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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cccattagaggctaaaatagattgtggtctatatggtggttaactggttaagtttctgtttgctgaatttgctactttgtctctctgttatgttttatagGCTAGTCTTCCTGTTATCACAAACAATGTCTGACGGTCAAGAATCAGACAAGAATATTGAGATATGGAAGATCAAGAAATTGATAAAGGCATTGGAAGCT

Basic information

species Glycine max
transcript GLYMA16G26600.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G26600.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g12240.t01 (Vitis vinifera), 3'ss of exon 2
---cccattagaggctaaaatagattgtggtctata---tggtggttaactggttaagtttctgtttgctgaatttgctac-tttgtctctctgttat-gttttatagGCTAGTCTTC-CTGTTATCACAA-----ACAATGTCTGACGGTCAAGAATCAGACAAGAATATTGAGATATGGAAGATCAAGAAATTGATAAAGGCATTGGAAGCT
     | ||      ||||  |   ||     | ||   |  |  |   |||   |   |     |  | |||||| | |  ||| | | |   ||   | |  ||  | |||  | | | ||||  ||       |||||| | || ||||| ||| |||| ||||| |||||||||||||||||||| || ||||| |              
tcatgcctttttttttaaaggaatctgcaccttttagttttcttttctcctgtgcataatcaaactcccagaattttcaaagtttattttttctttgcagGTAAATCAGTTAGCTTCCACAGTTAGTACCGTACTTACAATGGCAGATGGTCATGAAACAGATAAGAACATTGAGATATGGAAGATCAAAAAGTTGATCA--------------

upper sequence: GLYMA16G26600.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0041g00730.t01 (Vitis vinifera), 3'ss of exon 1
----cccattagaggctaaaatagattgtggtctatatggtggttaactggttaagtttctgtttgctgaatttgc-----tactttgtc-tctctgtt----atgttttatagGCTAGTCTTCCTGT--TATCACAAACAATGTCTGACGGTCAAGAATCAGACAAGAATATTGAGATATGGAAGATCAAGAAATTGATAAAGGCATTGGAAGCT
    | |||   ||| ||  |   |   |  |   | |  |  ||   |  |  |  | ||   | | |||||||      || | || | ||| ||      || ||   ||   |  ||   ||||  |||     |||||| |||| ||||| ||| |||| ||||| ||||||||||||||||||||||| |||||                
tcacctcatatcaggatattaagcaccatttttagttttattttttcattatggaactactagattcagaatttgagtttatattctgccatctttgcagGCAATTTTCATTAATTTCCTCAGTCTGTACTATATTGCACAATGGCTGATGGTCATGAAACAGATAAGAACATTGAGATATGGAAGATCAAGAAGTTGAT----------------
















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|193695102|gb|FK631268.1|FK631268
EST:     TTCAGTTTTCGCCCTCTTTTCTCATCTCCAACATCTTCGTCGTCACGGAG                         GCTAGTCTTCCTGTTATCACAAACAATGTCTGACGGTCAAGAATCAGACAA
genomic: TTCAGTTTTCGCCCTCTTTTCTCATCTCCAACATCTTCGTCGTCACGGAGgtacggtccc ... tgttttatagGCTAGTCTTCCTGTTATCACAAACAATGTCTGACGGTCAAGAATCAGACAA
EST: gi|8283523|gb|BE021082.1|BE021082
EST:     TTCAGTTTTCGCCCTCTTTTCTCATCTCCAACATCTTCGTCGTCACGGAG                         GCTAGTCTTCCTGTTATCACAAACAATGTCTGACGGTCAAGAATCAGACAA
genomic: TTCAGTTTTCGCCCTCTTTTCTCATCTCCAACATCTTCGTCGTCACGGAGgtacggtccc ... tgttttatagGCTAGTCTTCCTGTTATCACAAACAATGTCTGACGGTCAAGAATCAGACAA
EST: gi|18040129|gb|BM308423.1|BM308423
EST:     GTTTTCGCCCTCTTTTCTCATCTCCAACATCTTCGTCGTCACGGAG                         GCTAGTCTTCCTGTTATCACAAACAATGTCTGACGGTCAAGAATCAGACAA
genomic: GTTTTCGCCCTCTTTTCTCATCTCCAACATCTTCGTCGTCACGGAGgtacggtccc ... tgttttatagGCTAGTCTTCCTGTTATCACAAACAATGTCTGACGGTCAAGAATCAGACAA
EST: gi|208026699|gb|GD826749.1|GD826749
EST:     TTCAGTTTTCGCCCTCTTTTCTCATCTCCAACATCTTCGTCGTCACGGAG                         GCTAGTCTTCCTGTTATCACAAACAATGTCTGACGGTCAAGAATCAGACAA
genomic: TTCAGTTTTCGCCCTCTTTTCTCATCTCCAACATCTTCGTCGTCACGGAGgtacggtccc ... tgttttatagGCTAGTCTTCCTGTTATCACAAACAATGTCTGACGGTCAAGAATCAGACAA
EST: gi|13125768|gb|BG316338.1|BG316338
EST:     TTCAGTTTTCGCCCTCTTTTCTCATCTCCAACATCTTCGTCGTCACGGAG                         GCTAGTCTTCCTGTTATCACAAACAATGTCTGACGGTCAAGAATCAGACAA
genomic: TTCAGTTTTCGCCCTCTTTTCTCATCTCCAACATCTTCGTCGTCACGGAGgtacggtccc ... tgttttatagGCTAGTCTTCCTGTTATCACAAACAATGTCTGACGGTCAAGAATCAGACAA
EST: gi|193597931|gb|FK549253.1|FK549253
EST:     TCTTCGTCGTCACGGAG                         GCTAGTCTTCCTGTTATCACAAACAATGTCTGACGGTCAAGAATCAGACAA
genomic: TCTTCGTCGTCACGGAGgtacggtccc ... tgttttatagGCTAGTCTTCCTGTTATCACAAACAATGTCTGACGGTCAAGAATCAGACAA
EST: gi|8283475|gb|BE021034.1|BE021034
EST:     TTTCGCCCTCTTTTCTCATCTCCAACATCTTCGTCGTCACGGAG                         GCTAGTCTTCCTGTTATCACAAACAATGTCTGACGGTCAAGAATCAGACAA
genomic: TTTCGCCCTCTTTTCTCATCTCCAACATCTTCGTCGTCACGGAGgtacggtccc ... tgttttatagGCTAGTCTTCCTGTTATCACAAACAATGTCTGACGGTCAAGAATCAGACAA
EST: gi|213591320|gb|DB973809.1|DB973809
EST:     TTCAGTTTTCGCCCTCTTTTCTCATCTCCAACATCTTCGTCGTCACGGAG                         GCTAGTCTTCCTGTTATCACAAACAATGTCTGACGGTCAAGAATCAGACAA
genomic: TTCAGTTTTCGCCCTCTTTTCTCATCTCCAACATCTTCGTCGTCACGGAGgtacggtccc ... tgttttatagGCTAGTCTTCCTGTTATCACAAACAATGTCTGACGGTCAAGAATCAGACAA
EST: gi|208250832|gb|GE047799.1|GE047799
EST:     TTCAGTTTTCGCCCTCTTTTCTCATCTCCAACATCTTCGTCGTCACGGAG                         GCTAGTCTTCCTGTTATCACAAACAATGTCTGACGGTCAAGAATCAGACAA
genomic: TTCAGTTTTCGCCCTCTTTTCTCATCTCCAACATCTTCGTCGTCACGGAGgtacggtccc ... tgttttatagGCTAGTCTTCCTGTTATCACAAACAATGTCTGACGGTCAAGAATCAGACAA
EST: gi|151408431|gb|EV278239.1|EV278239
EST:     TTCAGTTTTCGCCCTCTTTTCTCATCTCCAACATCTTCGTCGTCACGGAG                         GCTAGTCTTCCTGTTATCACAAACAATGTCTGACGGTCAAGAATCAGACAA
genomic: TTCAGTTTTCGCCCTCTTTTCTCATCTCCAACATCTTCGTCGTCACGGAGgtacggtccc ... tgttttatagGCTAGTCTTCCTGTTATCACAAACAATGTCTGACGGTCAAGAATCAGACAA
EST: gi|193311561|gb|FK277277.1|FK277277
EST:     TTCGGTTTTCGCCCTCTTTTCTCATCTCCAACATCTTCGTCGTCACGGAG                         GCTAGTCTTCCTGTTATCACAAACAATGTCTGACGGTCAAGAATCAGACAA
genomic: TTCAGTTTTCGCCCTCTTTTCTCATCTCCAACATCTTCGTCGTCACGGAGgtacggtccc ... tgttttatagGCTAGTCTTCCTGTTATCACAAACAATGTCTGACGGTCAAGAATCAGACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttaagtttctgtttgctgaatttgctactttgtctctctgttatgttttatagGCTAGTCTTCCTGTTATCACAAACAATGTCTGACGGTCAAGAATCAGACAAGAATATTGAGATATGGAAGATCAAGAAATTGATAAAGGCATTGGAAGCT
                                        tgttatgttttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cccattagaggctaaaatagattgtggtctatatggtggttaactggttaagtttctgtttgctgaatttgctactttgtctctctgttatgttttatagGCTAGTCTTCCTGTTATCACAAACAATGTCTGACGGTCAAGAATCAGACAAGAATATTGAGATATGGAAGATCAAGAAATTGATAAAGGCATTGGAAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - -gattgtg
- - - - - - - - - - - - - - - - -tggtggt
- - - - - - - - - - - - - - - - - - - - - actggtt
- - - - - - - - - - - - - - - - - - - - - - - - - -gtttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgaa