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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctaattcagaagatccaaggtttccaacagctttggtgtcaattttctttttcgtgtttgttcctaatcataatgtagtttgtccgctttacattgtagGGTGTTGGACACAATGATCAGAAAGTTCTTGTTCTAGCAGCTACAAATACACCTTATGCTCTAGACCAG

Basic information

species Glycine max
transcript GLYMA12G09300.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G09300.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g04814.3 (Oryza sativa), 3'ss of exon 3
-cctaattcagaagatccaaggtt--tccaacagctttggtgtcaattttctttttcgtgtttgttcctaatcataatgtagtttgtccgctttacattgtagGGTGTTGGACACAATGATCAGAAAGTTCTTGTTCTAGCAGCTACAAATACACCTTATGCTCTAGACCAG
   ||  | |     |||| ||||  |  |||   || | || |  |||| ||   |    ||  |  ||    |    | ||||  | | |  |  |   |||||||||| || |||||| | ||||| || ||||| || |||||||| || || |||||||||||||||
tgttatctgaagcattccatggtttgttaaactatttagatgccctttttgttacaccaacttact--taccttttgctttgtttcgctggtgaatgtc-cagGGTGTTGGCCATAATGATGACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAG

upper sequence: GLYMA12G09300.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G088834_T01 (Zea mays), 3'ss of exon 3
------cctaattcagaagatccaaggtttccaacagctttggtgtcaattttctttttcgtgtttgttcctaatcataatgtagtttgtccgctttacattgtagGGTGTTGGACACAATGATCAGAAAGTTCTTGTTCTAGCAGCTACAAATACACCTTATGCTCTAGACCAG
        |  || ||| ||      |||| |   | ||  |   || ||    | |||  ||||        || || || |  | ||| |   ||   |   |||||||||| ||||||||| | |||||||||||||| || || || ||||| || |||||||| ||||||
ttctccgtttgtttagaggactt---gttttcttaatctcagcattctatgccttctttgatgttaaactgacatgatcatattttctgtac---ttgattcccagGGTGTTGGTCACAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACGCCATATGCTCTGGACCAG

upper sequence: GLYMA12G09300.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G126860_T01 (Zea mays), 3'ss of exon 3
---------cctaattcagaagatccaaggtttccaacagctttggtgtcaattttctttttcgtgtttgttcctaatcataatgtagtttgtccgctttacattgtagGGTGTTGGACACAATGATCAGAAAGTTCTTGTTCTAGCAGCTACAAATACACCTTATGCTCTAGACCAG
          ||   |   || | |||   ||    | | || |  | | |     | ||||| |||| |   || |  ||||| |  | ||| |    |   |   |||||||||| || |||||| | |||||||||||||| || || || ||||| || |||||||| ||||||
aatacactatctggctaccaata-ccataattaatcagaactgtattctaagc---ccttttcatgttaga--ctgacaataattttttctgtac---ctgattcccagGGTGTTGGTCATAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACGCCATATGCTCTGGACCAG

upper sequence: GLYMA12G09300.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G27600.1 (Arabidopsis thaliana), 3'ss of exon 3
cctaattcagaagatccaaggtttccaacagctttggtgtcaattttctttttcgtgtttgttcctaa----tcataatgtagtttgtccgctttacattgtagGGTGTTGGACACAATGATCAGAAAGTTCTTGTTCTAGCAGCTACAAATACACCTTATGCTCTAGACCAG
                    ||    | |   |  |   | || |   | | |  |  ||||  || |    ||    | |   || ||  ||||   || ||||||||||||||||||||| ||||||| ||||| || ||||| || |||||||| |||||||| || |||
--------------------gtgcatagcttatccgaactaaactccatgtcttttagttgtagctgaaatttccgtctctgacttatct-ctttttcttttagGGTGTTGGACACAATGATGAGAAAGTACTTGTACTTGCAGCAACCAATACACCCTATGCTCTTGATCAG

upper sequence: GLYMA12G09300.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0080g00160.t01 (Vitis vinifera), 3'ss of exon 3
cctaattcagaagatcc-aaggtttccaacagctttggtgtcaattttctttttcgtgtttgttcctaatcataatgtagtttgtccgctttacattgtagGGTGTTGGACACAATGATCAGAAAGTTCTTGTTCTAGCAGCTACAAATACACCTTATGCTCTAGACCAG
   |     ||| ||    |   ||   | || |    | |  | ||  ||    ||      || ||||  | |  | ||    |   |     ||  ||||||| |||||||||||||||||||| |||||||| || || |||||||| |||||||| || || |||
ttgagaagggaaaattttgaaacttttgatagttagattcttcagttctttccctgt-cccagtcttaatgttgagctggtggaccttatcctttttccagGGTGTAGGACACAATGATCAGAAAGTCCTTGTTCTTGCCGCCACAAATACTCCTTATGCCCTGGATCAG

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|51338581|gb|CO982447.1|CO982447
EST:     AGAGTGAAGCTTCAAGGCGTATTAAAACTGAGCTTCTGGTGCAGATGCAG                         GGTGTAGGACACAATGATCAGAAAGTTCTTGTTCTAGCAGCTACAAATACA
genomic: AGAGTGAAGCTTCAAGGCGTATTAAAACTGAGCTTCTGGTGCAGATGCAGgtaatgaatt ... tacattgtagGGTGTTGGACACAATGATCAGAAAGTTCTTGTTCTAGCAGCTACAAATACA
EST: gi|4296956|gb|AI442549.1|AI442549
EST:     AGTGAAGCTTTCAAG-CGTATTAAAACTGAGCCTTCTGGTGCAGATGCAG                         G-TGTTGGACACAATG
genomic: AGTGAAGCTT-CAAGGCGTATTAAAACTGAGC-TTCTGGTGCAGATGCAGgtaatgaatt ... tacattgtagGGTGTTGGACACAATG
EST: gi|193402079|gb|FK370182.1|FK370182
EST:     AGAGTGAAGCTTCAAGGCGTATTAAAACTGAGCTTCTGGTGCAGATGCAG                         GGTGTAGGACACAATGATCAGAAAGTTCTTGTTCTAGCAGCTACAAATACA
genomic: AGAGTGAAGCTTCAAGGCGTATTAAAACTGAGCTTCTGGTGCAGATGCAGgtaatgaatt ... tacattgtagGGTGTTGGACACAATGATCAGAAAGTTCTTGTTCTAGCAGCTACAAATACA
EST: gi|207769070|gb|GD741986.1|GD741986
EST:     AGAGTGAAGCTTCAAGGCGTATTAAAACTGAGCTTCTGGTGCAGATGCAG                         GGTGTAGGACACAATGATCAGAAAGTTCTTGTTCTAGCAGCTACAAATACA
genomic: AGAGTGAAGCTTCAAGGCGTATTAAAACTGAGCTTCTGGTGCAGATGCAGgtaatgaatt ... tacattgtagGGTGTTGGACACAATGATCAGAAAGTTCTTGTTCTAGCAGCTACAAATACA
EST: gi|193656125|gb|FK603591.1|FK603591
EST:     GAGTGAAGCTTCAAGGCGTAATTAAAACTGAGCTTCTGGTGCAGATGCAG                         GGTGTAGGACACAATGATCAGAAAGTTCTTGTTCTAGCAGCTACAAATACA
genomic: GAGTGAAGCTTCAAGGCGT-ATTAAAACTGAGCTTCTGGTGCAGATGCAGgtaatgaatt ... tacattgtagGGTGTTGGACACAATGATCAGAAAGTTCTTGTTCTAGCAGCTACAAATACA
EST: gi|208307913|gb|GE105435.1|GE105435
EST:     AGAGTGAAGCTTCAAGGCGTATTAAAACTGAGCTTCTGGTGCAGATGCAG                         GGTGTAGGACACAATGATCAGAAAGTTCTTGTTCTAGCAGCTACAAATACA
genomic: AGAGTGAAGCTTCAAGGCGTATTAAAACTGAGCTTCTGGTGCAGATGCAGgtaatgaatt ... tacattgtagGGTGTTGGACACAATGATCAGAAAGTTCTTGTTCTAGCAGCTACAAATACA
EST: gi|193360519|gb|FK328117.1|FK328117
EST:     AGAGTGAAGCTTCAAGGCGTATTAAAACTGAGCTTCTGGTGCAGATGCAG                         GGTGTAGGACACAATGATCAGAAAGTTCTTGTTTCTAGCAGCTACAAATAC
genomic: AGAGTGAAGCTTCAAGGCGTATTAAAACTGAGCTTCTGGTGCAGATGCAGgtaatgaatt ... tacattgtagGGTGTTGGACACAATGATCAGAAAGTTCTTG-TTCTAGCAGCTACAAATAC
EST: gi|193598592|gb|FK554632.1|FK554632
EST:     AGAGTGAAGCTTCAAGGCGTATTAAAACTGAGCTTCTGGTGCAGATGCAG                         GGTGTAGGACACAATGATCAGAAAGTTCTTGTTCTAGCAGCTACAAATACA
genomic: AGAGTGAAGCTTCAAGGCGTATTAAAACTGAGCTTCTGGTGCAGATGCAGgtaatgaatt ... tacattgtagGGTGTTGGACACAATGATCAGAAAGTTCTTGTTCTAGCAGCTACAAATACA
EST: gi|193354272|gb|FK319844.1|FK319844
EST:     AGAGTGAAGCTTCAAGGCGTATTAAAACTGAGCTTCTGGTGCAGATGCAG                         GGTGTAGGACACAATGATCAGAAAGTTCTTGTTCTAGCAGCTACAAATACA
genomic: AGAGTGAAGCTTCAAGGCGTATTAAAACTGAGCTTCTGGTGCAGATGCAGgtaatgaatt ... tacattgtagGGTGTTGGACACAATGATCAGAAAGTTCTTGTTCTAGCAGCTACAAATACA
EST: gi|208305898|gb|GE109577.1|GE109577
EST:     AGAGTGAAGCTTCAAGGCGTATTAAAACTGAGCTTCTGGTGCAGATGCAG                         GGTGTAGGACACAATGATCAGAAAGTTCTTGTTCTAGCAGCTACAAATACA
genomic: AGAGTGAAGCTTCAAGGCGTATTAAAACTGAGCTTCTGGTGCAGATGCAGgtaatgaatt ... tacattgtagGGTGTTGGACACAATGATCAGAAAGTTCTTGTTCTAGCAGCTACAAATACA
EST: gi|58014504|gb|CX701246.1|CX701246
EST:     AGAGTGAAGCTTCAAGGCGTATTAAAACTGAGCTTCTGGTGCAGATGCAG                         GGTGTTGGACACAATGATCAGAAAGTTCTTGTTCTAGCAGCTACAAATACA
genomic: AGAGTGAAGCTTCAAGGCGTATTAAAACTGAGCTTCTGGTGCAGATGCAGgtaatgaatt ... tacattgtagGGTGTTGGACACAATGATCAGAAAGTTCTTGTTCTAGCAGCTACAAATACA
EST: gi|208027498|gb|GD826204.1|GD826204
EST:     AGAGTGAAGCTTCAAGGCGTATTAAAACTGAGCTTCTGGTGCAGATGCAG                         GGTGTAGGACACAATGATCAGAAAGTTCTTGTTCTAGCAGCTACAAATACA
genomic: AGAGTGAAGCTTCAAGGCGTATTAAAACTGAGCTTCTGGTGCAGATGCAGgtaatgaatt ... tacattgtagGGTGTTGGACACAATGATCAGAAAGTTCTTGTTCTAGCAGCTACAAATACA
EST: gi|193367132|gb|FK329844.1|FK329844
EST:     AGAGTGAAGCTTCAAGGCGTATTAAAACTGAGCTTCTGGTGCAGATGCAG                         GGTGTAGGACACAATGATCAGAAAGTTCTTGTTCTAGCAGCTACAAATACA
genomic: AGAGTGAAGCTTCAAGGCGTATTAAAACTGAGCTTCTGGTGCAGATGCAGgtaatgaatt ... tacattgtagGGTGTTGGACACAATGATCAGAAAGTTCTTGTTCTAGCAGCTACAAATACA
EST: gi|193532173|gb|FK491909.1|FK491909
EST:     AGAGTGAAGCTTCAAGGCGTATCAAAACTGAGCTTCTGGTGCAGATGCAG                         GGTGTAGGACACAATGATC
genomic: AGAGTGAAGCTTCAAGGCGTATTAAAACTGAGCTTCTGGTGCAGATGCAGgtaatgaatt ... tacattgtagGGTGTTGGACACAATGATC
EST: gi|19346337|gb|BM891217.1|BM891217
EST:     AGAGTGAAGCTTCAAGGCGTATTAAAACTGAGCTTCTGGTGCAGATGCAG                         GGTGTTGGACACAATGATCAGAAAGTTCTTGTTCTAGCAGCTACAAATACA
genomic: AGAGTGAAGCTTCAAGGCGTATTAAAACTGAGCTTCTGGTGCAGATGCAGgtaatgaatt ... tacattgtagGGTGTTGGACACAATGATCAGAAAGTTCTTGTTCTAGCAGCTACAAATACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttttcgtgtttgttcctaatcataatgtagtttgtccgctttacattgtagGGTGTTGGACACAATGATCAGAAAGTTCTTGTTCTAGCAGCTACAAATACACCTTATGCTCTAGACCAG
                 tcctaat  putative branch site (score: 2)
                                      tccgcttt  putative PPT
                    taatcataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctaattcagaagatccaaggtttccaacagctttggtgtcaattttctttttcgtgtttgttcctaatcataatgtagtttgtccgctttacattgtagGGTGTTGGACACAATGATCAGAAAGTTCTTGTTCTAGCAGCTACAAATACACCTTATGCTCTAGACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - -tccaaca
- - - - - - - - - - - - - - - - - tggtgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgtag