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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacattgagaatctcgctgcctttttttcccctgcttgttttacattatttttttgctttaatttagattgtaagtaattgtgttgttctttatgtcattagACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAAAGGCTTAGAGGAAAAGATGATG

Basic information

species Glycine max
transcript GLYMA02G46620.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G46620.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv19s0090g01590.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------------------gtacattgagaatctcgctgc-ctttttttcccctgcttgttttacattatttttttgctttaatttagattgtaagtaattgtg-ttgttctttatgtcattagACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAAAGGCTTAGAGGAAAAGATGATG
                                        |  ||||    | |   | | |||| ||  |||      |||||  ||||  |  | | ||  | || | |     |   | |  || |  |||   | |  ||||||||||| |||||||||||||||| ||||||||||| ||  |  |||| ||| | |||||||| |||||||
gtatgagagaccatatgatatattgtaaactttgattggctgaattgtatttgtttttccactttattaaccccataaattttatgttatcctgataccttgctataaactaaggtttcctcttcttatcttttcccttaacagACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATG
















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|23727058|gb|BU761545.1|BU761545
EST:     AGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAAAG                         ACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAA
genomic: AGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAAAGgtacattgag ... atgtcattagACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAA
EST: gi|17153736|gb|BM143669.1|BM143669
EST:     AGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAAAG                         ACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAA
genomic: AGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAAAGgtacattgag ... atgtcattagACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAA
EST: gi|31468894|gb|CD410922.1|CD410922
EST:     AGAAGAAAGCTTTTAAAGGATCCTTCGTAGAAGCAGGGTCTTATGCAAAG                         ACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAA
genomic: AGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAAAGgtacattgag ... atgtcattagACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAA
EST: gi|26047850|gb|CA784505.1|CA784505
EST:     AGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAAAG                         ACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAA
genomic: AGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAAAGgtacattgag ... atgtcattagACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAA
EST: gi|298181833|gb|HO026008.1|HO026008
EST:     AGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAAAG                         ACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAA
genomic: AGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAAAGgtacattgag ... atgtcattagACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAA
EST: gi|298174609|gb|HO017832.1|HO017832
EST:     AGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAAAG                         ACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAA
genomic: AGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAAAGgtacattgag ... atgtcattagACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAA
EST: gi|9898882|gb|BE607850.1|BE607850
EST:     AGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAAAG                         ACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAA
genomic: AGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAAAGgtacattgag ... atgtcattagACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAA
EST: gi|298184523|gb|HO029736.1|HO029736
EST:     AGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAATG                         ACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAA
genomic: AGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAAAGgtacattgag ... atgtcattagACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAA
EST: gi|31311953|gb|CD397156.1|CD397156
EST:     AGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAAAG                         ACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAA
genomic: AGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAAAGgtacattgag ... atgtcattagACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAA
EST: gi|298178521|gb|HO024256.1|HO024256
EST:     AGGAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAAAG                         ACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAA
genomic: AGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAAAGgtacattgag ... atgtcattagACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAA
EST: gi|298181875|gb|HO026050.1|HO026050
EST:     AGAAGAAAGGTTTTAAAGGATCCTTTATAGAAGCAGGGTCTTATGCAAAG                         ACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAA
genomic: AGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAAAGgtacattgag ... atgtcattagACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAA
EST: gi|7925046|gb|AW831072.1|AW831072
EST:     AGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAAAG                         ACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAA
genomic: AGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAAAGgtacattgag ... atgtcattagACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAA
EST: gi|6071305|gb|AW100692.1|AW100692
EST:     AGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAAAG                         ACAATTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAA
genomic: AGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAAAGgtacattgag ... atgtcattagACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAA
EST: gi|24135852|gb|BU926362.1|BU926362
EST:     AGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAAAG                         ACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAA
genomic: AGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAAAGgtacattgag ... atgtcattagACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAA
EST: gi|298173707|gb|HO017043.1|HO017043
EST:     GAAGAAAGTGTTTTAAAGGATCCTTTGTAGAAGCATGGTCTTATGCAAAG                         ACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAA
genomic: GAAGAAAG-GTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAAAGgtacattgag ... atgtcattagACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAA
EST: gi|15337011|gb|BI497667.1|BI497667
EST:     AGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAAAG                         ACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAA
genomic: AGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAAAGgtacattgag ... atgtcattagACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAA
EST: gi|18041339|gb|BM309633.1|BM309633
EST:     AGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAAAG                         ACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAA
genomic: AGAAGAAAGGTTTTAAAGGATCCTTTGTAGAAGCAGGGTCTTATGCAAAGgtacattgag ... atgtcattagACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttttgctttaatttagattgtaagtaattgtgttgttctttatgtcattagACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAAAGGCTTAGAGGAAAAGATGATG
         ctttaat  putative branch site (score: 4)
                                       ttctttat  putative PPT
          tttaatttagattgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacattgagaatctcgctgcctttttttcccctgcttgttttacattatttttttgctttaatttagattgtaagtaattgtgttgttctttatgtcattagACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAAAGGCTTAGAGGAAAAGATGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG