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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcaacattcattttttcacttcttctacttccactgcaacattttctatgtttaggtattttggtcgtagatttcgattttgattattattccatcctctttcaattgatcaatggttgttttgatgcagGTGAACATGGAGTATGGTCTTGATCCCGCCGTTGGAAAAGCGATTATGCAAGCGGCACAAGAAGTGGCCGAGGGAAAACTAAACGACCATTTTCCTCTCG

Basic information

species Glycine max
transcript GLYMA02G01920.1
intron # 2
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 2
lower sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 3
gtcaacattcattttttcacttcttctacttccactgcaacattttctatgtttaggtattttggtcgtagatttcgattttgattattattccatcctctttcaattgatcaatggttgttttgatgcagGTGAACATGGAGTATGGTCTTGATCCCGCCGTTGGAAAAGCGATTATGCAAGCGGCACAAGAAGTGGCCGAGGGAAAACTAAACGACCATTTTCCTCTCG
                     |  |  | ||    || ||||| |||  |        |||||  |  | |  |  |   ||| ||  | |   ||   || |||||||        || || |  || |||| |||||||| ||||||||||||||  || | || ||||| || |||||||| || ||||||||| | |||||||||||||| || |||||||| ||||
----------------atgtatagttgatttt---tgtaacatcttcatta------cattttcatactggtctgagtaattggttgatgtaagatttactctcaattg------cattattctattgtagGTCAACATGGAATATGGTCTTGATCCATCCATAGGCAAAGCAATAATGCAAGCAGCCCAAGAAGTGTCAGAGGGAAAACTAAATGATCATTTTCCGCTCG
















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|15589604|gb|BI674220.1|BI674220
EST:     GAACCCAGGGAGGTCGCGCCTTTGGCGTCTTGAAGAAATGCGCTGCTAAG                         GTGAACATGGAGTATGGTCTTGATCCCGCCGTTGGAAAAGCGATTATGCAA
genomic: GAACCCATC-AT-TCGCGCCTTTGGCGTCTTGAAGAAATGCGCTGCTAAGgtcaacattc ... tttgatgcagGTGAACATGGAGTATGGTCTTGATCCCGCCGTTGGAAAAGCGATTATGCAA
EST: gi|19347447|gb|BM892327.1|BM892327
EST:     CCGAACCCATCATTCGCGCCTTTGGCGTCTTGAAGAAATGCGCTGCTAAG                         GTGAACATGGAGTATGGTCTTGATCCCGCCGTTGGAAAAGCGATTATGCAA
genomic: CCGAACCCATCATTCGCGCCTTTGGCGTCTTGAAGAAATGCGCTGCTAAGgtcaacattc ... tttgatgcagGTGAACATGGAGTATGGTCTTGATCCCGCCGTTGGAAAAGCGATTATGCAA
EST: gi|192310921|gb|FG998897.1|FG998897
EST:     CCGAACCCATCATTCGCGCCTTTGGCGTCTTGAAGAAATGCGCTGCTAAG                         GTGAACATGGAGTATGGTCTTGATCCCGCCGTTGGAAAAGCGATTATGCAA
genomic: CCGAACCCATCATTCGCGCCTTTGGCGTCTTGAAGAAATGCGCTGCTAAGgtcaacattc ... tttgatgcagGTGAACATGGAGTATGGTCTTGATCCCGCCGTTGGAAAAGCGATTATGCAA
EST: gi|298178427|gb|HO024162.1|HO024162
EST:     CCGAACCCATCATTCGCGCCTTTGGCGTCTTGAAGAAATGCGCTGCTAAG                         GTGAACATGGAGTATGGTCTTGATCCCGCCGTTGGAAAAGCGATTATGCAA
genomic: CCGAACCCATCATTCGCGCCTTTGGCGTCTTGAAGAAATGCGCTGCTAAGgtcaacattc ... tttgatgcagGTGAACATGGAGTATGGTCTTGATCCCGCCGTTGGAAAAGCGATTATGCAA
EST: gi|192322683|gb|FK015020.1|FK015020
EST:     CCGAACCCATCATTCGCGCCTTTGGCGTCTTGAAGAAATGCGCTGCTAAG                         GTGAACATGGAGTATGGTCTTGATCCCGCCGTTGGAAAAGCGATTATGCAA
genomic: CCGAACCCATCATTCGCGCCTTTGGCGTCTTGAAGAAATGCGCTGCTAAGgtcaacattc ... tttgatgcagGTGAACATGGAGTATGGTCTTGATCCCGCCGTTGGAAAAGCGATTATGCAA
EST: gi|192310776|gb|FK000290.1|FK000290
EST:     CCGAACCCATCATTCGCGCCTTTGGCGTCTTGAAGAAATGCGCTGCTAAG                         GTGAACATGGAGTATGGTCTTGATCCCGCCGTTGGAAAAGCGATTATGCAA
genomic: CCGAACCCATCATTCGCGCCTTTGGCGTCTTGAAGAAATGCGCTGCTAAGgtcaacattc ... tttgatgcagGTGAACATGGAGTATGGTCTTGATCCCGCCGTTGGAAAAGCGATTATGCAA
EST: gi|16281620|gb|BI944581.1|BI944581
EST:     CCGAACCCATCATTCGCGCCTTTGGCGTCTTGAAGAAATGCGCTGCTAAG                         GTGAACATGGAGTATGGTCTTGATCCCGCCGTTGGAAAAGCGATTATGCAA
genomic: CCGAACCCATCATTCGCGCCTTTGGCGTCTTGAAGAAATGCGCTGCTAAGgtcaacattc ... tttgatgcagGTGAACATGGAGTATGGTCTTGATCCCGCCGTTGGAAAAGCGATTATGCAA
EST: gi|209714881|gb|BW682046.1|BW682046
EST:     CCGAACCCATCATTCGCGCCTTTGGCGTCTTGAAGAAATGCGCTGCTAAG                         GTGAACATGGAGTATGGTCTTGATCCCGCCGTTGGAAAAGCGATTATGCAA
genomic: CCGAACCCATCATTCGCGCCTTTGGCGTCTTGAAGAAATGCGCTGCTAAGgtcaacattc ... tttgatgcagGTGAACATGGAGTATGGTCTTGATCCCGCCGTTGGAAAAGCGATTATGCAA
EST: gi|209717303|gb|BW659018.1|BW659018
EST:     CCGAACCCATCATTCGCGCCTTTGGCGTCTTGAAGAAATGCGCTGCTAAG                         GTGAACATGGAGTATGGTCTTGATCCCGCCGTTGGAAAAGCGATTATGCAA
genomic: CCGAACCCATCATTCGCGCCTTTGGCGTCTTGAAGAAATGCGCTGCTAAGgtcaacattc ... tttgatgcagGTGAACATGGAGTATGGTCTTGATCCCGCCGTTGGAAAAGCGATTATGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattttgattattattccatcctctttcaattgatcaatggttgttttgatgcagGTGAACATGGAGTATGGTCTTGATCCCGCCGTTGGAAAAGCGATTATGCAAGCGGCACAAGAAGTGGCCGAGGGAAAACTAAACGACCATTTTCCTCTCG
                                            ttttgat  putative branch site (score: 4)
                                         ttgtttt  CT-rich tract
     tgattattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaacattcattttttcacttcttctacttccactgcaacattttctatgtttaggtattttggtcgtagatttcgattttgattattattccatcctctttcaattgatcaatggttgttttgatgcagGTGAACATGGAGTATGGTCTTGATCCCGCCGTTGGAAAAGCGATTATGCAAGCGGCACAAGAAGTGGCCGAGGGAAAACTAAACGACCATTTTCCTCTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT