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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttggccttctaccatgttctgccatctgccactgataacactgcttgcatattaattaattcatgcaatgaccatcactcttcactctttaattcgcagTTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCCCTCCCCCTAATTCTGTTGGGAAAG

Basic information

species Glycine max
transcript GLYMA18G46140.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G46140.3 (Glycine max), 3'ss of exon 3
lower sequence: Vv15s0048g01890.t01 (Vitis vinifera), 3'ss of exon 2
tttggccttctaccatgttctgccatctgccactgataacactgcttgcatattaattaattcatgcaatgac-catcactcttcactctttaattcgcagTTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCCCTCCCCCTAATTCTGTTGGGAAAG
  | |    |  || |  |     |      |    | |   ||       ||||| | |||  |    | ||   | |   ||||  |||    | ||||||||||||||||||||||||| | || |||||| | || || || ||||| || || ||  || |||||||||||
-atagggggcacccttagtgcattaaaaaaaaaatctgatgttgaacttgcattaaatcattattattctaacgttttatgtttcatccttctgattgcagTTTGTCAATGACCTACATGCTCTTATTAGTCCAGCTCCTCAAGGGACTCCTCTTCCACTTGTTTTGTTGGGAAAG
















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|15815736|gb|BI788011.1|BI788011
EST:     ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAG                         TTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
genomic: ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAGgttaggttct ... taattcgcagTTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
EST: gi|11412081|gb|BF424092.1|BF424092
EST:     ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAG                         TTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
genomic: ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAGgttaggttct ... taattcgcagTTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
EST: gi|15001018|gb|BI321832.1|BI321832
EST:     ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAG                         TTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
genomic: ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAGgttaggttct ... taattcgcagTTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
EST: gi|298169267|gb|HO020627.1|HO020627
EST:     ATGTCGACAAAACAACCAGCTTGGCACGAAAAGCCTTCCGTCTTTTTAAG                         TTTGTCAATGACCTACGTGCTTTGATAAGTCCAACACCACAGGGCACTCCC
genomic: ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAGgttaggttct ... taattcgcagTTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
EST: gi|7926421|gb|AW832447.1|AW832447
EST:     ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAG                         TTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
genomic: ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAGgttaggttct ... taattcgcagTTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
EST: gi|58017723|gb|CX704465.1|CX704465
EST:     CGAAAAGTCTTCCGTCTTTTTAAG                         TTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
genomic: CGAAAAGTCTTCCGTCTTTTTAAGgttaggttct ... taattcgcagTTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
EST: gi|7284130|gb|AW596728.1|AW596728
EST:     ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAG                         TTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
genomic: ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAGgttaggttct ... taattcgcagTTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
EST: gi|23052758|gb|BU577249.1|BU577249
EST:     ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAG                         TTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
genomic: ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAGgttaggttct ... taattcgcagTTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
EST: gi|7691215|gb|AW759346.1|AW759346
EST:     ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAG                         TTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
genomic: ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAGgttaggttct ... taattcgcagTTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
EST: gi|13251950|gb|BG362853.1|BG362853
EST:     ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAG                         TTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
genomic: ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAGgttaggttct ... taattcgcagTTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
EST: gi|58023678|gb|CX710419.1|CX710419
EST:     ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAG                         TTTGTCAATGACNTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
genomic: ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAGgttaggttct ... taattcgcagTTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
EST: gi|7796633|gb|AW782030.1|AW782030
EST:     ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAG                         TTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
genomic: ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAGgttaggttct ... taattcgcagTTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
EST: gi|58014395|gb|CX701137.1|CX701137
EST:     CGAAAAGTCTTCCGTCTTTTTAAG                         TTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
genomic: CGAAAAGTCTTCCGTCTTTTTAAGgttaggttct ... taattcgcagTTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
EST: gi|6482692|gb|AW201929.1|AW201929
EST:     ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAG                         TTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
genomic: ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAGgttaggttct ... taattcgcagTTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
EST: gi|15663457|gb|BI700828.1|BI700828
EST:     ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAG                         TTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
genomic: ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAGgttaggttct ... taattcgcagTTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
EST: gi|209698252|gb|BW678023.1|BW678023
EST:     ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAG                         TTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
genomic: ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAGgttaggttct ... taattcgcagTTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
EST: gi|15814527|gb|BI786802.1|BI786802
EST:     ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAG                         TTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACATGGCACTCCC
genomic: ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAGgttaggttct ... taattcgcagTTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
EST: gi|151412092|gb|EV281904.1|EV281904
EST:     ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAG                         TTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
genomic: ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAGgttaggttct ... taattcgcagTTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
EST: gi|9564862|gb|BE474371.1|BE474371
EST:     ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAG                         TTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
genomic: ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAGgttaggttct ... taattcgcagTTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
EST: gi|58023559|gb|CX710300.1|CX710300
EST:     ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAG                         TTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
genomic: ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAGgttaggttct ... taattcgcagTTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
EST: gi|18725662|gb|BM523624.1|BM523624
EST:     ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAG                         TTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
genomic: ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAGgttaggttct ... taattcgcagTTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
EST: gi|27809248|gb|CB063670.1|CB063670
EST:     ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAG                         TTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
genomic: ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAGgttaggttct ... taattcgcagTTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
EST: gi|120530703|gb|EH258836.1|EH258836
EST:     ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAG                         TTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
genomic: ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAGgttaggttct ... taattcgcagTTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
EST: gi|4395943|gb|AI494940.1|AI494940
EST:     ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAG                         TTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
genomic: ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAGgttaggttct ... taattcgcagTTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
EST: gi|27446046|gb|CA953169.1|CA953169
EST:     ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAG                         TTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC
genomic: ATGTCGACAAAACAACCAGCTTGGCACGAAAAGTCTTCCGTCTTTTTAAGgttaggttct ... taattcgcagTTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcatattaattaattcatgcaatgaccatcactcttcactctttaattcgcagTTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCCCTCCCCCTAATTCTGTTGGGAAAG
                              tcactcttcactcttt  CT-rich tract
     tattaattaattcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttggccttctaccatgttctgccatctgccactgataacactgcttgcatattaattaattcatgcaatgaccatcactcttcactctttaattcgcagTTTGTCAATGACCTACATGCTTTGATAAGTCCAACACCACAGGGCACTCCCCTCCCCCTAATTCTGTTGGGAAAG

- - gccttct
- - - - - - -catgttc
- - - - - - - - - - - - - ctgccac
- - - - - - - - - - - - - - - - - - - -cactgct
- - - - - - - - - - - - - - - - - - - - - - - tgcatat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgca