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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcattatacgcccttctacacagtagtaatatttatgtaaattcttttgcactataagataaatatattcagcatttgaaaaacatttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG

Basic information

species Glycine max
transcript GLYMA20G23080.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G23080.2 (Glycine max), 3'ss of exon 8
lower sequence: AT1G56340.1 (Arabidopsis thaliana), 3'ss of exon 6
---------------------------------------gttcattat----acgcccttctacacagtagtaatatttat-gtaaattcttttgcactataagataa-atatattcagcatttg----aaaaacatttat------cagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG
                                       |||    ||    |      |  |   |  |||| ||||||| ||||  | |||    |  | |||||| || |  | || | |      ||  | ||  ||      |||| |||||||||||||| || || ||||| |||||||| |||||||| || ||  |||| |||||||||
gtaatttaggaatccgtatttatattcacctgaaatagagtttgagattctgatagttatggatgtaacagtagtatttattgtaagatttttgtttccctgagataatatctgataagtagtaagtctaagtatatcaatttgacacagAATTCAAGGATGACCCAGAACTCTATGTCTTCCCCAAATTGAAGTATGTTGGAGTTGAGTTGTGGCAG

upper sequence: GLYMA20G23080.2 (Glycine max), 3'ss of exon 8
lower sequence: Vv14s0060g01290.t01 (Vitis vinifera), 3'ss of exon 8
gttcat-tatacgc-ccttctacacagtagtaatatttatgtaaattcttttgcactataagataaatatattcagcatttgaaaaacatttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG
|||| | |  | || ||| || |      |  ||| |||| |   ||  ||||  ||  || ||  | | | | |  |  ||   |  ||||  |||| ||||| |||||||| ||  | |||||||||||| | |||||||| |||||||||||| | ||||||
gttcctatccatgcacctgcttcttctatgccatagttattt--tttggtttggtct-caacattcagacacttataaactgttca-tattttacagAGTTCAAAGATGACCCAGAGATCTATGTTTTCCCCGATTTGAAGTATGTGGGCATTGAACTCTGGCAG
















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|298193745|gb|HO040393.1|HO040393
EST:     GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG                         ATTTCAAGGATGACCCCGACCTATA
genomic: GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATA
EST: gi|193341174|gb|FK306414.1|FK306414
EST:     GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG                         ATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
genomic: GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
EST: gi|254340600|gb|GR850902.1|GR850902
EST:     GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG                         ATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
genomic: GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
EST: gi|31469544|gb|CD411572.1|CD411572
EST:     GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG                         ATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
genomic: GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
EST: gi|13790097|gb|BG652688.1|BG652688
EST:     GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAN                         ATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
genomic: GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
EST: gi|7147510|gb|AW509432.1|AW509432
EST:     GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG                         ATNTCAAGGATGACCCCGACCTATATGTNTTTCCC-AACTTGAAGTACGTG
genomic: GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGT-TTTCCCCAACTTGAAGTACGTG
EST: gi|6094883|gb|AW119550.1|AW119550
EST:     GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG                         ATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
genomic: GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
EST: gi|58021776|gb|CX708517.1|CX708517
EST:     GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG                         ATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
genomic: GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
EST: gi|213596806|gb|DB978038.1|DB978038
EST:     ATTGATTGATAACCCAG                         ATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
genomic: ATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
EST: gi|192307920|gb|FK003068.1|FK003068
EST:     GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG                         ATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
genomic: GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
EST: gi|26268307|gb|CA819370.1|CA819370
EST:     GAACTCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG                         ATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
genomic: GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
EST: gi|254340601|gb|GR850903.1|GR850903
EST:     GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG                         ATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
genomic: GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
EST: gi|5606713|gb|AI900811.1|AI900811
EST:     TATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG                         ATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
genomic: TATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
EST: gi|208042272|gb|GD839550.1|GD839550
EST:     CCCCAAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG                         ATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
genomic: CCCC-AACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
EST: gi|208301469|gb|GE099861.1|GE099861
EST:     AAAATGGAAGGCACCATTGATTGATAACCCAG                         ATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
genomic: AAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
EST: gi|16997164|gb|BM086536.1|BM086536
EST:     GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG                         ATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
genomic: GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
EST: gi|6915349|gb|AW396879.1|AW396879
EST:     GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG                         ATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
genomic: GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
EST: gi|5126765|gb|AI748501.1|AI748501
EST:     GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG                         ATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
genomic: GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
EST: gi|18040353|gb|BM308647.1|BM308647
EST:     GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG                         ATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
genomic: GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
EST: gi|254332430|gb|GR843907.1|GR843907
EST:     GGCACCATTGATTGATAACCCAG                         ATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
genomic: GGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
EST: gi|19934771|gb|BQ079801.1|BQ079801
EST:     GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG                         ATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
genomic: GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
EST: gi|24136456|gb|BU926966.1|BU926966
EST:     GAACCCCAAGTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG                         ATTTCAAGGATGACCCCGACCTATATGTTTTCCC
genomic: GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCC
EST: gi|208317285|gb|GE117494.1|GE117494
EST:     GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG                         ATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
genomic: GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
EST: gi|208091443|gb|GD886338.1|GD886338
EST:     GAGCCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG                         ATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTATGTGG
genomic: GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
EST: gi|192307919|gb|FK003067.1|FK003067
EST:     GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG                         ATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
genomic: GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
EST: gi|254348789|gb|GR852468.1|GR852468
EST:     AAGGAAAATGGAAGGCACCATTGA-TGATAACCCAG                         ATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
genomic: AAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
EST: gi|26047705|gb|CA784416.1|CA784416
EST:     GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG                         ATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
genomic: GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
EST: gi|208268672|gb|GE072089.1|GE072089
EST:     GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG                         ATTTCAAGGATGACCCCG
genomic: GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCG
EST: gi|22524331|gb|BU083142.1|BU083142
EST:     AACCCCAACTATAAAGGAAAATGGAAAGCACCATTGATTGATAAACCCAG                         ATTTCAAGGATGACCCCGACCTATATGTTATCCCCAACTT
genomic: AACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAA-CCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTT
EST: gi|26045988|gb|CA783372.1|CA783372
EST:     GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG                         ATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
genomic: GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG
EST: gi|15203979|gb|BI426756.1|BI426756
EST:     GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAG                         ATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTAAAGTACGTGG
genomic: GAACCCCAACTATAAAGGAAAATGGAAGGCACCATTGATTGATAACCCAGgttcattata ... catttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaattcttttgcactataagataaatatattcagcatttgaaaaacatttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG
            actataagataaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcattatacgcccttctacacagtagtaatatttatgtaaattcttttgcactataagataaatatattcagcatttgaaaaacatttatcagATTTCAAGGATGACCCCGACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG