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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggatgtaatgtgctattttaatttatttatgaacacccttgcttaagcctaaagttaaccaatactttccttgacaaacatggtattaatttgtttaatggtttgttggcagCCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTGAAGGACAACAAGGTTGTAAAAGAAGTTACTGGAGCTAAATACGATGATT

Basic information

species Glycine max
transcript GLYMA18G47850.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G47850.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G02730.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------------------------------------------------gtatggatgtaatgtgctattttaatt--tatttatgaacaccct-tgcttaagcctaaagtta--accaatactttccttgacaaacatggtattaatttgtttaa-tggtttgttgg--cagCCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTGAAGGACAACAAGGTTGTAAAAGAAGTTACTGGAGCTAAATACGATGATT
                                                       ||  ||  | ||  | ||    | |   |  || | | |  |  | | |     |   |||   || | ||| |  |||        || |  |||    || ||    ||  ||||  ||||| ||||||| |||||| ||||| | ||||||||| |||||||| ||| ||||||| ||||||||||| || ||||| || || || |||||||||||| 
gtctgagttctgctcttttatctctcttcttttggtaactcggttttcctaaaccatatatcaattgaaccatagctagtagcagctaaggataatcaatacctgtttttgttgttgctactactacctgtctttgttgt--tgctgctaagccattgaaactcttcattggtgcagCCATTGGCAAAAGAGCTAGGAATAAGAGTGGTTCCAACTTTCAAGATTTTGAAGGATAACAAGGTTGTCAAGGAAGTGACCGGTGCAAAATACGATGATC

upper sequence: GLYMA18G47850.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G16400.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatggatgtaatgtgctattttaatttatttatgaacacccttgcttaagcctaaagttaaccaatactttccttgacaaacatggtattaattt----gtttaatggtt--tgttggcagCCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTGAAGGACAACAAGGTTGTAAAAGAAGTTACTGGAGCTAAATACGATGATT
                                            | ||   | |    ||   |   |  |  ||| | |   ||| || | ||||      | ||    |  || | |||||| ||||| | |||||| ||||||| ||||||||| ||||| |||||  |||| ||||||||||| ||||| ||||| || || || ||||| || || |
--------------------------------------------gtttgttcttctttttccgctgaatgtgtctttatatttatgttacttatttcataactcaaaaactcttgcttgcagCCATTGGCGAAAGAGCTAGGAATTAGAGTGGTTCCAACTTTTAAAATCTTGAAAGACAACAAGGTAGTAAAGGAAGTGACCGGGGCAAAATATGAAGACT

upper sequence: GLYMA18G47850.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0023g00740.t01 (Vitis vinifera), 3'ss of exon 2
gtatggatgtaatgtgctattttaatttatttatgaacacccttgcttaagcctaaagttaaccaatactttccttgacaaacatggtattaatttgtttaatggtttgttggcagCCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTGAAGGACAACAAGGTTGTAAAAGAAGTTACTGGAGCTAAATACGATGATT
                               | || |  |  || | | | || ||  ||  |  ||||     |  || | | |   | | |||  | | | |   ||||||||| | |||||||  ||||||||||| |  |||||||| || ||||| || |||||||||| |||| | ||||| |||||||| || || ||||  || ||||
------------------------------gtctgtaatcttttacctgatcccaa--ttccctgatacaaa--tgcacgagc-tcacactgattcatctga-gaactgttggcagACTTTGGCAAAGGAGCTGGGAATCAGGGTGGTTCCTACCTTCAAGATCCTGAAGGACAGCAAGATCGTAAAGGAAGTTACAGGGGCCAAATTAGACGATT

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|208206678|gb|GE005815.1|GE005815
EST:     AGTATCTGGATGTTGTCTTTC-AAAGCTTGATTGCAACCAAGACAACAGG                         CCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCAC
genomic: AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGGgtatggatgt ... ttgttggcagCCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCAC
EST: gi|208291436|gb|GE094602.1|GE094602
EST:     AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGG                         CCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTG
genomic: AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGGgtatggatgt ... ttgttggcagCCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTG
EST: gi|208315959|gb|GE117871.1|GE117871
EST:     ATCTGGATGTTGTACTTTACTAAAAGCTTGATTGCAACCAAGACAACAGG                         CCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCATAATTCTG
genomic: ATCTGGATGTTGT-CTTT-CTAAA-GCTTGATTGCAACCAAGACAACAGGgtatggatgt ... ttgttggcagCCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTG
EST: gi|193573980|gb|FK529298.1|FK529298
EST:     AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGG                         CCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTG
genomic: AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGGgtatggatgt ... ttgttggcagCCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTG
EST: gi|193449274|gb|FK412025.1|FK412025
EST:     AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGG                         CCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTG
genomic: AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGGgtatggatgt ... ttgttggcagCCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTG
EST: gi|208235444|gb|GE029686.1|GE029686
EST:     AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGG                         CCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATT
genomic: AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGGgtatggatgt ... ttgttggcagCCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATT
EST: gi|10233522|gb|BE802410.1|BE802410
EST:     AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGG                         CCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTG
genomic: AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGGgtatggatgt ... ttgttggcagCCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTG
EST: gi|22523063|gb|BU081874.1|BU081874
EST:     GTATCTNGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGG                         CCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTG
genomic: GTATCT-GGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGGgtatggatgt ... ttgttggcagCCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTG
EST: gi|8669948|gb|BE191055.1|BE191055
EST:     AGTATCTGGATGTTGTCTNTCTAAAGCTTGATTGCAACCAAGACAACAGG                         CCCTTGGCAATAGAGCTGGGAATTAAAGTGGCTCCCACTTTCAAAATTCTG
genomic: AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGGgtatggatgt ... ttgttggcagCCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTG
EST: gi|15204667|gb|BI427435.1|BI427435
EST:     AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGG                         CCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTG
genomic: AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGGgtatggatgt ... ttgttggcagCCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTG
EST: gi|209718144|gb|BW657803.1|BW657803
EST:     AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGG                         CCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTG
genomic: AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGGgtatggatgt ... ttgttggcagCCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTG
EST: gi|193496027|gb|FK458607.1|FK458607
EST:     AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGG                         CCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTG
genomic: AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGGgtatggatgt ... ttgttggcagCCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTG
EST: gi|208097036|gb|GD894689.1|GD894689
EST:     AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGG                         CCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAAATTCT
genomic: AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGGgtatggatgt ... ttgttggcagCCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAA-TTCT
EST: gi|207820793|gb|GD791790.1|GD791790
EST:     AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGG                         CCCTGGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTG
genomic: AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGGgtatggatgt ... ttgttggcagCCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTG
EST: gi|208201450|gb|GE000014.1|GE000014
EST:     AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGG                         CCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCCACTTTCAAAATTCT
genomic: AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGGgtatggatgt ... ttgttggcagCCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCC-ACTTTCAAAATTCT
EST: gi|193666151|gb|FK612210.1|FK612210
EST:     AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGG                         CCCTTGGCAAATAAGAAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATT
genomic: AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGGgtatggatgt ... ttgttggcagCCCTTGGCAA-TA-GA-GCTGGGAATTAAAGTGGTTCCCACTTTCAAAATT
EST: gi|15204672|gb|BI427440.1|BI427440
EST:     AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGG                         CCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTG
genomic: AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGGgtatggatgt ... ttgttggcagCCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTG
EST: gi|208110738|gb|GD910892.1|GD910892
EST:     AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGG                         CCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTACT
genomic: AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGGgtatggatgt ... ttgttggcagCCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATT-CT
EST: gi|208178337|gb|GD978290.1|GD978290
EST:     AGCATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGG                         CCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTG
genomic: AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGGgtatggatgt ... ttgttggcagCCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTG
EST: gi|10844836|gb|BF068037.1|BF068037
EST:     AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAATACAACAGG                         CCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTG
genomic: AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGGgtatggatgt ... ttgttggcagCCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTG
EST: gi|10231562|gb|BE800450.1|BE800450
EST:     AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGG                         CCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTG
genomic: AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGGgtatggatgt ... ttgttggcagCCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTG
EST: gi|20498028|gb|BQ272958.1|BQ272958
EST:     AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGG                         CCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTG
genomic: AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGGgtatggatgt ... ttgttggcagCCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTG
EST: gi|5760472|gb|AI965835.1|AI965835
EST:     AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGG                         CCCTTGGCAATAGAGCTGTGAATTAAAGTGGTTCCCACTCTCAAAATTCTG
genomic: AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGGgtatggatgt ... ttgttggcagCCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTG
EST: gi|193413845|gb|FK378276.1|FK378276
EST:     AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGG                         CCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTG
genomic: AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGGgtatggatgt ... ttgttggcagCCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTG
EST: gi|208076715|gb|GD875644.1|GD875644
EST:     GTATCTGGATGTTAGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGG                         CCCTTGGCAATAGAGCTGGG
genomic: GTATCTGGATGTT-GTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGGgtatggatgt ... ttgttggcagCCCTTGGCAATAGAGCTGGG
EST: gi|208247694|gb|GE045278.1|GE045278
EST:     AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGG                         CCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCCACTTTCAAAATT
genomic: AGTATCTGGATGTTGTCTTTCTAAAGCTTGATTGCAACCAAGACAACAGGgtatggatgt ... ttgttggcagCCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCC-ACTTTCAAAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accaatactttccttgacaaacatggtattaatttgtttaatggtttgttggcagCCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTGAAGGACAACAAGGTTGTAAAAGAAGTTACTGGAGCTAAATACGATGATT
                          tattaatttgtttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggatgtaatgtgctattttaatttatttatgaacacccttgcttaagcctaaagttaaccaatactttccttgacaaacatggtattaatttgtttaatggtttgttggcagCCCTTGGCAATAGAGCTGGGAATTAAAGTGGTTCCCACTTTCAAAATTCTGAAGGACAACAAGGTTGTAAAAGAAGTTACTGGAGCTAAATACGATGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT