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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacttgtgataatacatatttatcttcattttatattatagatagttcataattgtatttaagacttgagaatccattttcttttttctgatcttttcagGTTATTGCAAACCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGTGGGAAGTTAGTGCACCCAAATGACCATGTCAATAGATCACAGTCTTCAAATGATA

Basic information

species Glycine max
transcript GLYMA02G01920.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G01920.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 3
tacttgtgataatacatatttatcttcattttatattatagatagttcata--attgtatt-taagacttgagaatccattttcttttttctgatcttttcagGTTATTGCAAACCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGTGGGAAGTTAGTGCACCCAAATGACCATGTCAATAGATCACAGTCTTCAAATGATA
   || | ||  |  ||  | || || |  |||   |      ||||  |   ||| || | ||| |  | |  ||   |  |||  |||   |  ||   |||||||||||||  | || || ||||||||| | |||||||| || | |||||| || ||||| ||||| ||||| || ||||||||||| ||||||||||
attttatcatgtttaattctcatgttaacattactgtgagctaagtttgtgttattatactgtaatatcttaccatttctgatctgcttttgcaattt---agGTTATTGCAAATAGGGCCGCTGAGATTCTTGGACATAAGCGTGGCGAGAAGTTTGTACACCCTAATGATCATGTGAACAGATCACAGTCCTCAAATGATA

upper sequence: GLYMA02G01920.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 3
---tacttgtgataatacatatttatcttcattttatattatagatagttcataattgtattta--agacttgagaatccattttcttttttctgatcttttcagGTTATTGCAAACCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGTGGGAAGTTAGTGCACCCAAATGACCATGTCAATAGATCACAGTCTTCAAATGATA
   |  |  ||  |    || || || |  |||||||  | |  |    ||||  || |    |     ||  |   |  ||  ||| ||||| ||    ||||||| ||||||||  | ||| | ||||| ||| | || ||||| |||| |||||| |||||||||||||||||||| ||||| ||||| |||||||||||||
tagttttcctgtaagctaatgttcatgtgaattttat--tgtgaacctatcatgcttctgccaactgtgctatattgtttatgatctcttttccgaa---ttcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATA

upper sequence: GLYMA02G01920.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G348729_T01 (Zea mays), 3'ss of exon 6
---tacttgtgataatacatatttatcttcattttatattatagatagttcataattgtatttaagacttgagaatccattttcttttttctgatcttttcagGTTATTGCAAACCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGTGGGAAGTTAGTGCACCCAAATGACCATGTCAATAGATCACAGTCTTCAAATGATA
   |  |  ||  |    || || || |  |||||||  |  |  |||    |   ||         ||  |   |  ||  ||| ||||| ||    ||||||| ||||||||  | ||| | ||||| ||| | || ||| | |||  |||||| |||||||||||||||||||| ||||| ||||| |||||||||||||
tagttttcctgtaagctaatgttcatgtgaattttattatgaacctagcatgtttctgccagctgtgctatattgtttatgatctcttttccgaa---ttcagGTAATTGCAAATAGGGCATCTGAGATCCTTGGACACAAGGGCGGTCAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATA

upper sequence: GLYMA02G01920.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G47510.1 (Arabidopsis thaliana), 3'ss of exon 4
------------tacttgtgataatacatatttat--cttcattttatatta-tagatagttcataa----ttgtatttaagacttgagaatccatttt----cttttttctgatcttttcagGTTATTGCAAACCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGTGGGAAGTTAGTGCACCCAAATGACCATGTCAATAGATCACAGTCTTCAAATGATA
             | || |    | |  | || |     ||||| |||||   ||| ||    | ||    || | |||| |  ||   | |   ||||     | || | || ||||  ||||| ||||| ||  ||||||| ||||||||| | |  || || |||| ||| |  |||||||||||||||||||| || |||||||| ||||| || || |
gtaatttctttgcagtttttgagacatctgttgaggatctcattgtatatagctagctacaagagaaggctttctgtttatgttttttcattttcttttggccttgttatttgctcttcacagGTCATTGCTAATAGAGCAGCTGAGATTCTTGGTCGCAAACGTGGTGAGAAATGTGTGCACCCAAATGACCATGTGAACAGATCACAATCTTCTAACGACA

upper sequence: GLYMA02G01920.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G50950.3 (Arabidopsis thaliana), 3'ss of exon 2
-tacttgtgataatacatatttatcttcatttt-atattatagatagttcataattgtatttaagacttgagaatccattttcttttttctgatcttttcagGTTATTGCAAACCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGTGGGAAGTTAGTGCACCCAAATGACCATGTCAATAGATCACAGTCTTCAAATGATA
 ||   || |  |   ||    || |  |   | || || |||||| || |  |    |  |  ||  | |  |  ||  |  |||| |  | | ||| ||||| ||||| ||  ||||||| ||||||||| | || || || ||||  ||  | |||||||||||||||||||| || |||||||| ||||| ||||| |
ttaagagttaagactaattacaatgtcaaaaatgattttttagatacttaaccaccagacgtccgaggtaattaaacagatcattttgt--gctttttacagGTCATTGCCAATAGAGCAGCTGAGATTCTTGGTCACAAACGTGGTGAAAAAATTGTGCACCCAAATGACCATGTGAACAGATCACAATCTTCTAATGACA

upper sequence: GLYMA02G01920.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 4
tacttgtgataatacatatttatcttc--attttatattatagatagttcataattgtatttaagacttgagaatccattttcttttttctgatctttt-cagGTTATTGCAAACCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGTGGGAAGTTAGTGCACCCAAATGACCATGTCAATAGATCACAGTCTTCAAATGATA
  |  |   || ||  | |||  || |  | | |||| |    ||  ||  | ||     |||   |||   | |    ||| |||||| | | || |  ||||||||||||||  ||||||| ||||||||| | ||| |||| ||||  || |  ||||| |||||||||||||| || |||||||| ||||| |||||||
--caggatttagtat-tctttgcctacgaactgtatacttgtcatttttggtgatgaatattacttctttttatttggatttattttttatcaactgtggcagGTTATTGCAAATAGAGCAGCTGAGATTCTTGGCCATCAGCGTGGTGAAAAATATGTGCATCCAAATGACCATGTTAACAGATCACAATCTTCTAATGATA

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|19347447|gb|BM892327.1|BM892327
EST:     TTGTATGGCAAACTGGCAGTGGCACTCAAAGTAACATGAATGCTAACGAG                         GTTATTGCAAACCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGT
genomic: TTGTATGGCAAACTGGCAGTGGCACTCAAAGTAACATGAATGCTAACGAGgttaattagt ... atcttttcagGTTATTGCAAACCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGT
EST: gi|151409155|gb|EV278963.1|EV278963
EST:     TTGTATGGCAAACTGGCAGTGGCACTCAAAGTAACATGAATGCTAACGAG                         GTTATTGCAAACCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGTGGGAAG
genomic: TTGTATGGCAAACTGGCAGTGGCACTCAAAGTAACATGAATGCTAACGAGgttaattagt ... atcttttcagGTTATTGCAAACCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGTGGGAAG
EST: gi|192310921|gb|FG998897.1|FG998897
EST:     TTGTATGGCAAACTGGCAGTGGCACTCAAAGTAACATGAATGCTAACGAG                         GTTATTGCAAACCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGTGGGAAG
genomic: TTGTATGGCAAACTGGCAGTGGCACTCAAAGTAACATGAATGCTAACGAGgttaattagt ... atcttttcagGTTATTGCAAACCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGTGGGAAG
EST: gi|298178427|gb|HO024162.1|HO024162
EST:     TTGTATGGCAAACTGGCAGTGGCACTCAAAGTAACATGAATGCTAACGAG                         GTTATTGCAAACCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGTGGGAAG
genomic: TTGTATGGCAAACTGGCAGTGGCACTCAAAGTAACATGAATGCTAACGAGgttaattagt ... atcttttcagGTTATTGCAAACCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGTGGGAAG
EST: gi|192322683|gb|FK015020.1|FK015020
EST:     TTGTATGGCAAACTGGCAGTGGCACTCAAAGTAACATGAATGCTAACGAG                         GTTATTGCAAACCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGTGGGAAG
genomic: TTGTATGGCAAACTGGCAGTGGCACTCAAAGTAACATGAATGCTAACGAGgttaattagt ... atcttttcagGTTATTGCAAACCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGTGGGAAG
EST: gi|192310776|gb|FK000290.1|FK000290
EST:     TTGTATGGCAAACTGGCAGTGGCACTCAAAGTAACATGAATGCTAACGAG                         GTTATTGCAAACCGGGCAGCAGAGATTCTTTGGCATAAGCGGGGTGGGAAG
genomic: TTGTATGGCAAACTGGCAGTGGCACTCAAAGTAACATGAATGCTAACGAGgttaattagt ... atcttttcagGTTATTGCAAACCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGTGGGAAG
EST: gi|16281620|gb|BI944581.1|BI944581
EST:     TTGTATGGCAAACTGGCAGTGGCACTCAAAGTAACATGAATGCTAACGAG                         GTTATTGCAAACCGAGCAGCAGAAATTCTTTGGCATAAGCGGTGTGCGAAG
genomic: TTGTATGGCAAACTGGCAGTGGCACTCAAAGTAACATGAATGCTAACGAGgttaattagt ... atcttttcagGTTATTGCAAACCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGTGGGAAG
EST: gi|209714881|gb|BW682046.1|BW682046
EST:     TTGTATGGCAAACTGGCAGTGGCACTCAAAGTAACATGAATGCTAACGAG                         GTTATTGCAAACCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGTGGGAAG
genomic: TTGTATGGCAAACTGGCAGTGGCACTCAAAGTAACATGAATGCTAACGAGgttaattagt ... atcttttcagGTTATTGCAAACCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGTGGGAAG
EST: gi|209717303|gb|BW659018.1|BW659018
EST:     TTGTATGGCAAACTGGCAGTGGCACTCAAAGTAACATGAATGCTAACGAG                         GTTATTGCAAACCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGTGGGAAG
genomic: TTGTATGGCAAACTGGCAGTGGCACTCAAAGTAACATGAATGCTAACGAGgttaattagt ... atcttttcagGTTATTGCAAACCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGTGGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcataattgtatttaagacttgagaatccattttcttttttctgatcttttcagGTTATTGCAAACCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGTGGGAAGTTAGTGCACCCAAATGACCATGTCAATAGATCACAGTCTTCAAATGATA
                                        ttctgat  putative branch site (score: 3)
                           tccattttcttttttc  CT-rich tract
     aattgtatttaaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacttgtgataatacatatttatcttcattttatattatagatagttcataattgtatttaagacttgagaatccattttcttttttctgatcttttcagGTTATTGCAAACCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGTGGGAAGTTAGTGCACCCAAATGACCATGTCAATAGATCACAGTCTTCAAATGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
-acttgtg
- - - - - - - - - - - -cttcatt