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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttaagctataattctgtttacaacatgggaaatcattcatctcaccttgcagaatttcattttgttcccatgtgattaagttattatctttcattgcagGAGCATCCTGAGTGGGAGATTAAGAATGGTAGTGTCTTTTTCCAAAAGGCAAAAGAATCTGCACCTTGCAAAGAAATACCCTCTCTGCAGCTCATCAACC

Basic information

species Glycine max
transcript GLYMA05G25730.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G25730.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv02s0025g02010.t01 (Vitis vinifera), 3'ss of exon 5
--tttaagctataattctgt-ttacaacatgggaaatcattcatctcaccttgcagaatttcattttgttcccatgtgattaagttattatctttcattgcagGAGCATCCTGAGTGGGAGATTAAGAATGGTAGTGTCTTTTTCCAAAAGGCAAAAGAATCTGCACCTTGCAAAGAAATACCCTCTCTGCAGCTCATCAACC
     |    ||    | |  || ||| |  |    || |  |        || |  |    | | | ||     |   || | |||| ||||    |||||||||||||||||||||||||| ||||| ||   ||| |||||||| | ||| |||||||||||||| |||||||| || || |||||||| ||||| ||||
cacacatatcatgcaccagaattgcaatacagttgctcttgtactctttactgaatgaagggaatct-ttgatgagcatttgaattatcatctgc--ttgcagGAGCATCCTGAGTGGGAGATAAAGAACGGCCATGTGTTTTTCCAGAGGGCGAAAGAATCTGCACCCTGCAAAGAGATTCCGTCTCTGCAACTCATTAACC
















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|192324155|gb|FK017886.1|FK017886
EST:     AAATGTTGCTGTTCTCCTCTGGCCAGGAACTCCTTGAATATATTAAAGAG                         GAGCATCCTGAGTGGGAGATTAAGAATGGTAGTGTCTTTTTCCAAAAGGCA
genomic: AAATGTTGCTGTTCTCCTCTGACCAGGAACTCCTTGAATATATTAAAGAGgtgagcattg ... ttcattgcagGAGCATCCTGAGTGGGAGATTAAGAATGGTAGTGTCTTTTTCCAAAAGGCA
EST: gi|7796600|gb|AW781997.1|AW781997
EST:     AAATGTTGCTGTTCTCCTCTGACCAGGAACTCCTTGAATATATTAAAGAG                         GAGCATCCTGAGTGGGAGATTAAGAATGGTAGTGTCTTTTTCCAAAAGGCA
genomic: AAATGTTGCTGTTCTCCTCTGACCAGGAACTCCTTGAATATATTAAAGAGgtgagcattg ... ttcattgcagGAGCATCCTGAGTGGGAGATTAAGAATGGTAGTGTCTTTTTCCAAAAGGCA
EST: gi|298178308|gb|HO024043.1|HO024043
EST:     AAATGTTGCTGTTCTCCTCAGACCAGGAACTCCTTGAATATATTAAAGAG                         GAGCATCCTGAGTGGGAGATTAAGAATGGTAGTGTCTTTTTCC
genomic: AAATGTTGCTGTTCTCCTCTGACCAGGAACTCCTTGAATATATTAAAGAGgtgagcattg ... ttcattgcagGAGCATCCTGAGTGGGAGATTAAGAATGGTAGTGTCTTTTTCC
EST: gi|208079531|gb|GD873661.1|GD873661
EST:     AAATGTTGCTGTTCTCCTCTGACCAGGAACTCCTTGAATATATTAAAGAG                         GAGCATCCTGAGTGGGAGATTAAGAATGGTAGTGTCTTTTTCCAAAAGGCA
genomic: AAATGTTGCTGTTCTCCTCTGACCAGGAACTCCTTGAATATATTAAAGAGgtgagcattg ... ttcattgcagGAGCATCCTGAGTGGGAGATTAAGAATGGTAGTGTCTTTTTCCAAAAGGCA
EST: gi|193721599|gb|FK658755.1|FK658755
EST:     AAATGTTGCTGTTCTCCTCTGACCAGGAACTCCTTGAATATATTAAAGAG                         GAGCATCCTGAGTGGGAGATTAAGAATGGTAGTGTCTTTT-CCAAAAGGCA
genomic: AAATGTTGCTGTTCTCCTCTGACCAGGAACTCCTTGAATATATTAAAGAGgtgagcattg ... ttcattgcagGAGCATCCTGAGTGGGAGATTAAGAATGGTAGTGTCTTTTTCCAAAAGGCA
EST: gi|4307283|gb|AI444025.1|AI444025
EST:     AAATGTTGCTGTTCTCCTCTGACCAGGAACTCCTTGAATATATTAAAGAG                         GAGCATCCTGAGTGGGAGATTAAGAATGGTAGTGTCTTTTTCCAAAAGGCA
genomic: AAATGTTGCTGTTCTCCTCTGACCAGGAACTCCTTGAATATATTAAAGAGgtgagcattg ... ttcattgcagGAGCATCCTGAGTGGGAGATTAAGAATGGTAGTGTCTTTTTCCAAAAGGCA
EST: gi|58022693|gb|CX709434.1|CX709434
EST:     AAATGTTGCTGTTCTCCTCTGACCAGGAACTCCTTGAATATATTAAAGAG                         GAGCATCCTGAGTGGGAGATTAAGAATGGTAGTGTCTTTTTCCAAAAGGCA
genomic: AAATGTTGCTGTTCTCCTCTGACCAGGAACTCCTTGAATATATTAAAGAGgtgagcattg ... ttcattgcagGAGCATCCTGAGTGGGAGATTAAGAATGGTAGTGTCTTTTTCCAAAAGGCA
EST: gi|58019686|gb|CX706428.1|CX706428
EST:     AAATGTTGCTGTTCTCCTCTGACCAGGAACTCCTTGAATATATTAAAGAG                         GAGCATCCTGAGTGGGAGATTAAGAATGGTAGTGTCTTTTTCCAAAAGGCA
genomic: AAATGTTGCTGTTCTCCTCTGACCAGGAACTCCTTGAATATATTAAAGAGgtgagcattg ... ttcattgcagGAGCATCCTGAGTGGGAGATTAAGAATGGTAGTGTCTTTTTCCAAAAGGCA
EST: gi|7234655|gb|AW569991.1|AW569991
EST:     AAATGTTGCTGTTCTCCTCTGACCAGGAACTCCTTGAATATATTAAAGAG                         GAGCATCCTGAGTGGGAGATTAAGAATGGTAG
genomic: AAATGTTGCTGTTCTCCTCTGACCAGGAACTCCTTGAATATATTAAAGAGgtgagcattg ... ttcattgcagGAGCATCCTGAGTGGGAGATTAAGAATGGTAG
EST: gi|207811622|gb|GD783991.1|GD783991
EST:     AAATGTTGCTGTTCTCCTCTGACCAGGAACTCCTTGAATATATTAAAGAG                         GAGCATCCTGAGTGGGAGATTAAGAATTGTAGTGTCTTTTTCCAAAAGGCA
genomic: AAATGTTGCTGTTCTCCTCTGACCAGGAACTCCTTGAATATATTAAAGAGgtgagcattg ... ttcattgcagGAGCATCCTGAGTGGGAGATTAAGAATGGTAGTGTCTTTTTCCAAAAGGCA
EST: gi|33389688|gb|CA852895.1|CA852895
EST:     AAATGTTGCTGTTCTCCTCAGACCAGGAACTCCTTGAATATATTAAAGAG                         GAGCATCCTGAGTGGGAGATTAAGAATGGTAGTGTCTTTTTCCAAAAGGCA
genomic: AAATGTTGCTGTTCTCCTCTGACCAGGAACTCCTTGAATATATTAAAGAGgtgagcattg ... ttcattgcagGAGCATCCTGAGTGGGAGATTAAGAATGGTAGTGTCTTTTTCCAAAAGGCA
EST: gi|23729081|gb|BU762625.1|BU762625
EST:     AAATGTTGCTGTTCTCCTCAGACCAGGAACTCCTTGAATATATTAAAGAG                         GAGCATCCTGAGTGGGAGATTAAGAATGGTAGTGTCTTTTTCCAAAAGGCA
genomic: AAATGTTGCTGTTCTCCTCTGACCAGGAACTCCTTGAATATATTAAAGAGgtgagcattg ... ttcattgcagGAGCATCCTGAGTGGGAGATTAAGAATGGTAGTGTCTTTTTCCAAAAGGCA
EST: gi|193396367|gb|FK362765.1|FK362765
EST:     AATGTTGCTGTTCTCCTCTGACCAGGAACTCCTTGAATATATTAAAAGAG                         GAGCATCCTGAAGTGGGAGATTAAGAATGGTAGTGTCTTTTTCC-AAAGG
genomic: AATGTTGCTGTTCTCCTCTGACCAGGAACTCCTTGAATATATT-AAAGAGgtgagcattg ... ttcattgcagGAGCATCCTG-AGTGGGAGATTAAGAATGGTAGTGTCTTTTTCCAAAAGG
EST: gi|58014496|gb|CX701238.1|CX701238
EST:     AAATGTTGCTGTTCTCCTCTGACCAGGAACTCCTTGAATATATTAAAGAG                         GAGCATCCTGAGTGGGAGATTAAGAATGGTAGTGTCTTTTTCCAAAAGGCA
genomic: AAATGTTGCTGTTCTCCTCTGACCAGGAACTCCTTGAATATATTAAAGAGgtgagcattg ... ttcattgcagGAGCATCCTGAGTGGGAGATTAAGAATGGTAGTGTCTTTTTCCAAAAGGCA
EST: gi|9820179|gb|BE555689.1|BE555689
EST:     AAATGTTGCTGTTCTCCTCTGACCAGGAACTCCTTGAATATATTAAAGAG                         GAGCATCCTGAGTGGGAGATTAAGAATGGTAGTGTCTTTTTCCAAAAGGCA
genomic: AAATGTTGCTGTTCTCCTCTGACCAGGAACTCCTTGAATATATTAAAGAGgtgagcattg ... ttcattgcagGAGCATCCTGAGTGGGAGATTAAGAATGGTAGTGTCTTTTTCCAAAAGGCA
EST: gi|151401431|gb|EV271245.1|EV271245
EST:     AAATGTTGCTGTTCTCCTCTGACCAGGAACTCCTTGAATATATTAAAGAG                         GAGCATCCTGAGTGGGAGATTAAGAATGGTAGTGTCTTTTTCCAAAAGGCA
genomic: AAATGTTGCTGTTCTCCTCTGACCAGGAACTCCTTGAATATATTAAAGAGgtgagcattg ... ttcattgcagGAGCATCCTGAGTGGGAGATTAAGAATGGTAGTGTCTTTTTCCAAAAGGCA
EST: gi|192306503|gb|FG996207.1|FG996207
EST:     AAATGTTGCTGTTTTCCTCTGACCAGGAACTCCTTGAATATATTAAAGAG                         GAGCATCCTGAGTGGGAGATTAAGAATGGTAGTGTCTTTTTCCAAAAGGCA
genomic: AAATGTTGCTGTTCTCCTCTGACCAGGAACTCCTTGAATATATTAAAGAGgtgagcattg ... ttcattgcagGAGCATCCTGAGTGGGAGATTAAGAATGGTAGTGTCTTTTTCCAAAAGGCA
EST: gi|6845858|gb|AW348148.1|AW348148
EST:     AATGTTGCTGTTCTCCTCTGACCAGGANNCTCCTTGAATATATTAAAGAG                         GAGCATCCTGAGTGGGAGATTAAGAATGGTAGTGTCTTTTTCCAAAAGGCA
genomic: AATGTTGCTGTTCTCCTCTGACCAGGA-ACTCCTTGAATATATTAAAGAGgtgagcattg ... ttcattgcagGAGCATCCTGAGTGGGAGATTAAGAATGGTAGTGTCTTTTTCCAAAAGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttgcagaatttcattttgttcccatgtgattaagttattatctttcattgcagGAGCATCCTGAGTGGGAGATTAAGAATGGTAGTGTCTTTTTCCAAAAGGCAAAAGAATCTGCACCTTGCAAAGAAATACCCTCTCTGCAGCTCATCAACC
                                       ttatctttc  CT-rich tract
                              attaagttattatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttaagctataattctgtttacaacatgggaaatcattcatctcaccttgcagaatttcattttgttcccatgtgattaagttattatctttcattgcagGAGCATCCTGAGTGGGAGATTAAGAATGGTAGTGTCTTTTTCCAAAAGGCAAAAGAATCTGCACCTTGCAAAGAAATACCCTCTCTGCAGCTCATCAACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - ttctgtt
- - - - - - - - - - - -acatggg
- - - - - - - - - - - - - - - - - cattcat
- - - - - - - - - - - - - - - - - - - - - - -ccttgca