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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttttttaccttgatcttgttttatgagaagtctcttgtctttggcagttcgtttacctagttcttcaccccttgtgcagGAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACACATTTTGGCTCTTTTGAAGCATTAGTACAAAAAGTTAATGCAGAAGGTG

Basic information

species Glycine max
transcript GLYMA04G39930.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G39930.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv13s0067g02990.t01 (Vitis vinifera), 3'ss of exon 2
gtaagtttttttac-----------cttgatcttgttttatgagaagtctcttgtctttggcagttcgtttacctagttcttcac----cccttgtgcagGAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACACATTTTGGCTCTTTTGAAGCATTAGTACAAAAAGTTAATGCAGAAGGTG
||||| || ||| |           |||| |||| | |  |      ||||||   | |  || | | | ||  | |  | ||        |    ||||||||||||||||||||| || || ||||||||||| ||||| || |||||||||||||| ||  | |||||||| |||  |||| ||||| |||||||||
gtaagcttgttttcttagctctttgcttgctcttttctatttgtttatctcttaagtctctcattacatctatttggcgcatcgtaaaattccatcgcagGAAGGAGGTGGTGAACCCCCAAAAGGTTCACTGGGTTGGGCTATAGACACACATTTTGGTTCCATGGAAGCATTGGTAGCAAAAATTAATTCAGAAGGTG
















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|15337599|gb|BI498255.1|BI498255
EST:     GTCACGTCAACCATTCTATTTTCTGGAAAA-TCTAGCTCCTGTTCGT                         GAAAGGAGGTGGTGAACCACC-AAGG
genomic: GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGTgtaagttttt ... ccttgtgcagGAA-GGAGGTGGTGAACCACCCAAGG
EST: gi|4313704|gb|AI460823.1|AI460823
EST:     GTCACGTCAACCATTCTATTTTCTGGGAAAATCTAGCTTCTGTTCGT                         GAAAGGAG-TGTTGAACCACCCA
genomic: GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGTgtaagttttt ... ccttgtgcagGAA-GGAGGTGGTGAACCACCCA
EST: gi|10233755|gb|BE802643.1|BE802643
EST:     GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT                         GAAGGAGGTGGTGAACCACCCAANGGTTCACTGGGATGGGCCATTGACACA
genomic: GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGTgtaagttttt ... ccttgtgcagGAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
EST: gi|298197610|gb|HO045089.1|HO045089
EST:     GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT                         GAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
genomic: GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGTgtaagttttt ... ccttgtgcagGAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
EST: gi|20076003|gb|BQ094786.1|BQ094786
EST:     GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT                         GAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
genomic: GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGTgtaagttttt ... ccttgtgcagGAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
EST: gi|18692743|gb|BM521591.1|BM521591
EST:     GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT                         GAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
genomic: GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGTgtaagttttt ... ccttgtgcagGAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
EST: gi|6070236|gb|AW099772.1|AW099772
EST:     GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT                         GAAGGAGGTGGTGAACCACCCAAGGGTTCACT
genomic: GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGTgtaagttttt ... ccttgtgcagGAAGGAGGTGGTGAACCACCCAAGGGTTCACT
EST: gi|16347621|gb|BI973216.1|BI973216
EST:     GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT                         GAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
genomic: GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGTgtaagttttt ... ccttgtgcagGAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
EST: gi|298173808|gb|HO017144.1|HO017144
EST:     GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT                         GAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
genomic: GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGTgtaagttttt ... ccttgtgcagGAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
EST: gi|298181231|gb|HO022670.1|HO022670
EST:     GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT                         GAAGGAGGTGGTGAACCACCCATGGGTTCACTGGGATGGGCCATTGACACA
genomic: GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGTgtaagttttt ... ccttgtgcagGAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
EST: gi|213608229|gb|DB970826.1|DB970826
EST:     GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT                         GAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
genomic: GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGTgtaagttttt ... ccttgtgcagGAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
EST: gi|298165022|gb|HO011071.1|HO011071
EST:     GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT                         GAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
genomic: GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGTgtaagttttt ... ccttgtgcagGAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
EST: gi|23730997|gb|BU763608.1|BU763608
EST:     GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT                         GAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
genomic: GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGTgtaagttttt ... ccttgtgcagGAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
EST: gi|298173236|gb|HO020220.1|HO020220
EST:     GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT                         GAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
genomic: GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGTgtaagttttt ... ccttgtgcagGAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
EST: gi|19347357|gb|BM892237.1|BM892237
EST:     GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT                         GAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
genomic: GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGTgtaagttttt ... ccttgtgcagGAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
EST: gi|7685971|gb|AW756619.1|AW756619
EST:     GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT                         GAAGGAGGTGGGTGAACCACCCAAGGGTTCACT
genomic: GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGTgtaagttttt ... ccttgtgcagGAAGGAGGTGG-TGAACCACCCAAGGGTTCACT
EST: gi|298174724|gb|HO014755.1|HO014755
EST:     GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT                         GAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
genomic: GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGTgtaagttttt ... ccttgtgcagGAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
EST: gi|298183088|gb|HO028351.1|HO028351
EST:     GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT                         GAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
genomic: GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGTgtaagttttt ... ccttgtgcagGAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
EST: gi|298166785|gb|HO010224.1|HO010224
EST:     GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT                         GAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
genomic: GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGTgtaagttttt ... ccttgtgcagGAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
EST: gi|120532869|gb|EH261002.1|EH261002
EST:     GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT                         GAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
genomic: GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGTgtaagttttt ... ccttgtgcagGAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
EST: gi|8826470|gb|BE210200.1|BE210200
EST:     GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT                         GAAGGAGGTGGTGAA
genomic: GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGTgtaagttttt ... ccttgtgcagGAAGGAGGTGGTGAA
EST: gi|298191328|gb|HO038807.1|HO038807
EST:     GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT                         GAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
genomic: GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGTgtaagttttt ... ccttgtgcagGAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
EST: gi|298164553|gb|HO014198.1|HO014198
EST:     GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT                         GAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
genomic: GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGTgtaagttttt ... ccttgtgcagGAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
EST: gi|213617768|gb|DB959380.1|DB959380
EST:     GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT                         GAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
genomic: GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGTgtaagttttt ... ccttgtgcagGAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
EST: gi|298195572|gb|HO043963.1|HO043963
EST:     GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT                         GAAGGAGGTGGTGAACCACCCAA
genomic: GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGTgtaagttttt ... ccttgtgcagGAAGGAGGTGGTGAACCACCCAA
EST: gi|209696790|gb|BW680411.1|BW680411
EST:     GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT                         GAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
genomic: GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGTgtaagttttt ... ccttgtgcagGAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
EST: gi|213587591|gb|DB969732.1|DB969732
EST:     GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT                         GAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
genomic: GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGTgtaagttttt ... ccttgtgcagGAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
EST: gi|298185168|gb|HO030381.1|HO030381
EST:     GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT                         GAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
genomic: GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGTgtaagttttt ... ccttgtgcagGAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
EST: gi|6566815|gb|AW234447.1|AW234447
EST:     GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGT                         GAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
genomic: GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGTgtaagttttt ... ccttgtgcagGAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACA
EST: gi|4313692|gb|AI460811.1|AI460811
EST:     GTCACGTCAACCATTCTANTTTCTGGAAAAATCTAGCTCCTGTTCGT                         GAAGGAGGTG-TGAACCACCCAAGG
genomic: GTCACGTCAACCATTCTATTTTCTGGAAAAATCTAGCTCCTGTTCGTgtaagttttt ... ccttgtgcagGAAGGAGGTGGTGAACCACCCAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagaagtctcttgtctttggcagttcgtttacctagttcttcaccccttgtgcagGAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACACATTTTGGCTCTTTTGAAGCATTAGTACAAAAAGTTAATGCAGAAGGTG
                                    ttcttcaccccttgt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttttttaccttgatcttgttttatgagaagtctcttgtctttggcagttcgtttacctagttcttcaccccttgtgcagGAAGGAGGTGGTGAACCACCCAAGGGTTCACTGGGATGGGCCATTGACACACATTTTGGCTCTTTTGAAGCATTAGTACAAAAAGTTAATGCAGAAGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC