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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGAGCTCGATAAGATTCTCTTCTTCTTCCCCGCCGGTTTGCCCTTTTCAAAGCAACTCTCCGTCATTGGCCTCAGCGAAGGACTCATCACTTTCACTAGgtttgtttgttaggttaccctgcttatctctcaaattattttactaattgattcattctgcaattccag

Basic information

species Glycine max
transcript GLYMA05G34400.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G34400.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv01s0011g06030.t01 (Vitis vinifera), 5'ss of exon 1
AAGAGCTCGATAAGATTCTCTTCTTCTTCCCCGCCGGTTTGCCCTTTTCAAAGCAACTCTCCGTCATTGGCCTCAGCGAAGGACTCATCACTTTCACTAGgtt---tgtttgt-taggtt---accctgcttatctctcaaattattt--tactaattgattcattctgcaattccag-----------------------
| ||||| || |||||| | |||||||  || || | |||||||||||| | ||| || ||||| || || ||||||||||| ||||||||||| || |||||   || |||| ||  ||   |   |   |     |||| |||| |  | | |||| || ||  |||   || |                         
AGGAGCTGGACAAGATTTTGTTCTTCTATCCAGCTGATTTGCCCTTTTCTACGCAGCTTTCCGTGATAGGGCTCAGCGAAGGGCTCATCACTTTTACAAGgttaggtgcttgtatatattggaaatttctgttataatcaatttatctcgtgcaaatttatccag-ctgagctttctttttggtgagtcattacccttgat
















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|298197699|gb|HO045178.1|HO045178
EST:     AAGCAACTCTCCGTCATTGGCCTCAGCGAAGGACTCATCACTTTCACTAG                         AATCTTCTCGCCAGAGGCTGGCCTGCGACGTCATCGAAGCAGAAAGACATT
genomic: AAGCAACTCTCCGTCATTGGCCTCAGCGAAGGACTCATCACTTTCACTAGgtttgtttgt ... gcaattccagAATCTTCTCGCCAGAGGCT-GCCTGCGACGTCATCGAAGCAGAAAGACATT
EST: gi|6482462|gb|AW201719.1|AW201719
EST:     AAGCAACTCTCCGTCATTGGCCTCAGCGAAGGACTCATCACTTTCACTAG                         AATCTTCTCGCCAGAGGCTGCCTGCGACGTCATCGAAGCAGAAAGACATTC
genomic: AAGCAACTCTCCGTCATTGGCCTCAGCGAAGGACTCATCACTTTCACTAGgtttgtttgt ... gcaattccagAATCTTCTCGCCAGAGGCTGCCTGCGACGTCATCGAAGCAGAAAGACATTC
EST: gi|298178758|gb|HO024493.1|HO024493
EST:     AAGCAACTCTCCGTCATTGGCCTCAGCGAAGGACTCATCACTTTCACTAG                         AATCTTCTCGCCAGAGGCTGCCTGCGACGTCATCGAAGCAGAAAGACATTC
genomic: AAGCAACTCTCCGTCATTGGCCTCAGCGAAGGACTCATCACTTTCACTAGgtttgtttgt ... gcaattccagAATCTTCTCGCCAGAGGCTGCCTGCGACGTCATCGAAGCAGAAAGACATTC
EST: gi|298196439|gb|HO041182.1|HO041182
EST:     AAGCAACTCTCCGTCATTGGCCTCAGCGAAGGACTCATCACTTTCACTAG                         AATCTTCTCGCCAGAGGCTGGCCTGCGACGTCATCGAAGCAGAAAGACATT
genomic: AAGCAACTCTCCGTCATTGGCCTCAGCGAAGGACTCATCACTTTCACTAGgtttgtttgt ... gcaattccagAATCTTCTCGCCAGAGGCTG-CCTGCGACGTCATCGAAGCAGAAAGACATT
EST: gi|18735130|gb|BM528581.1|BM528581
EST:     AAGCAACTCTCCGTCATTGGCCTCAGCGAAGGACTCATCACTTTCACTAG                         AATCTTCTCGCCAGAGGCTGCCTGCGACGTCATCGAAGCAGAAAGACATTC
genomic: AAGCAACTCTCCGTCATTGGCCTCAGCGAAGGACTCATCACTTTCACTAGgtttgtttgt ... gcaattccagAATCTTCTCGCCAGAGGCTGCCTGCGACGTCATCGAAGCAGAAAGACATTC
EST: gi|298194957|gb|HO043429.1|HO043429
EST:     AAGCAACTCTCCGTCATTGGCCTCAGCGAAGGACTCATCACTTTCACTAG                         AATCTTCTCGCCAGAGGCTGCCTGCGACGTCATCGAAGCAGAAAGACATTC
genomic: AAGCAACTCTCCGTCATTGGCCTCAGCGAAGGACTCATCACTTTCACTAGgtttgtttgt ... gcaattccagAATCTTCTCGCCAGAGGCTGCCTGCGACGTCATCGAAGCAGAAAGACATTC
EST: gi|298185750|gb|HO028061.1|HO028061
EST:     AAGCAACTCTCCGTCATTGGCCTCAGCGAAGGACTCATCACTTTCACTAG                         AATCTTCTCGCCAGAGGCTGGCCTGCGACGTCAACGAAGCAGAAAGACATT
genomic: AAGCAACTCTCCGTCATTGGCCTCAGCGAAGGACTCATCACTTTCACTAGgtttgtttgt ... gcaattccagAATCTTCTCGCCAGAGGCTG-CCTGCGACGTCATCGAAGCAGAAAGACATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGAGCTCGATAAGATTCTCTTCTTCTTCCCCGCCGGTTTGCCCTTTTCAAAGCAACTCTCCGTCATTGGCCTCAGCGAAGGACTCATCACTTTCACTAGgtttgtttgttaggttaccctgcttatctctcaaattattttactaattgattcattctgcaattccag

- - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA