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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttcctcgcaaatgcttccttgtgagcaagttaaaatgttaaacccagtttatttttcatcactaatttagttgaagctaatagctattttaccttgcagGTTTGAAGGAATGATGGTTCCAAGCAGAGGTCAAGCAGCGCTATTAACTTTTTGCACTTGCATCAGCTTGGCAAGTGTGGCACTTGTGCTTACCATAACC

Basic information

species Glycine max
transcript GLYMA16G26340.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G26340.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0068g01020.t01 (Vitis vinifera), 3'ss of exon 2
----------------------------------------------------------------------------------cttcctcgcaaatgcttccttgtgagcaagtt---aaaatgttaaacccagtttattt--ttcatcactaatttagttgaagctaatagctattttacc--ttgcagGTTTGAAGGAATGATGGTTCCAAGCAGAGGTCAAGCAGCGCTATTAACTTTTTGCACTTGCATCAGCTTGGCAAGTGTGGCACTTGTGCTTACCATAACC
                                                                                   || |  | |||||     ||| |  ||| |    |||    |||  | || |   |   || || | |  |||  |||   | ||||     ||      || |||||||||||| ||||||||||||||| |||| ||||||||  |  | || || ||||||||||| ||| ||||||| || |  ||||| ||||||||||| 
gtaagctgctgctgctaccacccgtctctcagtatcatctgtatttctcattttcactcaggctatgtttggttacggaaaatttgcgagaaaatgaaatgttggggacaaatggggaaaggcctaattctagatggatgagttgatgagtggtttc-ttggttccaatattggcttatttgattccagGTTTGAAGGCATGATGGTTCCAAGCCGAGGCCAAGCAGCATTGCTCACCTTCTGCACTTGCATAAGCCTGGCAAGCGTTGGCCTTGTTCTTACCATAACT
















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|298179428|gb|HO027899.1|HO027899
EST:     TTCTTCACTCGTAACAATTTTGCAGTGACTGACAGAGGAGAGACGATCAC                         GTTTGAAGGAATGATGGCTCCAAGC
genomic: TTCTTCACTCGTAACAATTTTGCAGTGACTGACAGAGGAGAGACAATCACgtatgttact ... taccttgcagGTTTGAAGGAATGATGGTTCCAAGC
EST: gi|192302487|gb|FG994809.1|FG994809
EST:     TTCTTCACTCGTAACAATTTTGCAGTGACTGACAGAGGAGAGACAATCAC                         GTTTGAAGGAATGATGGTTCCAAGCAGAGGTCAAGCAGCGCTATTAACTTT
genomic: TTCTTCACTCGTAACAATTTTGCAGTGACTGACAGAGGAGAGACAATCACgtatgttact ... taccttgcagGTTTGAAGGAATGATGGTTCCAAGCAGAGGTCAAGCAGCGCTATTAACTTT
EST: gi|31309305|gb|CD394508.1|CD394508
EST:     TTCTTCACTCGTAACAATTTTGCAGTGACTGACAGAGGAGAGACAATCAC                         GTTTGAAGGAATGATGGTTCCAAGCAGAGGTCAAGCAGCGCTATTAACTTT
genomic: TTCTTCACTCGTAACAATTTTGCAGTGACTGACAGAGGAGAGACAATCACgtatgttact ... taccttgcagGTTTGAAGGAATGATGGTTCCAAGCAGAGGTCAAGCAGCGCTATTAACTTT
EST: gi|31308755|gb|CD393958.1|CD393958
EST:     TTCTTCACTCGTAACAATTTTGCAGTGACTGACAGAGGAGAGACAATCAC                         GTTTGAAGGAATGATGGTTCCAAGCAGAGGTCAAGCAGCGCTATTAACTTT
genomic: TTCTTCACTCGTAACAATTTTGCAGTGACTGACAGAGGAGAGACAATCACgtatgttact ... taccttgcagGTTTGAAGGAATGATGGTTCCAAGCAGAGGTCAAGCAGCGCTATTAACTTT
EST: gi|20811369|gb|BQ295847.1|BQ295847
EST:     TTCTTCACTCGTAACAATTTTGCAGTGACTGACAGAGGAGAGACAATCAC                         GTTTGAAGGAATGATGGTTCCAAGCAGAGGTCAAGCAGCGCTATTAACTTT
genomic: TTCTTCACTCGTAACAATTTTGCAGTGACTGACAGAGGAGAGACAATCACgtatgttact ... taccttgcagGTTTGAAGGAATGATGGTTCCAAGCAGAGGTCAAGCAGCGCTATTAACTTT
EST: gi|151399988|gb|EV269859.1|EV269859
EST:     TTCTTCACTCGTAACAATTTTGCAGTGACTGACAGAGGAGAGACAATCAC                         GTTTGAAGGAATGATGGTTCCAAGCAGAGGTCAAGCAGCGCTATTAACTTT
genomic: TTCTTCACTCGTAACAATTTTGCAGTGACTGACAGAGGAGAGACAATCACgtatgttact ... taccttgcagGTTTGAAGGAATGATGGTTCCAAGCAGAGGTCAAGCAGCGCTATTAACTTT
EST: gi|31561633|gb|CD487471.1|CD487471
EST:     TTCTTCACTCGTAACAATTTTGCAGTGACTGACAGAGGAGAGACAATCAC                         GTTTGAAGGAATGATGGTTCCAAGCAGAGGTCAAGCAGCGCTATTAACTTT
genomic: TTCTTCACTCGTAACAATTTTGCAGTGACTGACAGAGGAGAGACAATCACgtatgttact ... taccttgcagGTTTGAAGGAATGATGGTTCCAAGCAGAGGTCAAGCAGCGCTATTAACTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtttatttttcatcactaatttagttgaagctaatagctattttaccttgcagGTTTGAAGGAATGATGGTTCCAAGCAGAGGTCAAGCAGCGCTATTAACTTTTTGCACTTGCATCAGCTTGGCAAGTGTGGCACTTGTGCTTACCATAACC
                                          ttttacctt  CT-rich tract
                                 taatagctatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttcctcgcaaatgcttccttgtgagcaagttaaaatgttaaacccagtttatttttcatcactaatttagttgaagctaatagctattttaccttgcagGTTTGAAGGAATGATGGTTCCAAGCAGAGGTCAAGCAGCGCTATTAACTTTTTGCACTTGCATCAGCTTGGCAAGTGTGGCACTTGTGCTTACCATAACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
cttcctc
- - - - - - tgcttcc
- - - - - - - - - - - - - - - - - - - - aaaccca