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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtactcatcactttcctatttctttcattttcttttctatagatccaattctctcatgctaattcctatttcttgttcgattcagGTTCTGCACATGGACAGGAATGACTATTACGGAGGAGAATCCACTTCGCTCAATCTTATTCAG

Basic information

species Glycine max
transcript GLYMA08G13300.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G13300.3 (Glycine max), 3'ss of exon 1
lower sequence: Vv05s0094g01550.t01 (Vitis vinifera), 3'ss of exon 1
--gtacgtactcatcacttt-----cctatttctttcatt----ttcttttctatagatccaattctctcatgctaattcctatttcttgttcgattcagGTTCTGCACATGGACAGGAATGACTATTACGGAGGAGAATCCACTTCGCTCAATCTTATTCAG
   |   | |  |||  |||     || |  |  | || |    || || |||    |  || ||   | ||| | |    |   | |  |  ||  ||||||||||||||||| || ||||||||||| |||||||| || | ||| |||||||||||||||
cattgtatccctatcgatttgaattccaaagtgatgcactgacattattatctgctcaagcagttggttgatgattaaaattgcatatattgtgaaccagGTTCTGCACATGGATAGAAATGACTATTATGGAGGAGAGTCAAGTTCACTCAATCTTATTCAG
















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|17023050|gb|BM094084.1|BM094084
EST:     GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAG                         GTTCTGCACATGGACAGGAATGACTATTACGGAGGAGAATCCACTTCGCTC
genomic: GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtacgtactc ... ttcgattcagGTTCTGCACATGGACAGGAATGACTATTACGGAGGAGAATCCACTTCGCTC
EST: gi|7590904|gb|AW706647.1|AW706647
EST:     GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAG                         GTTCTGCACATGGACAGGAATGACTATTACGGAGGAGAATCCACTTCGCTC
genomic: GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtacgtactc ... ttcgattcagGTTCTGCACATGGACAGGAATGACTATTACGGAGGAGAATCCACTTCGCTC
EST: gi|18848745|gb|BM567857.1|BM567857
EST:     GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAG                         GTTCTGCACATGGACAGGAATGACTATTACGGAGGAGAATCCACTTCGCTC
genomic: GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtacgtactc ... ttcgattcagGTTCTGCACATGGACAGGAATGACTATTACGGAGGAGAATCCACTTCGCTC
EST: gi|209700942|gb|BW683135.1|BW683135
EST:     GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAG                         GTTCTGCACATGGACAGGAATGACTATTACGGAGGAGAATCCACTTCGCTC
genomic: GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtacgtactc ... ttcgattcagGTTCTGCACATGGACAGGAATGACTATTACGGAGGAGAATCCACTTCGCTC
EST: gi|213598655|gb|DB958183.1|DB958183
EST:     GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAG                         GTTCTGCACATGGACAGGAATGACTATTACGGAGGAGAATCCACTTCGCTC
genomic: GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtacgtactc ... ttcgattcagGTTCTGCACATGGACAGGAATGACTATTACGGAGGAGAATCCACTTCGCTC
EST: gi|163927330|gb|EH040145.1|EH040145
EST:     GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAG                         GTTCTGCACATGGACAGGAATGACTATTACGGAGGAGAATCCACTTCGCTC
genomic: GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtacgtactc ... ttcgattcagGTTCTGCACATGGACAGGAATGACTATTACGGAGGAGAATCCACTTCGCTC
EST: gi|151394091|gb|EV263962.1|EV263962
EST:     GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAG                         GTTCTGCACATGGACAGGAATGACTATTACGGAGGAGAATCCACTTCGCTC
genomic: GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtacgtactc ... ttcgattcagGTTCTGCACATGGACAGGAATGACTATTACGGAGGAGAATCCACTTCGCTC
EST: gi|192328654|gb|FK023154.1|FK023154
EST:     GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAG                         GTTCTGCACATGGACAGGAATGACTATTACGGAGGAGAATCCACTTCGCTC
genomic: GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtacgtactc ... ttcgattcagGTTCTGCACATGGACAGGAATGACTATTACGGAGGAGAATCCACTTCGCTC
EST: gi|193706374|gb|FK648868.1|FK648868
EST:     GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAG                         GTTCTGCACATGGACAGGAATGACTATTAC
genomic: GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtacgtactc ... ttcgattcagGTTCTGCACATGGACAGGAATGACTATTAC
EST: gi|10842948|gb|BF066306.1|BF066306
EST:     GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAG                         GTTCTGCACATGGACAGGAATGACTATTACGGAGGAGAATCCACTTCGCTC
genomic: GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtacgtactc ... ttcgattcagGTTCTGCACATGGACAGGAATGACTATTACGGAGGAGAATCCACTTCGCTC
EST: gi|151407978|gb|EV277793.1|EV277793
EST:     GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAG                         GTTCTGCACATGGACAGGAATGACTATTACGGAGGAGAATCCACTTCGCTC
genomic: GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtacgtactc ... ttcgattcagGTTCTGCACATGGACAGGAATGACTATTACGGAGGAGAATCCACTTCGCTC
EST: gi|151411945|gb|EV281756.1|EV281756
EST:     GTCTCGAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAG                         GTTCTGCACATGGACAGGAATGACTATTACGGAGGAGAATCCACTTCGCTC
genomic: GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtacgtactc ... ttcgattcagGTTCTGCACATGGACAGGAATGACTATTACGGAGGAGAATCCACTTCGCTC
EST: gi|6667361|gb|AW278812.1|AW278812
EST:     GTCTCAAGGAGTGCATCCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAG                         GTTCTGCACATGGACAGGAATGAC
genomic: GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtacgtactc ... ttcgattcagGTTCTGCACATGGACAGGAATGAC
EST: gi|192327650|gb|FK020669.1|FK020669
EST:     GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAG                         GTTCTGCACATGGACAGGAATGACTATTACGGAGGAGAATCCACTTCGCTC
genomic: GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtacgtactc ... ttcgattcagGTTCTGCACATGGACAGGAATGACTATTACGGAGGAGAATCCACTTCGCTC
EST: gi|17021888|gb|BM092922.1|BM092922
EST:     GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAG                         GTTCTGCACATGGACAGGAATGACTATTACGGAGGAGAATCCACTTCGCTC
genomic: GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtacgtactc ... ttcgattcagGTTCTGCACATGGACAGGAATGACTATTACGGAGGAGAATCCACTTCGCTC
EST: gi|120532856|gb|EH260989.1|EH260989
EST:     GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAG                         GTTCTGCACATGGACAGGAATGACTATTACGGAGGAGAATCCACTTCGCTC
genomic: GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtacgtactc ... ttcgattcagGTTCTGCACATGGACAGGAATGACTATTACGGAGGAGAATCCACTTCGCTC
EST: gi|213589680|gb|DB965840.1|DB965840
EST:     GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAG                         GTTCTGCACATGGACAGGAATGACTATTACGGAGGAGAATCCACTTCGCTC
genomic: GTCTCAAGGAGTGCATTCTCAGCGGTCTTCTCTCCGTCGATGGCCTCAAGgtacgtactc ... ttcgattcagGTTCTGCACATGGACAGGAATGACTATTACGGAGGAGAATCCACTTCGCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttctatagatccaattctctcatgctaattcctatttcttgttcgattcagGTTCTGCACATGGACAGGAATGACTATTACGGAGGAGAATCCACTTCGCTCAATCTTATTCAG
                          tgctaat  putative branch site (score: 2)
                                ttcctatttcttgttc  CT-rich tract
                                    tatttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtactcatcactttcctatttctttcattttcttttctatagatccaattctctcatgctaattcctatttcttgttcgattcagGTTCTGCACATGGACAGGAATGACTATTACGGAGGAGAATCCACTTCGCTCAATCTTATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA