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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgcatattcaggccattgattgactatggtttgtttttaaaatacatttcatatatctttccgatgctgactttgggtgcatcttatctgtgtgcagGTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCTACCTAGATATCTTTACTAATTATGTATCTCTCTATAATACCACTATGAA

Basic information

species Glycine max
transcript GLYMA08G46570.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G46570.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G25040.1 (Arabidopsis thaliana), 3'ss of exon 1
ttttgcatattcaggccattgattgactatggtttgtttttaaaatacatttcatatatctttccgatgctgac--tttgggtgcatcttatctgtgtgcagGTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCTACCTAGATATCTTTACTAATTATGTATCTCTCTATAATACCACTATGAA
  ||| | ||  ||  | ||   | |   || |   || |     |     |  |   | | |  ||   |  |  |||   ||  |  ||| | | ||||||||| ||||||||||||||||||||||||||  | || |||||    || ||  | ||||| || || | || ||| ||||| || || ||| |||||||
--ttgaaaatgtagttcgttagatcagcttgctcgattctgtgtttgagaattttgcttttatgagaattttgcaatttttttgtttggtatatctttgcagGTGTTTCATTGAAGACTCAAGAACTCTATGCCATTGTCTTTGCGACGCGTTATTTGGATATTTTCACGAGTTTTGTGTCTCTGTACAACACCTCTATGAA
















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|193347785|gb|FK313517.1|FK313517
EST:     CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCG                         GTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
genomic: CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCGgtcggtacct ... ctgtgtgcagGTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
EST: gi|192306206|gb|FG996834.1|FG996834
EST:     CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCG                         GTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
genomic: CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCGgtcggtacct ... ctgtgtgcagGTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
EST: gi|7028432|gb|AW458215.1|AW458215
EST:     CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCG                         GTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
genomic: CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCGgtcggtacct ... ctgtgtgcagGTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
EST: gi|7693494|gb|AW761586.1|AW761586
EST:     CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCG                         GTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
genomic: CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCGgtcggtacct ... ctgtgtgcagGTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
EST: gi|207818212|gb|GD790215.1|GD790215
EST:     CGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCG                         GTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
genomic: CGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCGgtcggtacct ... ctgtgtgcagGTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
EST: gi|6566143|gb|AW233782.1|AW233782
EST:     CACACCATCAAATCCTGCGCCG                         GTGTCTCATTGAAGACTCAAGAGCTCTATGCACTCGTTTTTGCTTGTCGCT
genomic: CACACCATCAAATCCTGCGCCGgtcggtacct ... ctgtgtgcagGTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
EST: gi|24136565|gb|BU927075.1|BU927075
EST:     CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCG                         GTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
genomic: CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCGgtcggtacct ... ctgtgtgcagGTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
EST: gi|31561500|gb|CD487338.1|CD487338
EST:     CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCG                         GTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
genomic: CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCGgtcggtacct ... ctgtgtgcagGTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
EST: gi|24136162|gb|BU926672.1|BU926672
EST:     CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCG                         GTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
genomic: CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCGgtcggtacct ... ctgtgtgcagGTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
EST: gi|207767184|gb|GD739596.1|GD739596
EST:     CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCG                         GTGTCTCATTGAAGA
genomic: CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCGgtcggtacct ... ctgtgtgcagGTGTCTCATTGAAGA
EST: gi|193561865|gb|FK519852.1|FK519852
EST:     CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCG                         GTGTCTCATTGAAGACTCAAAGAACTCTATGCACTTCGTTTTTGCTTGTCG
genomic: CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCGgtcggtacct ... ctgtgtgcagGTGTCTCATTGAAGACTCAA-GAACTCTATGCACT-CGTTTTTGCTTGTCG
EST: gi|10232336|gb|BE801224.1|BE801224
EST:     CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCG                         GTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
genomic: CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCGgtcggtacct ... ctgtgtgcagGTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
EST: gi|208194630|gb|GD988501.1|GD988501
EST:     CGTCCTTCTTTCTTCAAGATCCACACCATCAAATCCTGCGCCG                         GTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTTCGC
genomic: CGTCCTTC-TTC-TCAAGATCCACACCATCAAATCCTGCGCCGgtcggtacct ... ctgtgtgcagGTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTG-TCGC
EST: gi|298188845|gb|HO035538.1|HO035538
EST:     CAGCGTCCTCGTCCTTCTTCCCAAGATCCACACCATCAAATCCTGCGCCG                         GTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
genomic: CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCGgtcggtacct ... ctgtgtgcagGTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
EST: gi|209715072|gb|BW677115.1|BW677115
EST:     CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCG                         GTGTCTCATTGAAGACTCAAGAGCTCTATGCACTCGTTTTTGCTTGTCGCT
genomic: CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCGgtcggtacct ... ctgtgtgcagGTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
EST: gi|208060969|gb|GD857549.1|GD857549
EST:     CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCG                         GTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
genomic: CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCGgtcggtacct ... ctgtgtgcagGTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
EST: gi|13252025|gb|BG362928.1|BG362928
EST:     CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCG                         GTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
genomic: CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCGgtcggtacct ... ctgtgtgcagGTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
EST: gi|7147282|gb|AW509204.1|AW509204
EST:     CTTCTCAAGATCCACACCATCAAATCCTGCGCCG                         GTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
genomic: CTTCTCAAGATCCACACCATCAAATCCTGCGCCGgtcggtacct ... ctgtgtgcagGTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
EST: gi|11412647|gb|BF424658.1|BF424658
EST:     CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCG                         GTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
genomic: CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCGgtcggtacct ... ctgtgtgcagGTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
EST: gi|207799923|gb|GD770602.1|GD770602
EST:     CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCG                         GTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
genomic: CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCGgtcggtacct ... ctgtgtgcagGTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
EST: gi|151401246|gb|EV271060.1|EV271060
EST:     CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCG                         GTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
genomic: CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCGgtcggtacct ... ctgtgtgcagGTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
EST: gi|7588285|gb|AW704084.1|AW704084
EST:     CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCG                         GTGTCTCATTGAAGACTCAAGAGCTCTATGCACTCGTTTTTGCTTGTCGCT
genomic: CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCGgtcggtacct ... ctgtgtgcagGTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
EST: gi|298185620|gb|HO030833.1|HO030833
EST:     CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCG                         GTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT
genomic: CAGCGTCCTCGTCCTTCTTCTCAAGATCCACACCATCAAATCCTGCGCCGgtcggtacct ... ctgtgtgcagGTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacatttcatatatctttccgatgctgactttgggtgcatcttatctgtgtgcagGTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCTACCTAGATATCTTTACTAATTATGTATCTCTCTATAATACCACTATGAA
                      tgctgac  putative branch site (score: 2)
                                       tcttatct  putative PPT
        atatatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgcatattcaggccattgattgactatggtttgtttttaaaatacatttcatatatctttccgatgctgactttgggtgcatcttatctgtgtgcagGTGTCTCATTGAAGACTCAAGAACTCTATGCACTCGTTTTTGCTTGTCGCTACCTAGATATCTTTACTAATTATGTATCTCTCTATAATACCACTATGAA

- -tgcatat
- - - - - tcaggcc
- - - - - - - - - - - - - - -tggtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgggtg