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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTTCATTCACTTAACACTCCTTTTAAGAGAGAAGGATCAAACATGGGAGCTGGAAGTTTCCTCAAGGTGGTTCTAAAAAATTTTGATGTTCTTGCTGGgtatgttttgctttttcctacttttctaacaaagcactttcctttcttccaaaaaaataaaataaaatgaaaaagcacttttcttttgttgctcttacat...

Basic information

species Glycine max
transcript GLYMA06G20570.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G20570.2 (Glycine max), 5'ss of exon 1
lower sequence: Vv17s0000g05990.t01 (Vitis vinifera), 5'ss of exon 1
------AGTTTCATTCACTTAACACTCCTTTTAAGAGAGAAGGATCAAACATGGGAGCTGGAAGTTTCCTCAAGGTGGTTCTAAAAAATTTTGATGTTCTTGCTGGgtatgttttgctttttcctacttttctaacaaagcactttcctttcttccaaaaaaataaaataaaatgaaaaagcact-tttcttttgttgctcttacat
      || |  |   |   || |     ||  ||  |   |||||       ||  |||||| ||| ||||||||||| || |||||  ||||||||||||| |||||||||  |  |||| | ||| ||| |      |   || ||     ||   |||| || ||  | |||||| | |    |||| |   | |||| ||  
GTAGAGAGATCAAAGGAGGAAAAAAATAATTGCAGGAAATGGGATCT------GGTACTGGAAATTTTCTCAAGGTGGTGCTCAAAAACATTGATGTTCTTGCCGGgtatgttc-gtctttttccactcttccacttttaccaatttctccaaacccctaaaaaaatattgagtgaaaatgaatcacttctctgagttctctcacgc
















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|209727462|gb|BW651957.1|BW651957
EST:     GCTGGAAGTTTCCTCAAGGTGGTTCTAAAAAATTTTGATGTTCTTGCTGG                         GCCTGTGCTTAGTCTTGCCTATCCTCT
genomic: GCTGGAAGTTTCCTCAAGGTGGTTCTAAAAAATTTTGATGTTCTTGCTGGgtatgttttg ... tctctttcagGCCTGTGCTTAGTCTTGCCTATCCTCT
EST: gi|298187817|gb|HO031774.1|HO031774
EST:     GCTGGAAGTTTCCTCAAGGTGGTTCTAAAAAATTTTGATGTTCTTGCTGG                         GCCTGTGCTTAGTCTTGCCTATCCTCT
genomic: GCTGGAAGTTTCCTCAAGGTGGTTCTAAAAAATTTTGATGTTCTTGCTGGgtatgttttg ... tctctttcagGCCTGTGCTTAGTCTTGCCTATCCTCT
EST: gi|298168324|gb|HO014499.1|HO014499
EST:     GCTGGAAGTTTCCTCAAGGTGGTTCTAAAAAATTTTGATGTTCTTGCTGG                         GCCTGTGCTTAGTCTTGCCTATCCTCT
genomic: GCTGGAAGTTTCCTCAAGGTGGTTCTAAAAAATTTTGATGTTCTTGCTGGgtatgttttg ... tctctttcagGCCTGTGCTTAGTCTTGCCTATCCTCT
EST: gi|192326557|gb|FK018834.1|FK018834
EST:     GCTGGAAGTTTCCTCAAGGTGGTTCTAAAAAATTTTGATGTTCTTGCTGG                         GCCTGTGCTTAGTCTTGCCTATCCTCT
genomic: GCTGGAAGTTTCCTCAAGGTGGTTCTAAAAAATTTTGATGTTCTTGCTGGgtatgttttg ... tctctttcagGCCTGTGCTTAGTCTTGCCTATCCTCT
EST: gi|298168765|gb|HO009695.1|HO009695
EST:     GCTGGAAGTTTCCTCAAGGTGGTTCTAAAAAATTTTGATGTTCTTGCTGG                         GCCTGTGCTTAGTCTTGCCTATCCTCT
genomic: GCTGGAAGTTTCCTCAAGGTGGTTCTAAAAAATTTTGATGTTCTTGCTGGgtatgttttg ... tctctttcagGCCTGTGCTTAGTCTTGCCTATCCTCT
EST: gi|26045617|gb|CA783151.1|CA783151
EST:     GCTGGAAGTTTCCTCAAGGTGGTTCTAAAAAATTTTGATGTTCTTGCTGG                         GCCTGTGCTTAGTCTTGCCTATCCTCT
genomic: GCTGGAAGTTTCCTCAAGGTGGTTCTAAAAAATTTTGATGTTCTTGCTGGgtatgttttg ... tctctttcagGCCTGTGCTTAGTCTTGCCTATCCTCT
EST: gi|193419106|gb|FK382280.1|FK382280
EST:     GCTGGAAGTTTCCTCAAGGTGGTTCTAAAAAATTTTGATGTTCTTGCTGG                         GCCTGTGCTTAGTCTTGCCTATCCTCT
genomic: GCTGGAAGTTTCCTCAAGGTGGTTCTAAAAAATTTTGATGTTCTTGCTGGgtatgttttg ... tctctttcagGCCTGTGCTTAGTCTTGCCTATCCTCT
EST: gi|192310282|gb|FK002610.1|FK002610
EST:     GCTGGAAGTTTCCTCAAGGTGGTTCTAAAAAATTTTGATGTTCTTGCTGG                         GCCTGTGCTTAGTCTTGCCTATCCTCT
genomic: GCTGGAAGTTTCCTCAAGGTGGTTCTAAAAAATTTTGATGTTCTTGCTGGgtatgttttg ... tctctttcagGCCTGTGCTTAGTCTTGCCTATCCTCT
EST: gi|6667545|gb|AW278996.1|AW278996
EST:     GCTGGAAGTTTCCTCAAGGTGGTTCTAAAAAATTTTGATGTTCTTGCTGG                         GCCTGTGCTTAGTCTTGCCTATCCTCT
genomic: GCTGGAAGTTTCCTCAAGGTGGTTCTAAAAAATTTTGATGTTCTTGCTGGgtatgttttg ... tctctttcagGCCTGTGCTTAGTCTTGCCTATCCTCT
EST: gi|192310283|gb|FK002611.1|FK002611
EST:     GCTGGAAGTTTCCTCAAGGTGGTTCTAAAAAATTTTGATGTTCTTGCTGG                         GCCTGTGCTTAGTCTTGCCTATCCTCT
genomic: GCTGGAAGTTTCCTCAAGGTGGTTCTAAAAAATTTTGATGTTCTTGCTGGgtatgttttg ... tctctttcagGCCTGTGCTTAGTCTTGCCTATCCTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTTCATTCACTTAACACTCCTTTTAAGAGAGAAGGATCAAACATGGGAGCTGGAAGTTTCCTCAAGGTGGTTCTAAAAAATTTTGATGTTCTTGCTGGgtatgttttgctttttcctacttttctaacaaagcactttcctttcttccaaaaaaataaaataaaatgaaaaagcacttttcttttgttgctcttacat

- - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG