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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACATGCAGAGAAGTATGTCCGAAGGGGTAGATTGGACTGGCCAGAGGGTGCAGCCTCACGAGAGAGTATTAAAGCTGTAATGAAGCTTCCCCGACTACAGgtttgttctcaaatctgtcatggaaaatatttattatgattttgaatgctttctgattttactaaatgaagcaatgttgacttcacttaacgtaatttttctttaataattgcag

Basic information

species Glycine max
transcript GLYMA06G18530.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G18530.1 (Glycine max), 5'ss of exon 10
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 5'ss of exon 11
ACATGCAGAGAAGTATGTCCGAAGGGGTAGATTGGACTGGCCAGAGGGTGCAGCCTCACGAGAGAGTATTAAAGCTGTAATGAAGCTTCCCCGACTACAGgtttgttctcaa-atctgtcatggaaaatatttattatgattttgaatgctttctga----ttttactaaatgaagcaatgttgacttcacttaacgtaatttttctttaataattgcag
|||||||||||||||||| |||||||||||||||||||||||||| |||||  | ||| | || ||||| ||||||||  | ||||| || || || |||||||||   ||     ||   |||   ||   ||  | | |||   |   | ||| |    | ||  |   |       |  ||  ||     ||  ||  | | |     |  | ||||
ACATGCAGAGAAGTATGTACGAAGGGGTAGATTGGACTGGCCAGAAGGTGCGACTTCAAGGGAAAGTATCAAAGCTGTTCTCAAGCTACCTCGCCTTCAGgtttgtgtacattgattgatttggttcattcataccaagttttgtgagcttgtctaaaggttctttatttgtattttggtcatgtgtttgacaaatctatatatgcaccttttttggcag
















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|10846474|gb|BF069349.1|BF069349
EST:     CAGCCTCACGAGAGAGTATTAAAGCTGTAATGAAGCTTCCCCGACTACAG                         AACATTATAATGCAACATGTTGATCATTCAGCTGGAGATCTTATACATCTT
genomic: CAGCCTCACGAGAGAGTATTAAAGCTGTAATGAAGCTTCCCCGACTACAGgtttgttctc ... ataattgcagAACATTATAATGCAGCATGTTGATCATTCAGCTGGAGATCTTATACATCTT
EST: gi|31464003|gb|CD406031.1|CD406031
EST:     CAGCCTCACGAGAGAGTATTAAAGCTGTAATGAAGCTTCCCCGACTACAG                         AACATTATAATGCAGCATGTTGATCATTCAGCTGGAGATCTTATACATCTT
genomic: CAGCCTCACGAGAGAGTATTAAAGCTGTAATGAAGCTTCCCCGACTACAGgtttgttctc ... ataattgcagAACATTATAATGCAGCATGTTGATCATTCAGCTGGAGATCTTATACATCTT
EST: gi|207829246|gb|GD798922.1|GD798922
EST:     CAGCCTCACGAGAGAGTATTAAAGCTGTAATGAAGCTTCCCCGACTACAG                         AACATTATAATGCAGCATGTTGATCATTCAGCTGGAGATCTTATACATCTT
genomic: CAGCCTCACGAGAGAGTATTAAAGCTGTAATGAAGCTTCCCCGACTACAGgtttgttctc ... ataattgcagAACATTATAATGCAGCATGTTGATCATTCAGCTGGAGATCTTATACATCTT
EST: gi|192330548|gb|FK021251.1|FK021251
EST:     CAGCCTCACGAGAGAGTATTAAAGCTGTAATGAAGCTTCCCCGACTACAG                         AACACTATAATGCAGCATGTTGATCATTCAGCTGGAGATCTTATACATCTT
genomic: CAGCCTCACGAGAGAGTATTAAAGCTGTAATGAAGCTTCCCCGACTACAGgtttgttctc ... ataattgcagAACATTATAATGCAGCATGTTGATCATTCAGCTGGAGATCTTATACATCTT
EST: gi|6963856|gb|AW432549.1|AW432549
EST:     CAGCCTCACGAGAGAGTATTAAAGCTGTAATGAAGCTTCCCCGACTACAG                         AACATTATAATGCAGCATGTTGATCATTCAGCTGGAGATCTTATACATCTT
genomic: CAGCCTCACGAGAGAGTATTAAAGCTGTAATGAAGCTTCCCCGACTACAGgtttgttctc ... ataattgcagAACATTATAATGCAGCATGTTGATCATTCAGCTGGAGATCTTATACATCTT
EST: gi|31307855|gb|CD393058.1|CD393058
EST:     CAGCCTCACGAGAGAGTATTAAAGCTGTAATGAAGCTTCCCCGACTACAG                         AACATTATAATGCAGCATGTTGATCATTCAGCTGGAGATCTTATACATCTT
genomic: CAGCCTCACGAGAGAGTATTAAAGCTGTAATGAAGCTTCCCCGACTACAGgtttgttctc ... ataattgcagAACATTATAATGCAGCATGTTGATCATTCAGCTGGAGATCTTATACATCTT
EST: gi|214004373|gb|DB985041.1|DB985041
EST:     CAGCCTCACGAGAGAGTATTAAAGCTGTAATGAAGCTTCCCCGACTACAG                         AACATTATAATGCAGCATGTTGATCATTCAGCTGGAGATCTTATACATCTT
genomic: CAGCCTCACGAGAGAGTATTAAAGCTGTAATGAAGCTTCCCCGACTACAGgtttgttctc ... ataattgcagAACATTATAATGCAGCATGTTGATCATTCAGCTGGAGATCTTATACATCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACATGCAGAGAAGTATGTCCGAAGGGGTAGATTGGACTGGCCAGAGGGTGCAGCCTCACGAGAGAGTATTAAAGCTGTAATGAAGCTTCCCCGACTACAGgtttgttctcaaatctgtcatggaaaatatttattatgattttgaatgctttctgattttactaaatgaagcaatgttgacttcacttaacgtaatttttctttaataattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC