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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcgagtaatcatggtatgggaggagtttgatttgtattactgctcatcaaactagtgtttgatcttgtagcattctaaacttcttccttctgcttgcagTGTTTAACTTGGAGAAAACATTCAAAACAACATTCTCTTTACTTGTGCTTCATATGTGGTTCTGTTTGCGTCGCTTGAAGCAAGAGGGAAAGGAGGGTGT

Basic information

species Glycine max
transcript GLYMA15G06170.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G06170.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os07g30790.1 (Oryza sativa), 3'ss of exon 2
-atcga--gtaatcatggtatgggaggagtttgatttgtattactgctcatcaaactagtgtttgatcttgtagca-ttctaaacttcttccttctgcttgcagTGTTTAACTTGGAGAAAACATTCAAAACAACATTCTCTTTACTTGTGCTTCATATGTGGTTCTGTTTGCGTCGCTTGAAGCAAGAGGGAAAGGAGGGTGT
 ||  |  | |  | || | ||| |   ||||| ||  | |   |  |  |     ||   | |  |      ||| ||    || | ||||||    || |||| ||| | |||||||||||||| ||||||||||| || |||||||| || ||||||||| |   | | |||||||||||  |||| || ||||| |||||
cattaactgcatacctgttttggtaactgtttgtttcatttccatctttttatgcttaagatatactgggtcggcaatttctgacattttcctt----ttacagTTTTTCAGTTGGAGAAAACATTTAAAACAACATTTTCATTACTTGTTCTCCATATGTGGCTTATTCTACGTCGCTTGAAAGAAGAAGGGAAGGATGGTGT

upper sequence: GLYMA15G06170.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G51220.1 (Arabidopsis thaliana), 3'ss of exon 2
atcgagtaatcatggtatgggaggagtttgatttgtattactgctcatcaaactagtgtttgatcttgtagcattctaaacttcttccttctgcttgcagTGTTTAACTTGGAGAAAACATTCAAAACAACATTCTCTTTACTTGTGCTTCATATGTGGTTCTGTTTGCGTCGCTTGAAGCAAGAGGGAAAGGAGGGTGT
 |    || |     |     |  | |||       |    |    ||  |   | | | || | |  |   ||           |   |||||| ||||| || |||||||||||||||||||||| ||| |  ||  | ||||| |||||||||||| |   ||| || ||||||||| |||| ||| |||| |||||
gtactttatttggtttccaacacaacttttgcaaacagagttatgtattta--cattttgtgctttgtttatatatcgggtgctctgtctctgct-gcagTATTCAACTTGGAGAAAACATTCAAAATAACGTATTCGCTGCTTGTCCTTCATATGTGGCTTGTTTTACGCCGCTTGAAGGAAGATGGACAGGAAGGTGT

upper sequence: GLYMA15G06170.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0013g01540.t01 (Vitis vinifera), 3'ss of exon 4
atcgagtaatcatggtatgggaggagtttgatttgtattactgctcatcaaactagtgtttgatct-tgtagcattctaa------acttcttccttctgcttgcagTGTTTAACTTGGAGAAAACATTCAAAACAACATTCTCTTTACTTGTGCTTCATATGTGGTTCTGTTTGCGTCGCTTGAAGCAAGAGGGAAAGGAGGGTGT
       ||  |||      | |   | | ||||    | |||||   ||  || |  ||  |||| | ||    |||||      | |   |  ||     |||||  ||||||||||||||||| || ||||||||||| ||| | ||| | |||||||||||| | || || || ||||||||  |||| |||||||| |||||
-------aacaatgtagatagtgatttgttattttacatgctgctttccatgctggctttgaatctctatattggtctaatgtaaaattatattatttcatatgcagCATTTAACTTGGAGAAAACCTTTAAAACAACATTTTCTCTGCTTATACTTCATATGTGGCTTTGCTTACGCCGCTTGAAAGAAGATGGAAAGGAAGGTGT

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|13478132|gb|BG507737.1|BG507737
EST:     TGTGTACCAAAGAATCATTTCTCAAGTTGATAAACCTCCCATTTATGAAG                         TGTTTAACTTGGAGAAAACATTCAAAACAACATTCTCTTTACTTGTGCTTC
genomic: TGTGTACCAAAGAATCATTTCTCAAGTTGATAAACCTCCCATTTATGAAGgtccattctg ... ctgcttgcagTGTTTAACTTGGAGAAAACATTCAAAACAACATTCTCTTTACTTGTGCTTC
EST: gi|151408835|gb|EV278643.1|EV278643
EST:     TGTGTACCAAAGAATCATTTCTCAAGTTGATAAACCTCCCATTTATGAAG                         TGTTTAACTTGGAGAAAACATTCAAAACAACATTCTCTTTACTTGTGCTTC
genomic: TGTGTACCAAAGAATCATTTCTCAAGTTGATAAACCTCCCATTTATGAAGgtccattctg ... ctgcttgcagTGTTTAACTTGGAGAAAACATTCAAAACAACATTCTCTTTACTTGTGCTTC
EST: gi|19054294|gb|BM732961.1|BM732961
EST:     TGTGTACCAAAGAATCATTTCTCAAGTTGATAAACCTCCCATTTATGAAG                         TGTTTAACTTGGAGAAAACATTCAAAACAACATTCTCTTTACTTGTGCTTC
genomic: TGTGTACCAAAGAATCATTTCTCAAGTTGATAAACCTCCCATTTATGAAGgtccattctg ... ctgcttgcagTGTTTAACTTGGAGAAAACATTCAAAACAACATTCTCTTTACTTGTGCTTC
EST: gi|193489286|gb|FK457193.1|FK457193
EST:     TGTGTACCAAAGAATCATTTCTCAAGTTGATAAACCTCCCATTTATGAAG                         TGTTTAACTTGGAGAAAACATTCAAAACAACATTCTCTTTACTTGTGCTTC
genomic: TGTGTACCAAAGAATCATTTCTCAAGTTGATAAACCTCCCATTTATGAAGgtccattctg ... ctgcttgcagTGTTTAACTTGGAGAAAACATTCAAAACAACATTCTCTTTACTTGTGCTTC
EST: gi|5606611|gb|AI900709.1|AI900709
EST:     TGTGTACCAAAGAATCATTTCTCAAGTTGATAAACCTCCCATTTATGAAG                         TGTTTAACTTGGAGAAAACATTCAAAACAACATTCTCTTTACTTGTGCTTC
genomic: TGTGTACCAAAGAATCATTTCTCAAGTTGATAAACCTCCCATTTATGAAGgtccattctg ... ctgcttgcagTGTTTAACTTGGAGAAAACATTCAAAACAACATTCTCTTTACTTGTGCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcaaactagtgtttgatcttgtagcattctaaacttcttccttctgcttgcagTGTTTAACTTGGAGAAAACATTCAAAACAACATTCTCTTTACTTGTGCTTCATATGTGGTTCTGTTTGCGTCGCTTGAAGCAAGAGGGAAAGGAGGGTGT
                            ttctaaa  putative branch site (score: 2)
                                   cttcttccttctgctt  CT-rich tract
                           attctaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcgagtaatcatggtatgggaggagtttgatttgtattactgctcatcaaactagtgtttgatcttgtagcattctaaacttcttccttctgcttgcagTGTTTAACTTGGAGAAAACATTCAAAACAACATTCTCTTTACTTGTGCTTCATATGTGGTTCTGTTTGCGTCGCTTGAAGCAAGAGGGAAAGGAGGGTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - tggtatg
- - - - - - - - - -ggaggag
- - - - - - - - - - - - - - tgatttg
- - - - - - - - - - - - - - - - - - - - ctgctca
- - - - - - - - - - - - - - - - - - - - - - - -tcaaact
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcattct