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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttgttatgtgattactaagcaagccaatcatgtcttagttgctattctaatgggtaatggatcaccattctaatgccacatatttgtcattgttgcagTTGAATTTTCTAATTACAGAAAATAGGCCGAGGGAAATTGTTGACCCTCTATGTGAAGGGGTGCAAATGGAGAGCCTTGATGCCTTGCTCTCTGTGGCTA

Basic information

species Glycine max
transcript GLYMA01G35390.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G35390.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv02s0087g00170.t01 (Vitis vinifera), 3'ss of exon 13
-agttgttatgtgattactaagcaagccaatcatgtcttagttgctattctaatgggtaatggatcaccattctaatgccacatatttgtcattgt----tgcagTTGAATTTTCTAATTACAGAAAATAGGCCGAGGGAAATTGTTGACCCTCTATGTGAAGGGGTGCAAATGGAGAGCCTTGATGCCTTGCTCTCTGTGGCTA
  ||    |||| |||  ||   |||      |  | || |||  ||  |||   | |  ||  |  ||| |    ||   ||| | | |  || |    ||||||||||||||||  |||||||||||||||   |||| |||||||| || | |||||||||||| ||    || || ||||||||| ||||||| || || |
atgtgcacatgt-attcatataaaagtggg--acattttggttaata--ctagatgttcttgtctatccaattggttgatccatctcttttgttttgccttgcagTTGAATTTTCTGGTTACAGAAAATAGGCAACGGGAGATTGTTGATCCACAATGTGAAGGGGTCCAGTCAGAAAGTCTTGATGCCCTGCTCTCGGTTGCCA
















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|192327322|gb|FK019569.1|FK019569
EST:     GGCCAACAGACACAGCATTCATTGAAAAGGGTCTCAATATTGTTGGTTGG                         TTGAATTTTCTAATTACAGAAAATAGGCCGAGGGAAATTGTTGACCCTCTA
genomic: GGCCAACAGACGCAGCATTCATTGAAAAGGGTCTCAATATTGTTGGTTGGgtatgtcatt ... attgttgcagTTGAATTTTCTAATTACAGAAAATAGGCCGAGGGAAATTGTTGACCCTCTA
EST: gi|151393318|gb|EV263193.1|EV263193
EST:     GGCCAACAGACGCAGCATTCATTGAAAAGG-TCTCAATATTGTTGGTTGG                         TTGAATTTTCTAATTACAGAAA
genomic: GGCCAACAGACGCAGCATTCATTGAAAAGGGTCTCAATATTGTTGGTTGGgtatgtcatt ... attgttgcagTTGAATTTTCTAATTACAGAAA
EST: gi|207812275|gb|GD784448.1|GD784448
EST:     TATTGTTGGTTGG                         TTGAATTTTCTAATTACAGAAAATAAGGCCGAGGGAAATTGTTGACCCTCT
genomic: TATTGTTGGTTGGgtatgtcatt ... attgttgcagTTGAATTTTCTAATTACAGAAAAT-AGGCCGAGGGAAATTGTTGACCCTCT
EST: gi|21601017|gb|BQ611348.1|BQ611348
EST:     GACCAACAGACGCAGCATTCATTGAAAAGGGCCTCAATATTGTTGGTTGG                         TTGAATTTTCTAATTACAGAAAATAGGCCGAGGGAAA
genomic: GGCCAACAGACGCAGCATTCATTGAAAAGGGTCTCAATATTGTTGGTTGGgtatgtcatt ... attgttgcagTTGAATTTTCTAATTACAGAAAATAGGCCGAGGGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctaatgggtaatggatcaccattctaatgccacatatttgtcattgttgcagTTGAATTTTCTAATTACAGAAAATAGGCCGAGGGAAATTGTTGACCCTCTATGTGAAGGGGTGCAAATGGAGAGCCTTGATGCCTTGCTCTCTGTGGCTA
                        ttctaat  putative branch site (score: 2)
                       attctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttgttatgtgattactaagcaagccaatcatgtcttagttgctattctaatgggtaatggatcaccattctaatgccacatatttgtcattgttgcagTTGAATTTTCTAATTACAGAAAATAGGCCGAGGGAAATTGTTGACCCTCTATGTGAAGGGGTGCAAATGGAGAGCCTTGATGCCTTGCTCTCTGTGGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- -tgttatg
- - - - - - - - ctaagca
- - - - - - - - - - - - -ccaatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcaccat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgccaca