGGCAGACATACTTATATTCCATTCAATgtaagtttct ... tgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
EST: gi|213594161|gb|DB981433.1|DB981433
EST:     GATTTACAGTTGGACTGGTCAACGGCAGACATACTTATACTCCATTCAAT                         AGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
genomic: GATTTACAGTTGGACTGGTCAACGGCAGACATACTTATATTCCATTCAATgtaagtttct ... tgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
EST: gi|193650647|gb|FK595854.1|FK595854
EST:     GATTTACAGTTGGACTGGTCAACGGCAGACATACTTATATTCCATTCAAT                         AGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
genomic: GATTTACAGTTGGACTGGTCAACGGCAGACATACTTATATTCCATTCAATgtaagtttct ... tgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
EST: gi|193371119|gb|FK337360.1|FK337360
EST:     GATTTACAGTTGGACTGGTCAACGGCAGACATACTTATATTCCATTCAAT                         AGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
genomic: GATTTACAGTTGGACTGGTCAACGGCAGACATACTTATATTCCATTCAATgtaagtttct ... tgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
EST: gi|207799035|gb|GD771016.1|GD771016
EST:     GATTTACAGTTGGACTGGTCAACGGCAGACATACTTATATTCCATTCAAT                         AGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
genomic: GATTTACAGTTGGACTGGTCAACGGCAGACATACTTATATTCCATTCAATgtaagtttct ... tgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
EST: gi|208215240|gb|GE010169.1|GE010169
EST:     TGGACTGGTCAACGGTCAGACATACTTATATTCCATTCAAT                         AGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
genomic: TGGACTGGTCAACGG-CAGACATACTTATATTCCATTCAATgtaagtttct ... tgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
EST: gi|208301127|gb|GE097364.1|GE097364
EST:     GATTTACAGTTGGACTGGTCAACGGCAGACATACTTATATTCCATTCAAT                         AGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
genomic: GATTTACAGTTGGACTGGTCAACGGCAGACATACTTATATTCCATTCAATgtaagtttct ... tgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
EST: gi|193526896|gb|FK485066.1|FK485066
EST:     GATTTACAGTTGGACTGGTCAACGGCAGACATACTTATATTCCATTCAAT                         AGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
genomic: GATTTACAGTTGGACTGGTCAACGGCAGACATACTTATATTCCATTCAATgtaagtttct ... tgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
EST: gi|209713675|gb|BW679374.1|BW679374
EST:     GATTTACAGTTGGACTGGTCAACGGCAGACATACTTATATTCCATTCAAT                         AGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA
genomic: GATTTACAGTTGGACTGGTCAACGGCAGACATACTTATATTCCATTCAATgtaagtttct ... tgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagatcaaaattgtccttcacaattgagaatttatcttcaaattttgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCAAGACTCCTTTCTTCAACCAACCAGCCTAGCTTTTTGAGCCCCAAAGATT
                                          ttttgat  putative branch site (score: 4)
                            aatttatcttcaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttattgcttctccaattttatattggtggtttgtattttcccaagatcaaaattgtccttcacaattgagaatttatcttcaaattttgatacccagAGAATCAATGAGAGGCAGAACAAGGTTGTGATTACTGACAGAATGTGGGCAAGACTCCTTTCTTCAACCAACCAGCCTAGCTTTTTGAGCCCCAAAGATT

- - - - -cttctcc
- - - - - - - - - - - - - tggtggt
- - - - - - - - - - - - - - - - - - - - ttcccaa