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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggctagattatgaaaatattgaaatagatatcaaaactatctgtctcaatgttgttgtttaccaaaggtttaattatgtacttcttaattttagGACATAAAAGCAAAGGAGAAGGAACTTCAAGCTAAAGAGGCTGAATTGAAAAGAAGGGAACAG

Basic information

species Glycine max
transcript GLYMA12G11820.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G11820.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0157g00150.t01 (Vitis vinifera), 3'ss of exon 2
gtaggctagattatgaaaatattgaaatagatatcaaaactatctgtctcaatgttgttgtttac--caaaggtttaattatgtacttcttaattttagGACATAAAAGCAAAGGAGAAGGAACTTCAAGCTAAAGAGGCTGAATTGAAAAGAAGGGAACAG------------------------------
||||   | |||    || |  |  | || || |    |         ||  ||      |  |   |||   |||| || |       | || ||||||||| ||| |||||||||| ||||||||| || |||||||||||| ||||||  || |||||                               
gtagatcaaatttgacaagttctatattacattttgttatctgtacattctgtgcaagcatgcatttcaagtttttagttcttctgcattcaactttagGACACAAAGGCAAAGGAGAGGGAACTTCAGGCCAAAGAGGCTGAACTGAAAAAGAGAGAACATGTACTTCAATCATCCTATGTCATATGGTAG

upper sequence: GLYMA12G11820.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 2
--------------------------------------------------------gtaggctagattatgaaaa-tattgaaatagatatcaaaactatctgtctcaatgttgt---------tgtttaccaaaggtttaattatgtacttcttaattttagGACATAAAAGCAAAGGAGAAGGAACTTCAAGCTAAAGAGGCTGAATTGAAAAGAAGGGAACAG
                                                          | || | |  |  |||| | || |  ||  ||| | |  |   | |||  |  ||           ||  |  |||   |||| || | |   | | |||| ||||||| ||| |||||||||| ||||||||| || |||||||||||| ||||||  || ||||||
gtagatcaaagttgacaaagatgtttcttatttatttatttatatttaaaaaaatgaaaagcgaaagaaaaaaaaatgttaagttatgtattacattttgttatctgtacattccgtgcaagcatgcatttcaagtttttagttcttttgctttcaattgtagGACACAAAGGCAAAGGAGAGGGAACTTCAGGCCAAAGAGGCTGAACTGAAAAAGAGAGAACAG
















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|26045882|gb|CA783314.1|CA783314
EST:     AGCCTTACGATCGTGGGGCAACTATTGACATCCCCCTTGATAATGCAAAG                         GACATAAAAGCAAAGGAGAAGGAACTTCAAGCTAAAGAGGCTGAATTGAAA
genomic: AGCCTTACGATCGTGGGGCAACTATTGACATCCCCCTTGATAATGCAAAGgtaggctaga ... ttaattttagGACATAAAAGCAAAGGAGAAGGAACTTCAAGCTAAAGAGGCTGAATTGAAA
EST: gi|213599371|gb|DB970347.1|DB970347
EST:     AGCCTTACGATCGTGGGGCAACTATTGACATCCCCCTTGATAATGCAAAG                         GACATAAAAGCAAAGGAGAAGGAACTTCAAGCTAAAGAGGCTGAATTGAAA
genomic: AGCCTTACGATCGTGGGGCAACTATTGACATCCCCCTTGATAATGCAAAGgtaggctaga ... ttaattttagGACATAAAAGCAAAGGAGAAGGAACTTCAAGCTAAAGAGGCTGAATTGAAA
EST: gi|298174331|gb|HO017667.1|HO017667
EST:     AGCCTTACGATCGTGGGGCAACTATTGACATCCCCCTTGATAATGCAAAG                         GACATAAAAGCAAAGGAGAAGGAACTTCAAGCTAAAGAGGCTGAATTGAAA
genomic: AGCCTTACGATCGTGGGGCAACTATTGACATCCCCCTTGATAATGCAAAGgtaggctaga ... ttaattttagGACATAAAAGCAAAGGAGAAGGAACTTCAAGCTAAAGAGGCTGAATTGAAA
EST: gi|15813443|gb|BI785718.1|BI785718
EST:     AGCCTTACGATCGTGGGGCAACTATTGACATCCCCCTTGATAATGCAAAG                         GACATAAAAGCAAAGGAGAAGGAACTTCAAGCTAAAGAGGCTGAATTGAAA
genomic: AGCCTTACGATCGTGGGGCAACTATTGACATCCCCCTTGATAATGCAAAGgtaggctaga ... ttaattttagGACATAAAAGCAAAGGAGAAGGAACTTCAAGCTAAAGAGGCTGAATTGAAA
EST: gi|7924737|gb|AW830763.1|AW830763
EST:     AGCCTTACGATCGTGGGGCAACTATTGACATCCCCCTTGATAATGCAAAG                         GACATAAAAGCAA
genomic: AGCCTTACGATCGTGGGGCAACTATTGACATCCCCCTTGATAATGCAAAGgtaggctaga ... ttaattttagGACATAAAAGCAA
EST: gi|13787288|gb|BG649880.1|BG649880
EST:     AGCCTTACGATCGTGGGGCAACTATTGACATCCCCCTTGATAATGCAAAG                         GACATAAAAGCAAAGGAGAAGGAACTTCAAGCTAAAGAGGCTGAATTGAAA
genomic: AGCCTTACGATCGTGGGGCAACTATTGACATCCCCCTTGATAATGCAAAGgtaggctaga ... ttaattttagGACATAAAAGCAAAGGAGAAGGAACTTCAAGCTAAAGAGGCTGAATTGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtctcaatgttgttgtttaccaaaggtttaattatgtacttcttaattttagGACATAAAAGCAAAGGAGAAGGAACTTCAAGCTAAAGAGGCTGAATTGAAAAGAAGGGAACAG
                                           tcttaat  putative branch site (score: 3)
                                       tacttctt  CT-rich tract
                             tttaattatgtacttc  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggctagattatgaaaatattgaaatagatatcaaaactatctgtctcaatgttgttgtttaccaaaggtttaattatgtacttcttaattttagGACATAAAAGCAAAGGAGAAGGAACTTCAAGCTAAAGAGGCTGAATTGAAAAGAAGGGAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG