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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatacactctgaaacaactactcaattgatgataatatgaaacttgttaggtatttctaatttatccgtgttcataataatgccacttgtgtttttacagGCTACTTTTGACTGTTTGCTGAAAACCTACGGTTTTCTAACACCTGAATTCTGGAAGGAGACTCGGTTCTCCAAATCACCATTCCAAGAGTACACTGATC

Basic information

species Glycine max
transcript GLYMA05G34570.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G34570.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0007g08370.t01 (Vitis vinifera), 3'ss of exon 1
tatacactctgaaacaactactcaattgatgataatatgaaacttgttaggtatttctaattta-tccgtgttcataataatgccacttgtgtttttacagGCTACTTTTGACTGTTTGCTGAAAACCTACGGTTTTCTAACACCTGAATTCTGGAAGGAGACTCGGTTCTCCAAATCACCATTCCAAGAGTACACTGATC
 | | |   ||     | |||| | |  |      || |     ||  ||  |  |  |  |   |   | | ||| || ||  ||  ||| | | | |||||||| ||||| ||| ||||||| || || |  |  || || ||||| ||||||| ||||||||||| | | ||||| |||||||||||| |||| ||||
aaaaaaacttgtggatattacttattatacttctgtaagttttatgcgagagagattcagctgggtgtatctacattatgat-tcatatgtttctctgcagGCTACCTTTGATTGTCTGCTGAAGACTTATGCGTACCTCACCCCTGACTTCTGGAGGGAGACTCGGTACACAAAATCCCCATTCCAAGAGCACACAGATC
















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|58022024|gb|CX708765.1|CX708765
EST:     TCTTCACTTCCTCCAGGGGTTCCACCAAAACCCTCGGAAATTTCGTCAAG                         GCTACTTTTGACTGTTTGCTGAAAACCTACGGTTTTCTAACACCTGAATTC
genomic: TCTTCACTTCCTCCAGGGGTTCCACCAAAACCCTCGGAAATTTCGTCAAGgttgttaact ... gtttttacagGCTACTTTTGACTGTTTGCTGAAAACCTACGGTTTTCTAACACCTGAATTC
EST: gi|10234053|gb|BE802941.1|BE802941
EST:     TCTTCACTTCCTCCAGGGGTTCCACCAAAACCCTCGGAAATTTCGTCAAG                         GCTACTTTTGACTGTATGCTGAAAACCTACGGTTNTCTAACACCTGAATTC
genomic: TCTTCACTTCCTCCAGGGGTTCCACCAAAACCCTCGGAAATTTCGTCAAGgttgttaact ... gtttttacagGCTACTTTTGACTGTTTGCTGAAAACCTACGGTTTTCTAACACCTGAATTC
EST: gi|58015153|gb|CX701895.1|CX701895
EST:     TCTTCACTTCCTCCAGGGGTTCCACCAAAACCCTCGGAAATTTCGTCAAG                         GCTACTTTTGACTGTTTGCTGAAAACCTACGGTTTTCTAACACCTGAATTC
genomic: TCTTCACTTCCTCCAGGGGTTCCACCAAAACCCTCGGAAATTTCGTCAAGgttgttaact ... gtttttacagGCTACTTTTGACTGTTTGCTGAAAACCTACGGTTTTCTAACACCTGAATTC
EST: gi|58025439|gb|CX712180.1|CX712180
EST:     TCTTCACTTCCTCCAGGGGTTCCACCAAAACCCTCGGAAATTTCGTCAAG                         GCTACTTTTGACTGTTTGCTGAAAACCTACGGTTTTCTAACACCTGAATTC
genomic: TCTTCACTTCCTCCAGGGGTTCCACCAAAACCCTCGGAAATTTCGTCAAGgttgttaact ... gtttttacagGCTACTTTTGACTGTTTGCTGAAAACCTACGGTTTTCTAACACCTGAATTC
EST: gi|11273939|gb|BF324327.1|BF324327
EST:     TCTTCACTTCCTCCAGGGGTTCCACCANAACCCTCGGAAATNTCGTCAAG                         GCTACTTTTGACTGTTTGCTGAAAACCTACGGTTTTCTAACACCTGAATTC
genomic: TCTTCACTTCCTCCAGGGGTTCCACCAAAACCCTCGGAAATTTCGTCAAGgttgttaact ... gtttttacagGCTACTTTTGACTGTTTGCTGAAAACCTACGGTTTTCTAACACCTGAATTC
EST: gi|12774140|gb|BG239067.1|BG239067
EST:     TCTTCACTTCCTCCAGGGGTTCCACCAAAACCCTCGGAAATTTCGTCAAG                         GCTACTTTTGACTGTTTGCTGAAAACCTACGGTTTTCTAACACCTGAATTC
genomic: TCTTCACTTCCTCCAGGGGTTCCACCAAAACCCTCGGAAATTTCGTCAAGgttgttaact ... gtttttacagGCTACTTTTGACTGTTTGCTGAAAACCTACGGTTTTCTAACACCTGAATTC
EST: gi|20449489|gb|BQ253613.1|BQ253613
EST:     TCTTCACTTCCTCCAGGGGTTCCACCAAAACCCTCGGAAATTTCGTCAAG                         GCTACTTTTGACTGGTTGCTGAAAAC-TACGGTTTTC
genomic: TCTTCACTTCCTCCAGGGGTTCCACCAAAACCCTCGGAAATTTCGTCAAGgttgttaact ... gtttttacagGCTACTTTTGACTGTTTGCTGAAAACCTACGGTTTTC
EST: gi|15812495|gb|BI784770.1|BI784770
EST:     GTTCCACCAAAACCCTCGGAAATTTCGTCAAG                         GCTACTTTTGACTGTTTGCTGAAAACCTACGGTTTTCTAACACCTGAATTC
genomic: GTTCCACCAAAACCCTCGGAAATTTCGTCAAGgttgttaact ... gtttttacagGCTACTTTTGACTGTTTGCTGAAAACCTACGGTTTTCTAACACCTGAATTC
EST: gi|31466087|gb|CD408115.1|CD408115
EST:     TCTTCACTTCCTCCAGGGGTTCCACCAAAACCCTCGGAAATTTCGTCAAG                         GCTACTTTTGACTGTTTGCTGAAAACCTACGGTTTTCTAACACCTGAATTC
genomic: TCTTCACTTCCTCCAGGGGTTCCACCAAAACCCTCGGAAATTTCGTCAAGgttgttaact ... gtttttacagGCTACTTTTGACTGTTTGCTGAAAACCTACGGTTTTCTAACACCTGAATTC
EST: gi|6912807|gb|AW394291.1|AW394291
EST:     TCTTCACTTCCTCCAGGGGTTCCACCAAAACCCTCGGAAATTTCGTCAAG                         GCTACTTTTGACTGTTTGCTGAAAACCTACGGTTTTCTAACACCTGAATTC
genomic: TCTTCACTTCCTCCAGGGGTTCCACCAAAACCCTCGGAAATTTCGTCAAGgttgttaact ... gtttttacagGCTACTTTTGACTGTTTGCTGAAAACCTACGGTTTTCTAACACCTGAATTC
EST: gi|6072906|gb|AW102293.1|AW102293
EST:     CACCAAAACCCTCTGAAATTTCGTCAAG                         GCTACTTTTGACTGTTTGCTGAAAACCTACGGTTTTCTAACACCTGAATTC
genomic: CACCAAAACCCTCGGAAATTTCGTCAAGgttgttaact ... gtttttacagGCTACTTTTGACTGTTTGCTGAAAACCTACGGTTTTCTAACACCTGAATTC
EST: gi|31466417|gb|CD408445.1|CD408445
EST:     TCTTCACTGCCTCCAGGGGTTCCACCAAAACCCTCGGAAATTTCGTCAAG                         GCTACTTTTGACTGTTTGCTGAAAACCTACGGTTTTCTAACACCTGAATTC
genomic: TCTTCACTTCCTCCAGGGGTTCCACCAAAACCCTCGGAAATTTCGTCAAGgttgttaact ... gtttttacagGCTACTTTTGACTGTTTGCTGAAAACCTACGGTTTTCTAACACCTGAATTC
EST: gi|31307363|gb|CD392566.1|CD392566
EST:     TCTTCACTTCCTCCAGGGGTTCCACCAAAACCCTCGGAAATTTCGTCAAG                         GCTACTTTTGACTGTTTGCTGAAAACCTACGGTTTTCTAACACCTGAATTC
genomic: TCTTCACTTCCTCCAGGGGTTCCACCAAAACCCTCGGAAATTTCGTCAAGgttgttaact ... gtttttacagGCTACTTTTGACTGTTTGCTGAAAACCTACGGTTTTCTAACACCTGAATTC
EST: gi|58017154|gb|CX703896.1|CX703896
EST:     TCTTCACTTCCTCCAGGGGTTCCACCAAAACCCTCGGAAATTTCGTCAAG                         GCTACTTTTGACTGTTTGCTGAAAACCTACGGTTTTCTAACACCTGAATTC
genomic: TCTTCACTTCCTCCAGGGGTTCCACCAAAACCCTCGGAAATTTCGTCAAGgttgttaact ... gtttttacagGCTACTTTTGACTGTTTGCTGAAAACCTACGGTTTTCTAACACCTGAATTC
EST: gi|4313612|gb|AI460731.1|AI460731
EST:     TCTTCACTTCCTCCAGGGGTTCCACCAAAACCCTCGGAAATNTCGTCAAG                         GCTACTTTTGACTGTTTGCTGAAAACCTACGGTTNTCTAACACCTGAATTC
genomic: TCTTCACTTCCTCCAGGGGTTCCACCAAAACCCTCGGAAATTTCGTCAAGgttgttaact ... gtttttacagGCTACTTTTGACTGTTTGCTGAAAACCTACGGTTTTCTAACACCTGAATTC
EST: gi|31469619|gb|CD411647.1|CD411647
EST:     TCTTCACTTCCTCCAGGGGTTCCACCAAAACCCTCGGAAATTTCGTCAAG                         GCTACTTTTGACTGTTTGCTGAAAACCTACGGTTTTCTAACACCTGAATTC
genomic: TCTTCACTTCCTCCAGGGGTTCCACCAAAACCCTCGGAAATTTCGTCAAGgttgttaact ... gtttttacagGCTACTTTTGACTGTTTGCTGAAAACCTACGGTTTTCTAACACCTGAATTC
EST: gi|58017600|gb|CX704342.1|CX704342
EST:     TCTTCACTTCCTCCAGGGGTTCCACCAAAACCCTCGGAAATTTCGTCAAG                         GCTACTTTTGACTGTTTGCTGAAAACCTACGGTTTTCTAACACCTGAATTC
genomic: TCTTCACTTCCTCCAGGGGTTCCACCAAAACCCTCGGAAATTTCGTCAAGgttgttaact ... gtttttacagGCTACTTTTGACTGTTTGCTGAAAACCTACGGTTTTCTAACACCTGAATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttaggtatttctaatttatccgtgttcataataatgccacttgtgtttttacagGCTACTTTTGACTGTTTGCTGAAAACCTACGGTTTTCTAACACCTGAATTCTGGAAGGAGACTCGGTTCTCCAAATCACCATTCCAAGAGTACACTGATC
         ttctaat  putative branch site (score: 2)
                                            tgttttt  putative PPT
      tatttctaatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatacactctgaaacaactactcaattgatgataatatgaaacttgttaggtatttctaatttatccgtgttcataataatgccacttgtgtttttacagGCTACTTTTGACTGTTTGCTGAAAACCTACGGTTTTCTAACACCTGAATTCTGGAAGGAGACTCGGTTCTCCAAATCACCATTCCAAGAGTACACTGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- tacactc
- - - - - - - - -ctactca
- - - - - - - - - - - - - tgatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccgtgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgccact