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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgctttcttttcttcttcggttttgcgtctgtttttgtcttagaattttgattttgagatttttgtttttttgttctcgattgttgcagTTTTGCCTACTATGAGTGTGCAAGAGCACGCTGGGAACGAGAAATCTTGCGTTTGGCACGCTAGGGATTTTGCTGATGGTGAACTCAAGGACGAGCTTTT

Basic information

species Glycine max
transcript GLYMA20G31070.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G31070.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G07140.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------gtatgtgctttcttttctt-cttcggttttgcgtctgtttttgtcttagaattttgattttgagatttttgtttttttgttctcg-attgttgcagTTTTGCCTACTATGAGTGTGCAAGAGCACGCTGGGAACGAGAAATCTTGCGTTTGGCACGCTAGGGATTTTGCTGATGGTGAACTCAAGGACGAGCTTTT
            | ||  ||   || | ||  ||  |  |||| ||||  | ||| ||    ||    |||    || |  || || |  ||||   |||  |||||||    |    |||||||| || || |||| |||||| || || || || || ||||||||| | || ||||||||||||||||||||||| ||||||||
gtataatttctatttggactactttgtgttgtttttgagttgcatctggatctgtatttaggttactgtttccttatcta-gtcttatgcttctgatatttctgcagTTAAATCGGGCATGAGTGTTCAGGAACACGTTGGGAATGAAAAGTCATGTGTGTGGCACGCTCGTGACTTTGCTGATGGTGAACTCAAGGATGAGCTTTT
















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|254339434|gb|GR848192.1|GR848192
EST:     GCTTCTCATGAGGCAATCCAAGACGCTCAAGATCTGCGCCAATCATCTCA                         TTTTGCCTACTATGAGTGTGCAAGAGCACGCTGGGAACGAGAAATCTTGCG
genomic: GCTTCTCATGAGGCAATCCAAGACGCTCAAGATCTGCGCCAATCATCTCAgtatgtgctt ... attgttgcagTTTTGCCTACTATGAGTGTGCAAGAGCACGCTGGGAACGAGAAATCTTGCG
EST: gi|151396243|gb|EV266120.1|EV266120
EST:     GCTTCTCATGAGGCAATCCAAGACGCTCAAGATCTGCGCCAATCATCTCA                         TTTTGCCTACTATGAGTGTGCAAGAGCACGCTGGGAACGAGAAATCTTGCG
genomic: GCTTCTCATGAGGCAATCCAAGACGCTCAAGATCTGCGCCAATCATCTCAgtatgtgctt ... attgttgcagTTTTGCCTACTATGAGTGTGCAAGAGCACGCTGGGAACGAGAAATCTTGCG
EST: gi|192333111|gb|FK026440.1|FK026440
EST:     GATCTGCGCCAATCATCTCA                         TTTTGCCTACTATGAGTGTGCAAGAGCACGCTGGGAACGAGAAATCTTGCG
genomic: GATCTGCGCCAATCATCTCAgtatgtgctt ... attgttgcagTTTTGCCTACTATGAGTGTGCAAGAGCACGCTGGGAACGAGAAATCTTGCG
EST: gi|23727133|gb|BU761585.1|BU761585
EST:     GCTTCTCATGAGGCAATCCAAGACGCTCAAGATCTGCGCCAATCATCTCA                         TTTTGCCTACTATGAGTGTGCAAGAGCACGCTGGGAACGAGAAATCTTGCG
genomic: GCTTCTCATGAGGCAATCCAAGACGCTCAAGATCTGCGCCAATCATCTCAgtatgtgctt ... attgttgcagTTTTGCCTACTATGAGTGTGCAAGAGCACGCTGGGAACGAGAAATCTTGCG
EST: gi|193482815|gb|FK446598.1|FK446598
EST:     GCTTCTCATGAGGCAATCCAAGACGCTCAAGATCTGCGCCAATCATCTCA                         TTTTGCCTACTATGAGTGTGCAAGAGCACGCTGGGAACGAGAAATCTTGCG
genomic: GCTTCTCATGAGGCAATCCAAGACGCTCAAGATCTGCGCCAATCATCTCAgtatgtgctt ... attgttgcagTTTTGCCTACTATGAGTGTGCAAGAGCACGCTGGGAACGAGAAATCTTGCG
EST: gi|298165930|gb|HO008901.1|HO008901
EST:     GCTTCTCATGAGGCAATCCAAGACGCTCAAGATCTGCGCCAATCATCTCA                         TTTTGCCTACTATGAGTGTGCAAGAGCACGCTGGGAACGAGAGATCTTGCG
genomic: GCTTCTCATGAGGCAATCCAAGACGCTCAAGATCTGCGCCAATCATCTCAgtatgtgctt ... attgttgcagTTTTGCCTACTATGAGTGTGCAAGAGCACGCTGGGAACGAGAAATCTTGCG
EST: gi|209718189|gb|BW657821.1|BW657821
EST:     GCTTCTCATGAGGCAATCCAAGACGCTCAAGATCTGCGCCAATCATCTCA                         TTTTGCCTACTATGAGTGTGCAAGAGCACGCTGGGAACGAGAAATCTTGCG
genomic: GCTTCTCATGAGGCAATCCAAGACGCTCAAGATCTGCGCCAATCATCTCAgtatgtgctt ... attgttgcagTTTTGCCTACTATGAGTGTGCAAGAGCACGCTGGGAACGAGAAATCTTGCG
EST: gi|254337710|gb|GR845280.1|GR845280
EST:     GCTTCTCATGAGGCAATCCAAGACGCTCAAGATCTGCGCCAATCATCTCA                         TTTTGCCTACTATGAGTGTGCAAGAGCACGCTGGGAACGAGAAATCTTGCG
genomic: GCTTCTCATGAGGCAATCCAAGACGCTCAAGATCTGCGCCAATCATCTCAgtatgtgctt ... attgttgcagTTTTGCCTACTATGAGTGTGCAAGAGCACGCTGGGAACGAGAAATCTTGCG
EST: gi|7030389|gb|AW460172.1|AW460172
EST:     GCTTCTCATGAGGCAATCCAAGACGCTCAAGATCTGCGCCAATCATCTCA                         TTTTGCCTACTATGAGTGTGCAAGAGCACGCTGGGAACGAGAAATCTTGCG
genomic: GCTTCTCATGAGGCAATCCAAGACGCTCAAGATCTGCGCCAATCATCTCAgtatgtgctt ... attgttgcagTTTTGCCTACTATGAGTGTGCAAGAGCACGCTGGGAACGAGAAATCTTGCG
EST: gi|254337711|gb|GR845281.1|GR845281
EST:     TCTGCGCCAATCATCTCA                         TTTTG-CTACTATGAGTGTGCAAGAGCACGCTGGGAACGAGAAATCTTGCG
genomic: TCTGCGCCAATCATCTCAgtatgtgctt ... attgttgcagTTTTGCCTACTATGAGTGTGCAAGAGCACGCTGGGAACGAGAAATCTTGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtcttagaattttgattttgagatttttgtttttttgttctcgattgttgcagTTTTGCCTACTATGAGTGTGCAAGAGCACGCTGGGAACGAGAAATCTTGCGTTTGGCACGCTAGGGATTTTGCTGATGGTGAACTCAAGGACGAGCTTTT
           ttttgat  putative branch site (score: 4)
         aattttgattttgaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgctttcttttcttcttcggttttgcgtctgtttttgtcttagaattttgattttgagatttttgtttttttgttctcgattgttgcagTTTTGCCTACTATGAGTGTGCAAGAGCACGCTGGGAACGAGAAATCTTGCGTTTGGCACGCTAGGGATTTTGCTGATGGTGAACTCAAGGACGAGCTTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT