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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaacactaatgttcaaattgagcttctgagagaaaattaagaaattgggtatgtgtttaaagttgaatttaatgggttggtgttgatttctttctgcagGAGTCAAGCAAGAGCATACAGATTGAAGCATTTCATGTTTTCAAG

Basic information

species Glycine max
transcript GLYMA15G12220.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G12220.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv10s0405g00020.t01 (Vitis vinifera), 3'ss of exon 8
----tgaacactaatgttcaa-attgagcttctgagagaaaattaagaaattgggtatgtgtttaaagttgaatttaatgggttggtgttgatttctttctgcagGAGTCAAGCAAGAGCATACAGATTGAAGCATTTCATGTTTTCAAG
    |   | | | | |  |  | | |   | | ||    || |   ||| |    |    ||| ||      ||| ||   |  |  ||   ||||||   ||||||||||||||||| || ||||||||||| |||||||||||||||
accatcttcccaagtatgaaggactaaaaattttagt---aactgctaaactaatgagacattttaacaaagctttgataaatgtggattatcttctttt--cagGAGTCAAGCAAGAGTATTCAGATTGAAGCTTTTCATGTTTTCAAG
















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|14991297|gb|BI316970.1|BI316970
EST:     GATATGTGAGCTCAAGAGACAACTTGAGGATTTTAATGAATCTTCTTAGA                         GAGTCAAGCAAGAGCATACAGATTGAAGCATTTCATGTTTTCAAG
genomic: GATATGTGAGCTCAAGAGACAACTTGAGGATTTTAATGAATCTTCTTAGAgtatgtctta ... ctttctgcagGAGTCAAGCAAGAGCATACAGATTGAAGCATTTCATGTTTTCAAG
EST: gi|31463880|gb|CD405908.1|CD405908
EST:     GATATGTGAGCTCAAGAGACAACTTGAGGATTTTAATGAATCTTCTTAGA                         GAGTCAAGCAAGAGCATACAGATTGAAGCATTTCATGTTTTCAAG
genomic: GATATGTGAGCTCAAGAGACAACTTGAGGATTTTAATGAATCTTCTTAGAgtatgtctta ... ctttctgcagGAGTCAAGCAAGAGCATACAGATTGAAGCATTTCATGTTTTCAAG
EST: gi|21994680|gb|BQ786208.1|BQ786208
EST:     GATATGTGAGCTCAAGAGACAACTTGAGGATTTTAATGAATCTTCTTAGA                         GAGTCAAGCAAGAGCATACAGATTGAAGCATTTCATGTTTTCAAG
genomic: GATATGTGAGCTCAAGAGACAACTTGAGGATTTTAATGAATCTTCTTAGAgtatgtctta ... ctttctgcagGAGTCAAGCAAGAGCATACAGATTGAAGCATTTCATGTTTTCAAG
EST: gi|22932404|gb|BU549543.1|BU549543
EST:     GATATGTGAGCTCAAGAGACAACTTGAGGATTTTAATGAATCTTCTTAGA                         GAGTCAAGCAAGAGCATACAGATTGAAGCATTTCATGTTTTCAAG
genomic: GATATGTGAGCTCAAGAGACAACTTGAGGATTTTAATGAATCTTCTTAGAgtatgtctta ... ctttctgcagGAGTCAAGCAAGAGCATACAGATTGAAGCATTTCATGTTTTCAAG
EST: gi|23734444|gb|BU765448.1|BU765448
EST:     GACAACTTGAGGATTTTAATGAATCTTCTTAGA                         GAGTCAAGCAAGAGCATACAGATTGAAGCATTTCATGTTTTCAAG
genomic: GACAACTTGAGGATTTTAATGAATCTTCTTAGAgtatgtctta ... ctttctgcagGAGTCAAGCAAGAGCATACAGATTGAAGCATTTCATGTTTTCAAG
EST: gi|31474015|gb|CD416043.1|CD416043
EST:     GATATGTGAGCTCAAGAGACAACTTGAGGATTTTAATGAATCTTCTTAGA                         GAGTCAAGCAAGAGCATACAGATTGAAGCATTTCATGTTTTCAAG
genomic: GATATGTGAGCTCAAGAGACAACTTGAGGATTTTAATGAATCTTCTTAGAgtatgtctta ... ctttctgcagGAGTCAAGCAAGAGCATACAGATTGAAGCATTTCATGTTTTCAAG
EST: gi|13312864|gb|BG406515.1|BG406515
EST:     GATATGTGAGCTCAAGAGACAACTTGAGGATTTTAATGAATCTTCTTAGA                         GAGTCAAGCAAGAGCATACAGATTGAAGCATTTCATGTTTTCAAG
genomic: GATATGTGAGCTCAAGAGACAACTTGAGGATTTTAATGAATCTTCTTAGAgtatgtctta ... ctttctgcagGAGTCAAGCAAGAGCATACAGATTGAAGCATTTCATGTTTTCAAG
EST: gi|22928039|gb|BU545178.1|BU545178
EST:     GATATGTGAGCTCAAGAGACAACTTGAGGATTTTAATGAATCTTCNNNGA                         GAGTCAAGCAAGAGCATACAGATTGAAGCATTTCATGTTTTCAAG
genomic: GATATGTGAGCTCAAGAGACAACTTGAGGATTTTAATGAATCTTCTTAGAgtatgtctta ... ctttctgcagGAGTCAAGCAAGAGCATACAGATTGAAGCATTTCATGTTTTCAAG
EST: gi|9901558|gb|BE610526.1|BE610526
EST:     GTGAGCTCAAGAGACAACTTGAGGATTTTAATGAATCTTCTTAGA                         GAGTCAAGCAAGAGCATACAGATTGAAGCATTTCATGTTTTCAAG
genomic: GTGAGCTCAAGAGACAACTTGAGGATTTTAATGAATCTTCTTAGAgtatgtctta ... ctttctgcagGAGTCAAGCAAGAGCATACAGATTGAAGCATTTCATGTTTTCAAG
EST: gi|254318122|gb|GR832290.1|GR832290
EST:     GAGACAACTTGAGGATTTTAATGAATCTTCTTAGA                         GAGTCAAGCAAGAGCATACAGATTGAAGCATTTCATGTTTTCAAG
genomic: GAGACAACTTGAGGATTTTAATGAATCTTCTTAGAgtatgtctta ... ctttctgcagGAGTCAAGCAAGAGCATACAGATTGAAGCATTTCATGTTTTCAAG
EST: gi|6724491|gb|AW308890.1|AW308890
EST:     GATATGTGAGCTCAAGAGACAACTTGAGGATTTTAATGAATCTTCTTAGA                         GAGTCAAGCAAGAGCATACAGATTGAAGCATTTCATGTTTTCAAG
genomic: GATATGTGAGCTCAAGAGACAACTTGAGGATTTTAATGAATCTTCTTAGAgtatgtctta ... ctttctgcagGAGTCAAGCAAGAGCATACAGATTGAAGCATTTCATGTTTTCAAG
EST: gi|33389396|gb|CA852603.1|CA852603
EST:     ACAACTTGAGGATTTTAATGAATCTTCTTAGA                         GAGTCAAGCAAGAGCATACAGATTGAAGCATTTCATGTTTTCAAG
genomic: ACAACTTGAGGATTTTAATGAATCTTCTTAGAgtatgtctta ... ctttctgcagGAGTCAAGCAAGAGCATACAGATTGAAGCATTTCATGTTTTCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgggtatgtgtttaaagttgaatttaatgggttggtgttgatttctttctgcagGAGTCAAGCAAGAGCATACAGATTGAAGCATTTCATGTTTTCAAG
                                    tgttgat  putative branch site (score: 4)
                                          tttctttctgc  CT-rich tract
           tttaaagttgaattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaacactaatgttcaaattgagcttctgagagaaaattaagaaattgggtatgtgtttaaagttgaatttaatgggttggtgttgatttctttctgcagGAGTCAAGCAAGAGCATACAGATTGAAGCATTTCATGTTTTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - gcttctg
- - - - - - - - - - - - - - - - -aaaattaa
- - - - - - - - - - - - - - - - - - - - - - - - -gtatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgat