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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttacatgatattcttttgagtatttaaaaaatctaatgttgatactttacttacatttctgtttattaaattctcaaaacaagttatcgcttatcaggttttctcgaattgtatcatcagATAATAAGACCTGTCCGATCTAAGCATTGCCCAACTTGTAAGCGATGTGTGGAACAGTTCGACCACCACTGTCCATGGATATCTAACTGTGTTGGGAAG

Basic information

species Glycine max
transcript GLYMA07G30380.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G30380.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os11g34860.1 (Oryza sativa), 3'ss of exon 9
---------------------------------------------------gtttacatgatattcttttgagtatttaaaaaatctaatgttgatactttacttacatttctgtttattaaattctcaaaacaagtt---atcgcttatcaggttttctcgaattgtatcatcagATAATAAGACCTGTCCGATCTAAGCATTGCCCAACTTGTAAGCGATGTGTGGAACAGTTCGACCACCACTGTCCATGGATATCTAACTGTGTTGGGAAG
                                                    ||    | ||||| || ||  | | |  | | |  ||||   |||  |   |   || | | ||| ||    |    |   | ||    |   |  || |  | || |     ||  | | ||||||||  | ||  | || || || ||||| |||||||||||||  ||||| || ||||| ||||| |||||||| |||||||| || |||||||| | |
gtattgtaagaacctattttatttttattctttttaattccaaattccttttttcctttcatatttttgtgtatttcttcatactgaaatgaccatatctgcatatgatatttatttttttctattcttatgtatgtcagaaataccaattacatcttttttttgtgacttaccagATAATTCGCCCAATGCGCTCCAAACATTGTCCAACTTGTAAGCACTGTGTTGAGCAGTTTGACCATCACTGTCCTTGGATATCAAATTGTGTTGGAAGG

upper sequence: GLYMA07G30380.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G14255.1 (Arabidopsis thaliana), 3'ss of exon 9
gtttacatgatattcttttgagtatttaaaaaatctaatgttgatactttacttacatttctgtttattaaattctcaaaacaagttatcgcttatcaggttttctcga--attgtatcatcagATAATAAGACCTGTCCGATCTAAGCATTGCCCAACTTGTAAGCGATGTGTGGAACAGTTCGACCACCACTGTCCATGGATATCTAACTGTGTTGGGAAG
                                               ||| || |    |   || |    |||  |   | |  || |   || ||    |      |  ||| | || ||||||||| ||||| || ||||||||||| ||||| ||||||||||| || || |||||||| ||||| ||||| || ||||| || ||||||||||| |||
---------------------------------------------gttttcctcaatccttatttcaggggattacctcgatattttctttgttttctaactacaattatcattttttcttcagATAATTAGACCGGTGCGATCTAAGCACTGCCCCACTTGTAAGCGCTGCGTTGAACAGTTTGACCATCACTGCCCCTGGATTTCCAACTGTGTTGGTAAG

upper sequence: GLYMA07G30380.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv03s0088g01260.t01 (Vitis vinifera), 3'ss of exon 9
gtttacatgatattcttttgagtatttaaaaaatctaatgttgatactttacttacatttctgtttattaaattctcaaaacaagttatcgcttatcaggttttctcgaattgtatcatcagATAATAAGACCTGTCCGATCTAAGCATTGCCCAACTTGTAAGCGATGTGTGGAACAGTTCGACCACCACTGTCCATGGATATCTAACTGTGTTGGGAAG
             | || | |||      ||  | |  | |  | |    |  | ||||  || ||   | | | ||  ||  || | | |  |  ||   |   ||   || | |  ||||||||| |||||||| || || ||||| ||||| || |||||||| ||||||||||| || ||||||||||| || ||||| || || ||||| ||||||
------------gttttctcagtg-----aactttttctttcaaaagaacagatgcattaatgcttgaaatactgtcctaaacagatttggtgtg-cattctcaatcttgtt-tcttttcagATAATTAGACCTGTTCGCTCAAAGCACTGCCCTACATGTAAGCGCTGTGTGGAACAATTTGACCACCACTGCCCTTGGATTTCAAATTGTGTAGGGAAG

upper sequence: GLYMA07G30380.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ29308 (Selaginella moellendorffii), 3'ss of exon 3
gtttacatgatattcttttgagtatttaaaaaatctaatgttgatactttacttacatttctgtttattaaattctcaaaacaagttatcgcttatcaggttttctcgaattgtatcatcagATAATAAGACCTGTCCGATCTAAGCATTGCCCAACTTGTAAGCGATGTGTGGAACAGTTCGACCACCACTGTCCATGGATATCTAACTGTGTTGGGAAG
                                                              ||  | ||| || |         | |||  |||   | | |   | |||| |     |||||| | || |||||  |||| ||||| ||  | | ||| || || ||||| || |||||||| ||||| ||||| |||||||| |||||||||||||||
--------------------------------------------------------------gtagactaatttttg-----ctttcatcttttagtcgttgtgagcaaatttttattgcagATAGTGAGGCCTGTAAGATCCAAGCACTGTTCGATTTGCAACCGCTGTGTAGAGCAGTTCGATCACCATTGTCCTTGGATATCAAACTGTGTTGGGAAG

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|193728572|gb|FK667170.1|FK667170
EST:     TTCCTCTTGTTTGGATGGGAAATTGGTCTCAACTTTGCCCTACCTGCAAG                         ATAATAAGACCTGTCCGATCTAAGCATTGCCCAACTTGTAAGCGATG
genomic: TTCCTC-TGTTTGGATGGGAAATTGGTCTCAACTTTGCCCTACCTGCAAGgtttacatga ... gtatcatcagATAATAAGACCTGTCCGATCTAAGCATTGCCCAACTTGTAAGCGATG
EST: gi|193422348|gb|FK389737.1|FK389737
EST:     GTTCCTCTGTTTGGATGGGAAATTGGTCTCAACTTTGCCCTACCTGCAAG                         ATAATAAGACCTGTCCGATCTAAGCATTGCCCAACTTGTAAGCGATGTGTG
genomic: GTTCCTCTGTTTGGATGGGAAATTGGTCTCAACTTTGCCCTACCTGCAAGgtttacatga ... gtatcatcagATAATAAGACCTGTCCGATCTAAGCATTGCCCAACTTGTAAGCGATGTGTG
EST: gi|193718537|gb|FK649091.1|FK649091
EST:     GTTCCTCTGTTTGGATGGGAAATTGGTCTCAACTTTGCCCTACCTGCAAG                         ATAATAAGACCTGTCCGATCTAAGCATT
genomic: GTTCCTCTGTTTGGATGGGAAATTGGTCTCAACTTTGCCCTACCTGCAAGgtttacatga ... gtatcatcagATAATAAGACCTGTCCGATCTAAGCATT
EST: gi|193670139|gb|FK608651.1|FK608651
EST:     GTTCCTCTGTTTGGATGGGAAATTGGTCTCAACTTTGCCCTACCTGCAAG                         ATAATAAGACCTGTCCGATCTAAGCATTGCCCAACTTGTAAGCGATGTGTG
genomic: GTTCCTCTGTTTGGATGGGAAATTGGTCTCAACTTTGCCCTACCTGCAAGgtttacatga ... gtatcatcagATAATAAGACCTGTCCGATCTAAGCATTGCCCAACTTGTAAGCGATGTGTG
EST: gi|193486106|gb|FK450864.1|FK450864
EST:     GTTCCTCTGTT-GGATGGGAAATTGGTCTCAACTTTGCCCTACCTGCAAG                         ATAATAAGACCTGTCCGATCTAAGC
genomic: GTTCCTCTGTTTGGATGGGAAATTGGTCTCAACTTTGCCCTACCTGCAAGgtttacatga ... gtatcatcagATAATAAGACCTGTCCGATCTAAGC
EST: gi|193465602|gb|FK432843.1|FK432843
EST:     GTTCCTCTGTTTGGATGGGAAATTGGTCTCAACTTTGCCCTACCTGCAAG                         ATAATAAGACCTGTCCGATCTAAGCATTGCCCAACTTGTAAGCGATGTGTG
genomic: GTTCCTCTGTTTGGATGGGAAATTGGTCTCAACTTTGCCCTACCTGCAAGgtttacatga ... gtatcatcagATAATAAGACCTGTCCGATCTAAGCATTGCCCAACTTGTAAGCGATGTGTG
EST: gi|193407162|gb|FK375281.1|FK375281
EST:     GTTCCTCTGTTTGGATGGGAAATTGGTCTCAACTTTGCCCTACCTGCAAG                         ATAATAAGACCTGTCCGATCTAAGCATTGCCCAACTTGTAAGCGATGTGTG
genomic: GTTCCTCTGTTTGGATGGGAAATTGGTCTCAACTTTGCCCTACCTGCAAGgtttacatga ... gtatcatcagATAATAAGACCTGTCCGATCTAAGCATTGCCCAACTTGTAAGCGATGTGTG
EST: gi|193322662|gb|FK289934.1|FK289934
EST:     GTTCCTCTGTTTGGATGGGAAATTGGTCCCAACTTTGCCCTACCTGCAAG                         ATAATAAGACCTGTCCGATCTAAGCAATTGCCCAACTTG
genomic: GTTCCTCTGTTTGGATGGGAAATTGGTCTCAACTTTGCCCTACCTGCAAGgtttacatga ... gtatcatcagATAATAAGACCTGTCCGATCTAAGCA-TTGCCCAACTTG
EST: gi|193551071|gb|FK507940.1|FK507940
EST:     GTTCCTCTGTTTGGATGGGAAATTGGTCTCAACTTTGCCCTACCTGCAAG                         ATAATAAGACCTGTCCGATCTAAGCATTGCCCAAACTTAGTAAGCGATG
genomic: GTTCCTCTGTTTGGATGGGAAATTGGTCTCAACTTTGCCCTACCTGCAAGgtttacatga ... gtatcatcagATAATAAGACCTGTCCGATCTAAGCATTGCCCAA-CTT-GTAAGCGATG
EST: gi|193410793|gb|FK376360.1|FK376360
EST:     GTTCCTCTGTTTGGATGGGAAATTGGTCTCAACTTTGCCCTACCTGCAAG                         ATAATAAGACCTGTCCGATCTAAGCATTGCCCAACTTGTAAGCGATGTGTG
genomic: GTTCCTCTGTTTGGATGGGAAATTGGTCTCAACTTTGCCCTACCTGCAAGgtttacatga ... gtatcatcagATAATAAGACCTGTCCGATCTAAGCATTGCCCAACTTGTAAGCGATGTGTG
EST: gi|193483837|gb|FK452352.1|FK452352
EST:     GTTCCTCTGTTTGGATGGGAAATTGGTCTCAACTTTGCCCTACCTGCAAG                         ATAATAAGACCTGTCCGATCTAAGCATTGCCCAACTTGTAAGCGATGTGTG
genomic: GTTCCTCTGTTTGGATGGGAAATTGGTCTCAACTTTGCCCTACCTGCAAGgtttacatga ... gtatcatcagATAATAAGACCTGTCCGATCTAAGCATTGCCCAACTTGTAAGCGATGTGTG
EST: gi|193499891|gb|FK464248.1|FK464248
EST:     GTTCCTCTGTTTGGATGGGAAATTGGTCTCAACTTTGCCCTACCTGCAAG                         ATAATAAGACCTGTCCGATCTAAGCATTGCCCAACTTGTAAGCGATGTGTG
genomic: GTTCCTCTGTTTGGATGGGAAATTGGTCTCAACTTTGCCCTACCTGCAAGgtttacatga ... gtatcatcagATAATAAGACCTGTCCGATCTAAGCATTGCCCAACTTGTAAGCGATGTGTG
EST: gi|193715236|gb|FK649827.1|FK649827
EST:     GTTCCTCTGTTTGGATGGGAAATTGGTCTCAACTTTGCCCTACCTGCAAG                         ATAATAAGACCTGTCCGATCTAAGCATTGCCCAACTTGTAAGCGATG
genomic: GTTCCTCTGTTTGGATGGGAAATTGGTCTCAACTTTGCCCTACCTGCAAGgtttacatga ... gtatcatcagATAATAAGACCTGTCCGATCTAAGCATTGCCCAACTTGTAAGCGATG
EST: gi|193556412|gb|FK511061.1|FK511061
EST:     GTTCCTCTGTTTGGNTGGGAAATTGGTCTCAACTTTGCCCTACCTGCAAG                         ATAATAAGACCTGTCCGATCTAAGCATTGCCCAACTTGTAAGCGATGTGTG
genomic: GTTCCTCTGTTTGGATGGGAAATTGGTCTCAACTTTGCCCTACCTGCAAGgtttacatga ... gtatcatcagATAATAAGACCTGTCCGATCTAAGCATTGCCCAACTTGTAAGCGATGTGTG
EST: gi|193324203|gb|FK292609.1|FK292609
EST:     GTTCCTCTGTTTGGATGGGAAATTGGTCTCAACTTTGCCCTACCTGCAAG                         ATAATAAGACCTGTCCGATCTAAGCATTGCCCAACTTGTAAGCGATGTGTG
genomic: GTTCCTCTGTTTGGATGGGAAATTGGTCTCAACTTTGCCCTACCTGCAAGgtttacatga ... gtatcatcagATAATAAGACCTGTCCGATCTAAGCATTGCCCAACTTGTAAGCGATGTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaattctcaaaacaagttatcgcttatcaggttttctcgaattgtatcatcagATAATAAGACCTGTCCGATCTAAGCATTGCCCAACTTGTAAGCGATGTGTGGAACAGTTCGACCACCACTGTCCATGGATATCTAACTGTGTTGGGAAG
                                         aattgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttacatgatattcttttgagtatttaaaaaatctaatgttgatactttacttacatttctgtttattaaattctcaaaacaagttatcgcttatcaggttttctcgaattgtatcatcagATAATAAGACCTGTCCGATCTAAGCATTGCCCAACTTGTAAGCGATGTGTGGAACAGTTCGACCACCACTGTCCATGGATATCTAACTGTGTTGGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA