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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

tttgtcattggaaaactgtgttttgggcatattgtatttcactagttgagcctttttcaacaatgaaagaaaataaatatttcatttaagttttatttatttatagtgtagcttctatttttctattttgtcatttacttttcaaaatctatcagatgttacattcaattttagatttcatttgcaggAAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGG

Basic information

species Glycine max
transcript GLYMA18G08230.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G08230.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 2
tttgtcattggaaaactgtgttttgggcatattgtatttcactagttgagcctttttcaacaatgaaagaaaataaatatttcatttaagttttatttatttatagtgtagcttctatttttctattttgtcatttacttttcaaaatctatcagatgttacattcaattttagatttcatttgcaggAAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGG
                   ||||  ||   ||||       ||  ||      |||||  |  | |  |||||| ||||   | ||   | ||||| ||| || |   ||           |  |  |  || |      |    |||||    | |||  |  ||   |   |   ||   ||||||| ||||||||| ||||  |||||||||| ||||| || |||||| |||||||||||||| 
-------------------gtttgtgggtgattgc----tgctgctttctttcttttcttctcttag-gaaaatgaatacaactttcttgctttatgtatgtacacaatacacatacaccatacacatgatcgtga----tgagtaatctg--ggttgtggcgctcttgtcctggcatc--ctgcagGAGGAGTTTCAGCTGGCGCTGTTCAAGACTAATAAGAAGGAAAGTTTGTTTGCTGATCGG-

upper sequence: GLYMA18G08230.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 4
tttgtcattggaaaactgtgttttgggcatattgtatttcactagttgagcctttttcaacaatgaaagaaaataaatatttcatttaagttttatttatttatagtgtagcttctatttttctattttgtcatttacttttcaaaatctatcagatgttacattcaattttagatttcatttgcaggAAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGG
                                                           |  | | |||   || | ||| |   ||   |   | | | ||||| |       | | |  |  || |||  |  | |||||  | |||  |      ||    |  |  |    | || ||  |||||||| |||||||| || ||||||||||||||||||||||| ||  ||||||| || ||| 
---------------------------------------------------------gtatgaaggaagggcatcattatatgtcttttatgccactcacttatactcc--tcacgaatcatgcatattgctacgt-cttttggacatccttttctgattttccttgacctgtcttgtcgtt--cagGAAGAATTTCAGTTAGCCTTGTTCAAGACAAATAAAAAAGAGAGCTTGTTTGCAGACCGG-

upper sequence: GLYMA18G08230.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 4
tttgtcattggaaaactgtgttttgggcatattgtatttcactagttgagcctttttcaacaatgaaagaaaataaatatttcatttaagttttatttatttatagtgtagcttctatttttctattttgtcatttact--tttcaaaatctatcagatgttacattcaattttagatttcatttgcaggAAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGG
                                                                                    | ||| | | | || |||    | |   | ||  |||  ||     | | | | |  | | | ||||| ||  || |   | |||  | | | ||  ||   |||||||||||||||||||| ||||| ||||||||||||||||| ||| ||||||| |||||| 
-----------------------------------------------------------------------------------gtataactctaacttgttt--gatcttcttcctcatttggtaaagctttagtgattgatctaacaatctgtctaattt---actcatctcttgtttgtat---cagGAAGAGTTTCAGTTGGCTTTGTTTAAGACAAATAAAAAAGAGAGTTTGTTTGCAGATCGG-

upper sequence: GLYMA18G08230.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0015g01070.t01 (Vitis vinifera), 3'ss of exon 2
tttgtcattggaaaactgtgttttgggcatattgtatttcactagttgagccttt-ttcaaca-atgaaagaaaataaatatttcatttaagt--tttatttatttatagtgtagcttctatttttctattttgtcatttacttttcaaaatctatcagatgttacattcaatttta-gatttcat-ttgcaggAAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGG
                                     |||| ||| | |||  || |||||   ||       | |  | || | |||  |||  |  |  |      | |  | ||  |  || |||    |  |||||  | ||    | ||||     || |       || || | |  ||| || |||||||||||||| ||||| |||||||| ||||| ||||| |||||  | |||||||||||| 
------------------------------------gttca-tagataagctattattcaatttataggcagtattggaaatctgattgtagtaatgcacctcacatgaataaatctcttgattctctcccattccatttgttgtttcccaactatagttagtaattgatgtttctacggtaccatattacagGAAGAGTTTCAATTGGCTTTGTTCAAAACAAACAAAAAGGAAAGCTTATTTGCTGATCGG-

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|151397479|gb|EV267352.1|EV267352
EST:     CTTCAAAAAGATTAGCAGTGCTGTAATCGACGATGGGTTGATTAACAAGG                         AAGAGTTTCAGTTGGCATCGTTCAAGACAAATAAAAAAGAAAGTCTGTTTG
genomic: CTTCAAAAAGATTAGCAGTGCTGTAATCGACGATGGGTTGATTAACAAGGtttgtcattg ... catttgcaggAAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTG
EST: gi|38192551|gb|CF921757.1|CF921757
EST:     CTTCAAAAAGATTAGCAGTGCTGTAATCGACGATGGGTTGATTAACAAGG                         AAGAGTTTCAGTTGGCATTGTTCAAGAC
genomic: CTTCAAAAAGATTAGCAGTGCTGTAATCGACGATGGGTTGATTAACAAGGtttgtcattg ... catttgcaggAAGAGTTTCAGTTGGCATTGTTCAAGAC
EST: gi|16349164|gb|BI974759.1|BI974759
EST:     CTTCAAAAAGATTAGCAGTGCTGTAATCGACGATGGGTTGATTAACAAGG                         AAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTG
genomic: CTTCAAAAAGATTAGCAGTGCTGTAATCGACGATGGGTTGATTAACAAGGtttgtcattg ... catttgcaggAAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTG
EST: gi|192298955|gb|FG987700.1|FG987700
EST:     CTTCAAAAAGATTAGCAGTGCTGTAATCGACGATGGGTTGATTAACAAGG                         AAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTG
genomic: CTTCAAAAAGATTAGCAGTGCTGTAATCGACGATGGGTTGATTAACAAGGtttgtcattg ... catttgcaggAAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTG
EST: gi|18848425|gb|BM567661.1|BM567661
EST:     CTTCAAAAAGATTAGCAGTGCTGTAATCGACGATGGGTTGATTAACAAGG                         AAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTG
genomic: CTTCAAAAAGATTAGCAGTGCTGTAATCGACGATGGGTTGATTAACAAGGtttgtcattg ... catttgcaggAAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTG
EST: gi|8284959|gb|BE022518.1|BE022518
EST:     CTTCAAAAAGATTAGCAGTGCTGTAATCGACGATGGGTTGATTAACAAGG                         AAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTG
genomic: CTTCAAAAAGATTAGCAGTGCTGTAATCGACGATGGGTTGATTAACAAGGtttgtcattg ... catttgcaggAAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTG
EST: gi|13791269|gb|BG653860.1|BG653860
EST:     CTTCAAAAAGATTAGCAGTGCTGTAATCGACGATGGGTTGATTAACAAGG                         AAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTG
genomic: CTTCAAAAAGATTAGCAGTGCTGTAATCGACGATGGGTTGATTAACAAGGtttgtcattg ... catttgcaggAAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTG
EST: gi|8283189|gb|BE020750.1|BE020750
EST:     CTTCAAAAAGATTAGCAGTGCTGTAATCGACGATGGGTTGATTAACAAGG                         AAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGGTTG
genomic: CTTCAAAAAGATTAGCAGTGCTGTAATCGACGATGGGTTGATTAACAAGGtttgtcattg ... catttgcaggAAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTG
EST: gi|192334402|gb|FK025551.1|FK025551
EST:     CTTCAAAAAGATTAGCAGTGCTGTAATCGACGATGGGTTGATTAACAAGG                         AAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTG
genomic: CTTCAAAAAGATTAGCAGTGCTGTAATCGACGATGGGTTGATTAACAAGGtttgtcattg ... catttgcaggAAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTG
EST: gi|209718662|gb|BW674764.1|BW674764
EST:     CTTCAAAAAGATTAGCAGTGCTGTAATCGACGATGGGTTGATTAACAAGG                         AAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTG
genomic: CTTCAAAAAGATTAGCAGTGCTGTAATCGACGATGGGTTGATTAACAAGGtttgtcattg ... catttgcaggAAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTG
EST: gi|254347752|gb|GR854001.1|GR854001
EST:     CTTCAAAAAGATTAGCAGTGCTGTAATCGACGATGGGTTGATTAACAAGG                         AAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTG
genomic: CTTCAAAAAGATTAGCAGTGCTGTAATCGACGATGGGTTGATTAACAAGGtttgtcattg ... catttgcaggAAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTG
EST: gi|192320225|gb|FK014239.1|FK014239
EST:     CTTCAAAAAGATTAGCAGTGCTGTAATCGACGATGGGTTGATTAACAAGG                         AAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTG
genomic: CTTCAAAAAGATTAGCAGTGCTGTAATCGACGATGGGTTGATTAACAAGGtttgtcattg ... catttgcaggAAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTG
EST: gi|213592918|gb|DB966023.1|DB966023
EST:     CTTCAAAAAGATTAGCAGTGCTGTAATCGACGATGGGTTGATTAACAAGG                         AAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTG
genomic: CTTCAAAAAGATTAGCAGTGCTGTAATCGACGATGGGTTGATTAACAAGGtttgtcattg ... catttgcaggAAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTG
EST: gi|254324275|gb|GR840592.1|GR840592
EST:     CTTCAAAAAGATTAGCAGTGCTGTAATCGACGATGGGTTGATTAACAAGG                         AAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTG
genomic: CTTCAAAAAGATTAGCAGTGCTGTAATCGACGATGGGTTGATTAACAAGGtttgtcattg ... catttgcaggAAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTG
EST: gi|308098080|gb|HO761251.1|HO761251
EST:     CTTCAAAAAGATTAGCAGTGCTGTAATCGACGATGGGTTGATTAACAAGG                         AAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTA
genomic: CTTCAAAAAGATTAGCAGTGCTGTAATCGACGATGGGTTGATTAACAAGGtttgtcattg ... catttgcaggAAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttacttttcaaaatctatcagatgttacattcaattttagatttcatttgcaggAAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGG
                                          tttcattt  CT-rich tract
                             attcaattttagattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgtcattggaaaactgtgttttgggcatattgtatttcactagttgagcctttttcaacaatgaaagaaaataaatatttcatttaagttttatttatttatagtgtagcttctatttttctattttgtcatttacttttcaaaatctatcagatgttacattcaattttagatttcatttgcaggAAGAGTTTCAGTTGGCATTGTTCAAGACAAATAAAAAAGAAAGTCTGTTTGCTGATCGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT