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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttactaggcaatttcccctgcatctctgtctctcttaaactattatttctcatataaccgttttctctctctctctctctctctctctttacatgcagTACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGA

Basic information

species Glycine max
transcript GLYMA20G36960.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G36960.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0081g00200.t01 (Vitis vinifera), 3'ss of exon 1
-----atttactaggcaatttcccctgcatctctgtctctcttaaactattatttctcatataaccgttttctctctctctctctctctctctctttacatgcagTACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGA
     ||| |||   | |||     ||  |    | |||  || || | | |||| |   |||    ||  ||  |  | | | | | | | | |||   || |||| || ||||| |||||||| ||||| |||||||||||||| ||||||||||| || ||  |||  || ||||||||
ccattattaactctaccattgtatatgtcttctagcctcattttaatt-taatttttttaata----ttggcttgcaatttatttatttatttttttttgtgtagTATCTTGATGAAAACAAGTCATTGATTCTGAAGATTGTTGAGAGCCAGAATTCAGGAAAATTGACTGAATGTGCAGA
















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|298165632|gb|HO011681.1|HO011681
EST:     TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAG                         TACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
genomic: TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAGgtcctttcct ... ttacatgcagTACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
EST: gi|207842021|gb|GD817209.1|GD817209
EST:     ACCACTGATCACATTCAACAG                         TACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
genomic: ACCACTGATCACATTCAACAGgtcctttcct ... ttacatgcagTACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
EST: gi|298182194|gb|HO026369.1|HO026369
EST:     TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAG                         TACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
genomic: TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAGgtcctttcct ... ttacatgcagTACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
EST: gi|298165119|gb|HO011168.1|HO011168
EST:     TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAG                         TACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGC-AGAAT
genomic: TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAGgtcctttcct ... ttacatgcagTACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
EST: gi|298198807|gb|HO042170.1|HO042170
EST:     TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAG                         TACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
genomic: TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAGgtcctttcct ... ttacatgcagTACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
EST: gi|192298039|gb|FG991319.1|FG991319
EST:     TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAG                         TACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
genomic: TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAGgtcctttcct ... ttacatgcagTACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
EST: gi|298165702|gb|HO008673.1|HO008673
EST:     TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAG                         TACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
genomic: TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAGgtcctttcct ... ttacatgcagTACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
EST: gi|298177026|gb|HO023387.1|HO023387
EST:     TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAG                         TACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
genomic: TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAGgtcctttcct ... ttacatgcagTACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
EST: gi|298195040|gb|HO043568.1|HO043568
EST:     TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAG                         TACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
genomic: TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAGgtcctttcct ... ttacatgcagTACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
EST: gi|193563360|gb|FK517063.1|FK517063
EST:     TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAG                         TACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
genomic: TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAGgtcctttcct ... ttacatgcagTACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
EST: gi|298163735|gb|HO012468.1|HO012468
EST:     TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAG                         TACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
genomic: TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAGgtcctttcct ... ttacatgcagTACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
EST: gi|213606189|gb|DB961333.1|DB961333
EST:     TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAG                         TACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
genomic: TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAGgtcctttcct ... ttacatgcagTACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
EST: gi|298196444|gb|HO041187.1|HO041187
EST:     TCATGGCAGCCTACTACCCCAACAACGTCGCCACTGATCACATTCAACAG                         TACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
genomic: TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAGgtcctttcct ... ttacatgcagTACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
EST: gi|298181704|gb|HO025879.1|HO025879
EST:     TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAG                         TACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
genomic: TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAGgtcctttcct ... ttacatgcagTACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
EST: gi|193633235|gb|FK585173.1|FK585173
EST:     TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAG                         TACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
genomic: TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAGgtcctttcct ... ttacatgcagTACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
EST: gi|209701831|gb|BW652284.1|BW652284
EST:     TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAG                         TACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
genomic: TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAGgtcctttcct ... ttacatgcagTACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
EST: gi|151408071|gb|EV277879.1|EV277879
EST:     TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAG                         TACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
genomic: TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAGgtcctttcct ... ttacatgcagTACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
EST: gi|193492554|gb|FK455706.1|FK455706
EST:     TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAG                         TACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
genomic: TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAGgtcctttcct ... ttacatgcagTACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
EST: gi|151409819|gb|EV279627.1|EV279627
EST:     TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAG                         TACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
genomic: TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAGgtcctttcct ... ttacatgcagTACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
EST: gi|298163796|gb|HO012529.1|HO012529
EST:     TCATGGCGGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAG                         TACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
genomic: TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAGgtcctttcct ... ttacatgcagTACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
EST: gi|208095937|gb|GD892415.1|GD892415
EST:     TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAG                         TACCTGGATGAGAACAAGTCCTTG
genomic: TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAGgtcctttcct ... ttacatgcagTACCTGGATGAGAACAAGTCCTTG
EST: gi|193559161|gb|FK515920.1|FK515920
EST:     TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAG                         TACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT
genomic: TCATGGCAGCCTACTACCCCAACAACGTCACCACTGATCACATTCAACAGgtcctttcct ... ttacatgcagTACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttctcatataaccgttttctctctctctctctctctctctctttacatgcagTACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGA
        atataac  putative branch site (score: 3)
              ccgttttctctctctc  CT-rich tract
      tcatataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttactaggcaatttcccctgcatctctgtctctcttaaactattatttctcatataaccgttttctctctctctctctctctctctctttacatgcagTACCTGGATGAGAACAAGTCCTTGATCCTGAAGATTGTTGAAAGCCAGAATTCTGGCAAGCTGAGCGAGTGTGCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - -tttcccc
- - - - - - - - - - tgcatct
- - - - - - - - - - - - - -ctgtctc