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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatcattagttctattgtatccatcctatgtattgctctaatttcaatatgtttgctttcacaatttcaaattagaactaattttttgcttttgtgaagGCTTATGCAATTTCAGCACTGTTGAAAATTTATGCATTTGAAGTAGCAGCTGGGAGGAAAGTGGATATCCTATCTGAG

Basic information

species Glycine max
transcript GLYMA01G35650.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G35650.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv02s0087g00690.t01 (Vitis vinifera), 3'ss of exon 8
-----ttatcattagttctattgtatccatcctatgtattgctctaatttcaatatgtttgctttcacaatttcaaattagaactaattttttgctt---ttgtgaagGCTTATGCAATTTCAGCACTGTTGAAAATTTATGCATTTGAAGTAGCAGCTGGGAGGAAAGTGGATATCCTATCTGAG
     |||     | |||| | ||||  |   ||| |||||||  | ||        ||  |||  |   | |  || |     ||||| |||||||   || ||||||| |||||  || |||| ||| ||||| | |||||||||||| ||||||| || || ||||||||||| ||| | |||
ggtatttagagacatttct-tggtattgaaattat-tattgctgaagttat------ttctcttaaattctcttgaagtgatggtaattctttgcttgttttttgaagGCATATGCTGTTACAGCGCTGATGAAAGTATATGCATTTGAAATAGCAGCAGGAAGAAAAGTGGATATGCTACCAGAG
















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|208312667|gb|GE112129.1|GE112129
EST:     GGAAGTTATGTGACATTGCAGAGGCGTATTCCAATGATGAAAATGTTAAG                         GCTTATGCAATTTCAGCACTGTT
genomic: GGAAGTTATGTGACATTGCAGAGGCATATTCCAATGATGAAAATGTTAAGgtatttatta ... ttttgtgaagGCTTATGCAATTTCAGCACTGTT
EST: gi|207835325|gb|GD807842.1|GD807842
EST:     AATGATGAAAATGTTAAG                         GCTTATGCAATTTCAGCACTGTTGAAAATTTAT
genomic: AATGATGAAAATGTTAAGgtatttatta ... ttttgtgaagGCTTATGCAATTTCAGCACTGTTGAAAATTTAT
EST: gi|207774490|gb|GD744648.1|GD744648
EST:     GGAAGTTATGTGACATTGCAGAGGCATATTCCAATGATGAAAATGTTAAG                         GCTTATGCAATTTCAGCACTGTTGAAAATTTATGCATTTGAAGTAGCAGCT
genomic: GGAAGTTATGTGACATTGCAGAGGCATATTCCAATGATGAAAATGTTAAGgtatttatta ... ttttgtgaagGCTTATGCAATTTCAGCACTGTTGAAAATTTATGCATTTGAAGTAGCAGCT
EST: gi|193326525|gb|FK291552.1|FK291552
EST:     GGAAGTTATGTGACATTGCAGAGGCATATTCCAATGATGAAAATGTTAAG                         GCTTATGCAATTTCAGCACTGTTGAAAATTTATGCATTTGAAGTAGCAGCT
genomic: GGAAGTTATGTGACATTGCAGAGGCATATTCCAATGATGAAAATGTTAAGgtatttatta ... ttttgtgaagGCTTATGCAATTTCAGCACTGTTGAAAATTTATGCATTTGAAGTAGCAGCT
EST: gi|207684276|gb|GD664627.1|GD664627
EST:     GGAAGTTGTGTGACATTGCAGAGGCATATTCCAATGATGAAAATGTTAAG                         GCTTATGCAATTTC
genomic: GGAAGTTATGTGACATTGCAGAGGCATATTCCAATGATGAAAATGTTAAGgtatttatta ... ttttgtgaagGCTTATGCAATTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatatgtttgctttcacaatttcaaattagaactaattttttgcttttgtgaagGCTTATGCAATTTCAGCACTGTTGAAAATTTATGCATTTGAAGTAGCAGCTGGGAGGAAAGTGGATATCCTATCTGAG
                               aactaat  putative branch site (score: 2)
                                     ttttttgcttttgt  CT-rich tract
                acaatttcaaattaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatcattagttctattgtatccatcctatgtattgctctaatttcaatatgtttgctttcacaatttcaaattagaactaattttttgcttttgtgaagGCTTATGCAATTTCAGCACTGTTGAAAATTTATGCATTTGAAGTAGCAGCTGGGAGGAAAGTGGATATCCTATCTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - tccatcc