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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtggcatttgtttgtttgtccaccttgtcgctttcaaagaagttgaatccatcttggaaatctaggcgtaaaattaaattcattgctatcttttttctttttctttttcttttttacagGGAACTGGTTCTGCAGGGGCTACGGTTAGAGTGTACATTGAACAGTTTGAACCAGATGTCTCTAAACATGATGTTGATGCTCAAATTGCCTTAAAACCAT

Basic information

species Glycine max
transcript GLYMA10G38590.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G38590.1 (Glycine max), 3'ss of exon 20
lower sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 20
gtatgtggcatttgtttgtttgtccaccttgtcgctttcaaagaagttgaatccatcttggaaatctaggcgtaaaattaaattcattgctatcttttttctttttctttttcttttttacagGGAACTGGTTCTGCAGGGGCTACGGTTAGAGTGTACATTGAACAGTTTGAACCAGATGTCTCTAAACATGATGTTGATGCTCAAATTGCCTTAAAACCAT
          | ||||      ||   ||| |    || ||  || ||  ||   | ||  |  | |||    | | |       ||  |  |    |  |||    |   ||||| || ||||||||||| || || || ||||| ||  || | ||||||||||| ||||| ||||| || || ||||||||||| ||||| ||||| ||  | ||||| |
---------gtatgttgtagattctttctttttttctttaatcaaattccat--gttttatatgtatagagacacattggcccctatcacagtgaactaacttagaat---tctttgttccagGGAACTGGCTCAGCTGGAGCTACAGTGCGAATATACATTGAACAATTTGAGCCAGACGTTTCAAAACATGATGTGGATGCACAAATAGCTCTTAAACCTT

upper sequence: GLYMA10G38590.1 (Glycine max), 3'ss of exon 20
lower sequence: Vv16s0022g02320.t01 (Vitis vinifera), 3'ss of exon 20
gtatgtggcatttgtttgtttgtccaccttgtcgctttcaaagaagttgaatccatcttggaaatctaggcgtaaaattaaattcattgctatcttttttctttttctttttcttttttacagGGAACTGGTTCTGCAGGGGCTACGGTTAGAGTGTACATTGAACAGTTTGAACCAGATGTCTCTAAACATGATGTTGATGCTCAAATTGCCTTAAAACCAT
||| |   ||||  |     | |  |   | || |||  |           | | ||||||  ||| |    || || |    |    |  |          | ||   | || | |||||||||||| ||||||||||| || || |||||| | || |||||||||||||| ||||||||||||||||||||  | ||||| |||   || || || ||||
gtaggcatcattaatcaacctattta---tatctcttcta-----------ttcctcttggggatcca--tttacaactgtggtggaagtaac---------tattgggtctcatatttacagGGAACCGGTTCTGCAGGTGCAACTGTTAGAATTTATATTGAACAGTTTGAGCCAGATGTCTCTAAACATGAAATGGATGCCCAAGCAGCATTGAAGCCAT
















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|120495856|gb|EH224023.1|EH224023
EST:     GTGTTCGGTTTGTTTTTACAGACGGTTCAAGGATTATATATCGTTTATCA                         GGAACTGGTTCTGCAGGGGCTACGGTTAGAGTGTACATTGAACAGTTTGAA
genomic: GTGTTCGGTTTGTTTTTACAGACGGTTCAAGGATTATATATCGTTTATCAgtatgtggca ... ttttttacagGGAACTGGTTCTGCAGGGGCTACGGTTAGAGTGTACATTGAACAGTTTGAA
EST: gi|4260048|gb|AI416544.1|AI416544
EST:     GTGTTCGGTTTGTTTTTACAGACGGTTCAAGGATTATATATCGTTTATCA                         GGAACTGGTTCTGCAGGGGCTACGGTTAGAGTGTACATTGAACAGTTTGAA
genomic: GTGTTCGGTTTGTTTTTACAGACGGTTCAAGGATTATATATCGTTTATCAgtatgtggca ... ttttttacagGGAACTGGTTCTGCAGGGGCTACGGTTAGAGTGTACATTGAACAGTTTGAA
EST: gi|57574855|gb|CX547830.1|CX547830
EST:     GTGTTCGGTTTGTTTTTACAGACGGTTCAAGGATTATATATCGTTTATCA                         GGAACTGGTTCTGCAGGGGCTACGGTTAGAGTGTACATTGAACAGTTTGAA
genomic: GTGTTCGGTTTGTTTTTACAGACGGTTCAAGGATTATATATCGTTTATCAgtatgtggca ... ttttttacagGGAACTGGTTCTGCAGGGGCTACGGTTAGAGTGTACATTGAACAGTTTGAA
EST: gi|120494277|gb|EH222444.1|EH222444
EST:     GTGTTCGGTTTGTTTTTACAGACGGTTCAAGGATTATATATCGTTTATCA                         GGAACTGGTTCTGCAGGGGCTACGGTTAGAGTGTACATTGAACAGTTTGAA
genomic: GTGTTCGGTTTGTTTTTACAGACGGTTCAAGGATTATATATCGTTTATCAgtatgtggca ... ttttttacagGGAACTGGTTCTGCAGGGGCTACGGTTAGAGTGTACATTGAACAGTTTGAA
EST: gi|58020248|gb|CX706990.1|CX706990
EST:     GTGTTCGGTTTGTTTTTACAGACGGTTCAAGGATTATATATCGTTTATCA                         GGAACTGGTTCTGCAGGGGCTACGGTTAGAGTGTACATTGAACAGTTTGAA
genomic: GTGTTCGGTTTGTTTTTACAGACGGTTCAAGGATTATATATCGTTTATCAgtatgtggca ... ttttttacagGGAACTGGTTCTGCAGGGGCTACGGTTAGAGTGTACATTGAACAGTTTGAA
EST: gi|192333011|gb|FK024660.1|FK024660
EST:     GTGTTCGGTTTGTTTTTACAGACGGTTCAAGGATTATATATCGTTTATCA                         GGAACTGGTTCTGCAGGGGCTACGGTTAGAGTGTACATTGAACAGTTTGAA
genomic: GTGTTCGGTTTGTTTTTACAGACGGTTCAAGGATTATATATCGTTTATCAgtatgtggca ... ttttttacagGGAACTGGTTCTGCAGGGGCTACGGTTAGAGTGTACATTGAACAGTTTGAA
EST: gi|120494776|gb|EH222943.1|EH222943
EST:     GTGTTCGGTTTGTTTTTACAGACGGTTCAAGGATTATATATCGTTTATCA                         GGAACTGGTTCTGCAGGGGCTACGGTTAGAGTGTACATTGAACAGTTTGAA
genomic: GTGTTCGGTTTGTTTTTACAGACGGTTCAAGGATTATATATCGTTTATCAgtatgtggca ... ttttttacagGGAACTGGTTCTGCAGGGGCTACGGTTAGAGTGTACATTGAACAGTTTGAA
EST: gi|4259997|gb|AI416493.1|AI416493
EST:     TGTTCGGTTTG-TTTTACAGACGGGTCAAAGGATTATATATCGTTTATCA                         GGAACTGGTTCTGCAGGGGCTACGGTNAGAGTGTACATTGAACAGTTTGAA
genomic: TGTTCGGTTTGTTTTTACAGACGGTTC-AAGGATTATATATCGTTTATCAgtatgtggca ... ttttttacagGGAACTGGTTCTGCAGGGGCTACGGTTAGAGTGTACATTGAACAGTTTGAA
EST: gi|31310494|gb|CD395697.1|CD395697
EST:     GTGTTCGGTTTGTTTTTACAGACGGTTCAAGGATTATATATCGTTTATCA                         GGAACTGGTTCTGCAGGGGCTACGGTTAGAGTGTACATTGAACAGTTTGAA
genomic: GTGTTCGGTTTGTTTTTACAGACGGTTCAAGGATTATATATCGTTTATCAgtatgtggca ... ttttttacagGGAACTGGTTCTGCAGGGGCTACGGTTAGAGTGTACATTGAACAGTTTGAA
EST: gi|58015952|gb|CX702694.1|CX702694
EST:     GTGTTCGGTTTGTTTTTACAGACGGTTCAAGGATTATATATCGTTTATCA                         GGAACTGGTTCTGCAGGGGCTACGGTTAGAGTGTCCATTGACCAGTTTGAA
genomic: GTGTTCGGTTTGTTTTTACAGACGGTTCAAGGATTATATATCGTTTATCAgtatgtggca ... ttttttacagGGAACTGGTTCTGCAGGGGCTACGGTTAGAGTGTACATTGAACAGTTTGAA
EST: gi|120494261|gb|EH222428.1|EH222428
EST:     GTGTTCGGTTTGTTTTTACAGACGGTTCAAGGATTATATATCGTTTATCA                         GGAACTGGTTCTGCAGGGGCTACGGTTAGAGTGTACCTTGAACAGTTTGAA
genomic: GTGTTCGGTTTGTTTTTACAGACGGTTCAAGGATTATATATCGTTTATCAgtatgtggca ... ttttttacagGGAACTGGTTCTGCAGGGGCTACGGTTAGAGTGTACATTGAACAGTTTGAA
EST: gi|10231645|gb|BE800533.1|BE800533
EST:     GTGTTCGGTTTGTTTTTACAGACGGTTCAAGGATTATATATCGTTTATCA                         GGAACTGGTTCTGCAGGGGCTACGGTTAGAGTGTACATTGAACAGTTTGAA
genomic: GTGTTCGGTTTGTTTTTACAGACGGTTCAAGGATTATATATCGTTTATCAgtatgtggca ... ttttttacagGGAACTGGTTCTGCAGGGGCTACGGTTAGAGTGTACATTGAACAGTTTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcgtaaaattaaattcattgctatcttttttctttttctttttcttttttacagGGAACTGGTTCTGCAGGGGCTACGGTTAGAGTGTACATTGAACAGTTTGAACCAGATGTCTCTAAACATGATGTTGATGCTCAAATTGCCTTAAAACCAT
              ttcattgctatctttt  CT-rich tract
                      tatcttttttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtggcatttgtttgtttgtccaccttgtcgctttcaaagaagttgaatccatcttggaaatctaggcgtaaaattaaattcattgctatcttttttctttttctttttcttttttacagGGAACTGGTTCTGCAGGGGCTACGGTTAGAGTGTACATTGAACAGTTTGAACCAGATGTCTCTAAACATGATGTTGATGCTCAAATTGCCTTAAAACCAT

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