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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTGTAGCAACTACAACTGGAACAGCCACAAATGCAACTGCTGTTGCTGCTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTGgtgagctattttagattgaaccaactcgaacccaaagacaacttgtatgtcaatataaaaagttcaaaatttaattgttaacttctggtatttgaatttg...

Basic information

species Glycine max
transcript GLYMA14G36520.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G36520.2 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os07g12530.1 (Oryza sativa), 5'ss of exon 10
AGTTGTAGCAACTACAACTGGAACAGCCACAAATGCAACTGCTGTTGCTGCTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTGgtgagctattttagattgaac--caactcgaac---ccaaagacaacttgtatgtca-atataaaaagttcaaaatttaattgttaacttctggtatttg--aatttg--------------------------------------------------------------------------
 |  ||   |  | |||| | || | |  |  |||| || || ||  | |||||| | || ||||| ||||| |||||||||||| | ||||||||| |||||||||| |||   ||      |   | ||||     | ||| ||||| ||  | | | ||    |   |   || |  |||||      || |   ||  |   ||                                                                          
TGAAGTCATAGTTGCAACAGCAAGAACTCCTGATGCTACAGCAGTATCGGCTAATGTTGTCGTTGACGAGAGACAGATGAATGCATTGTTTCTTGATCTGgtgagctactttcttttctctctcggttagaacaaggtagagagaacttctaccttatacattcgtatcactgtatgttcttgttggtaaatgttgcctgccagcgtgtattgttttcacgaaagaagagagatgagggaaaaaaaacaatgctgacaattctgttgctctgcgtcttccag

upper sequence: GLYMA14G36520.2 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G031780_T02 (Zea mays), 5'ss of exon 8
AGTTGTAGCAACTACAACTGGAACAGCCACAAATGCAACTGCTGTTGCTGCTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTGgtgagctattttagattgaa---ccaactcgaacccaaagacaacttgtatgtcaatataaaaagttcaaaatttaattgttaacttctggtatttgaatttg
 |   |   |    |||| | ||   || |  |||| || || ||  |||||||| | ||  |||||||||||||||||||||| || ||||||||| ||||||| || |||    || |   |   || ||||    | |   ||  ||   ||| | |||| |||  | ||   ||  | | ||      || | | ||| 
TGAAATCATAGTGGCAACAGCAAGGACCCCTGATGCTACAGCAGTATCTGCTAATGTTGTCCTTGATGAGAGGCAGATGAATGCTCTTTTTCTTGATCTGgtgagttactttcttctgcaactctgtctagaacagtgaaaggtctactaccgcaa-acaaaaggtt--acataggataataagctgtaaaaatgttattttc

upper sequence: GLYMA14G36520.2 (Glycine max), 5'ss of exon 9
lower sequence: AT5G05200.1 (Arabidopsis thaliana), 5'ss of exon 10
AGTTGTAGCAACTACAACTGGAACAGCCACAAATGCAACTGCTGTTGCTGCTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTGgtgagctattttagattgaaccaactc-gaacccaaagacaacttgtatgtcaatataaaaagttcaaaatttaattgt-------taacttctggtatttgaatttg--------------------------------
||| || || ||  |   |||||||    || |  | |||||||||||||||||  ||||| | |||||||| ||||||||||| || || || ||  |||| |||  ||  |||   ||     |  | |            ||| | ||   ||  |  |  |  || ||  ||||        |||   |  | ||||||  ||                                 
AGTAGTGGCTACAGCTCGTGGAACAAATTCAGACACTACTGCTGTTGCTGCTAACGTAGTTATGGATGAGAGACAGATGAATGCTCTTTTCCTCGACCTGgtaagcagtt--agacgtaatttcttaaggatttttttttggtttgaaagttgttaagaggatatagaagttgcattgagttaagataaaccccaggatttgagctttcagcagttgaaaataagttcactttcttatag

upper sequence: GLYMA14G36520.2 (Glycine max), 5'ss of exon 9
lower sequence: Vv13s0067g03210.t01 (Vitis vinifera), 5'ss of exon 10
AGTTGTAGCAACTACAACTGGAACAGCCACAAATGCAACTGCTGTTGCTGCTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTGgtgagctattttagattgaaccaactcgaacccaaagacaacttgtatgtcaatataaaaagttcaaaatttaattgttaacttctggtatttgaatttg-----
  |||| ||||| || |  ||  || |||||||  ||||||| |||||||||||| ||||||||||||||||||||||||||||||| |||||||||||||| |||  ||  |   | ||     |  ||   ||   | | || ||   ||   |   |||   |   ||| |||| | |  |  ||| |       ||     
TATTGTTGCAACAACCAGAGGCCCATCCACAAACACAACTGCAGTTGCTGCTAATGTAGTTGTTGATGAGAGGCAGATGAATGCACTTTTTCTTGATGTGgtaagcctttcaattctaaattg--tgcaaatgaatttccaattata---caggcttgtaagcatatggtttcattggttaaattaggtgtaaagccatgggtct

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|20813181|gb|BQ297659.1|BQ297659
EST:     CTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTG                         GTTCGGGTTAGTGAATCATATGGATTGAAGTTTCCTAGAGAATTTGCTCTT
genomic: CTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTGgtgagctatt ... tgctctacagGTTCGGGTTAGTGAATCATATGGATTGAAGTTTCCTAGAGAATTTGCTCTT
EST: gi|20812402|gb|BQ296880.1|BQ296880
EST:     CTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTG                         GTTCGGGTTAGTGAATCATATGGATTGAAGTTTCCTAGAGAATTTGCTCTT
genomic: CTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTGgtgagctatt ... tgctctacagGTTCGGGTTAGTGAATCATATGGATTGAAGTTTCCTAGAGAATTTGCTCTT
EST: gi|11689259|gb|BF596935.1|BF596935
EST:     CTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTG                         GTTCGGGTTAGTGAATCATATGGATTGAAGTTTCCTAGAGAATTTGCTCTT
genomic: CTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTGgtgagctatt ... tgctctacagGTTCGGGTTAGTGAATCATATGGATTGAAGTTTCCTAGAGAATTTGCTCTT
EST: gi|27426538|gb|CA938058.1|CA938058
EST:     CTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTG                         GTTCGGGTTAGTGAATCATATGGATTGAAGTTTCCTAGAGAATTTGCTCTT
genomic: CTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTGgtgagctatt ... tgctctacagGTTCGGGTTAGTGAATCATATGGATTGAAGTTTCCTAGAGAATTTGCTCTT
EST: gi|120494194|gb|EH222361.1|EH222361
EST:     CTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTG                         GTTCGGGTTAGTGAATCATATGGATTGAAGTTTCCTAGAGAATTTGCTCTT
genomic: CTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTGgtgagctatt ... tgctctacagGTTCGGGTTAGTGAATCATATGGATTGAAGTTTCCTAGAGAATTTGCTCTT
EST: gi|7693429|gb|AW761521.1|AW761521
EST:     CTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTG                         GTTCGGGTTAGTGAATCATATGGAT
genomic: CTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTGgtgagctatt ... tgctctacagGTTCGGGTTAGTGAATCATATGGAT
EST: gi|27424131|gb|CA935651.1|CA935651
EST:     CTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTG                         GTTCGGGTTAGTGAATCATATGGATTGAAGTTTCCTAGA
genomic: CTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTGgtgagctatt ... tgctctacagGTTCGGGTTAGTGAATCATATGGATTGAAGTTTCCTAGA
EST: gi|151394405|gb|EV264276.1|EV264276
EST:     CTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTG                         GTTCGGGTTAGTGAATCATATGGATTGAAGTTTCCTAGAGAATTTGCTCTT
genomic: CTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTGgtgagctatt ... tgctctacagGTTCGGGTTAGTGAATCATATGGATTGAAGTTTCCTAGAGAATTTGCTCTT
EST: gi|209714640|gb|BW671558.1|BW671558
EST:     CTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTG                         GTTCGGGTTAGTGAATCATATGGATTGAAGTTTCCTAGAGAATTTGCTCTT
genomic: CTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTGgtgagctatt ... tgctctacagGTTCGGGTTAGTGAATCATATGGATTGAAGTTTCCTAGAGAATTTGCTCTT
EST: gi|31310955|gb|CD396158.1|CD396158
EST:     CTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTG                         GTTCGGGTTAGTGAATCATATGGATTGAAGTTTCCTAGAGAATTTGCTCTT
genomic: CTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTGgtgagctatt ... tgctctacagGTTCGGGTTAGTGAATCATATGGATTGAAGTTTCCTAGAGAATTTGCTCTT
EST: gi|120495353|gb|EH223520.1|EH223520
EST:     CTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTG                         GTTCGGGTTAGTGAATCATATGGATTGAAGTTTCCTAGAGAATTTGCTCTT
genomic: CTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTGgtgagctatt ... tgctctacagGTTCGGGTTAGTGAATCATATGGATTGAAGTTTCCTAGAGAATTTGCTCTT
EST: gi|22524562|gb|BU083373.1|BU083373
EST:     CTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTG                         GTTCGGGTTAGTGAATCATATGGATTGAAGTTTCCTAGAGAATTTGCTCTT
genomic: CTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTGgtgagctatt ... tgctctacagGTTCGGGTTAGTGAATCATATGGATTGAAGTTTCCTAGAGAATTTGCTCTT
EST: gi|31457794|gb|CD399822.1|CD399822
EST:     CTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTG                         GTTCGGGTTAGTGAATCATATGGATTGAAGTTTCCTAGAGAATTTGCTCTT
genomic: CTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTGgtgagctatt ... tgctctacagGTTCGGGTTAGTGAATCATATGGATTGAAGTTTCCTAGAGAATTTGCTCTT
EST: gi|16104932|gb|BI892672.1|BI892672
EST:     CTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTG                         GCTCGGGTTAGTGAATCATATGGATTGAAGT
genomic: CTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTGgtgagctatt ... tgctctacagGTTCGGGTTAGTGAATCATATGGATTGAAGT
EST: gi|9900691|gb|BE609659.1|BE609659
EST:     CTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTG                         GTTCGGGTTAGTGAATCATATGGATTGAAGTTTCCTAGAGAATTTGCTCTT
genomic: CTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTGgtgagctatt ... tgctctacagGTTCGGGTTAGTGAATCATATGGATTGAAGTTTCCTAGAGAATTTGCTCTT
EST: gi|22928845|gb|BU545984.1|BU545984
EST:     CTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTG                         GTTCGGGTTAGTGAATCATATGGATTGAAGTTTCCTAGAGAATTTGCTCTT
genomic: CTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTGgtgagctatt ... tgctctacagGTTCGGGTTAGTGAATCATATGGATTGAAGTTTCCTAGAGAATTTGCTCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTGTAGCAACTACAACTGGAACAGCCACAAATGCAACTGCTGTTGCTGCTAATATAGTTGTTGATGAGAGGCAGATGAATGCACTCTTTCTTGATGTGgtgagctattttagattgaaccaactcgaacccaaagacaacttgtatgtcaatataaaaagttcaaaatttaattgttaacttctggtatttgaatttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG