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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAAGGTTTATGAGGGAATTCCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAAgtaagtgttcttttatcttttcctgaactgtttttaatggtaatatttaatgtttaatctataaattatttgagttgttttttcctcttgtgaatattgaactaatcaatgaaaaatgaaatcag

Basic information

species Glycine max
transcript GLYMA16G13580.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G13580.1 (Glycine max), 5'ss of exon 2
lower sequence: AT3G24830.1 (Arabidopsis thaliana), 5'ss of exon 2
CAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAAGGTTTATGAGGGAATTCCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAAgtaagtgttcttttatcttttcctgaactgtttttaatggtaatatttaatgt--ttaatctataaatta--tttgagttgttttttcctcttgtgaatattgaactaatcaatgaaaaatgaaatcag
| |||||||| |  || ||||| || ||||||||||| | ||||||| | || ||||| ||||||||| | |||||||||||  |||| |||||||| |||||| ||||  |  | ||||     | ||  |  |  |||| || || |||||  || | || | || |   |||   ||||||| |  | ||  |                                 
CCAAGCGTGGTGCTGCTGCTCTTGCACGTTTGAAGGTGTTTGAGGGAGTACCACCTCCTTATGACAAGGTCAAGAGAATGGTCATTCCTGATGCTCTCAAgtaa-tgtttctgcaactttgttctatcttgtaattttggttatgttcaatgtgttttagctgtcaactggttttcgtttgttttgttttgtttag---------------------------------

upper sequence: GLYMA16G13580.1 (Glycine max), 5'ss of exon 2
lower sequence: AT4G13170.1 (Arabidopsis thaliana), 5'ss of exon 2
CAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAAGGTTTATGAGGGAATTCCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAAgtaagtgttcttttatcttttcctgaactgtttttaatggtaatatt-taatgtttaatctataaattatttgagttgttttttcctcttgtgaatattgaactaatcaatgaaaaatgaaatcag
| |||||||| |  || || || ||||| |||||||||| ||||||||| || ||||| || |||||||| |||||||||||| |||| |||||||| ||||||||  |||||| | ||||  | |  ||||||   |  | ||  | ||||  ||||| |  ||||  | | | |  | | ||  | || | |  |                             
CCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGAAGGTTTTTGAGGGAATCCCACCTCCTTACGACAAGATTAAGAGAATGGTTATTCCTGATGCTCTTAAgtaagttctcttttgtttttttgtta--tgttttgtttcatgattctgtaatagttaatgtccaaat-gtgttaatgatctgttgattttttaatcag----------------------------

upper sequence: GLYMA16G13580.1 (Glycine max), 5'ss of exon 2
lower sequence: AT3G07110.1 (Arabidopsis thaliana), 5'ss of exon 2
CAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAAGGTTTATGAGGGAATTCCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAAgtaagtgttcttttatcttttcctgaactgtttttaatggtaatatttaatgtttaatctataaattatttgagttgttttttcctcttgtgaatattgaactaatcaatgaaaaatgaaatcag
| |||||||| |     || || || || |||||||| | ||| ||| ||||| |||||||||||||||| ||||| ||||| ||||| |||||||| ||||   ||| |||||| | |||| |   |  |||||    ||    || | |  |  |  || || |   |  |||   | |      |||    |       | ||||                 
CTAAGCGTGGAGCTAATGCACTTGCCCGCTTGAAGGTCTTTGAAGGAGTTCCTACTCCATATGACAAGATCAAGAGGATGGTCGTTCCTGATGCTCTCAAgtt--tgtccttttaccctttcattttcattttttttcagtttccttcatttat--acttacaagtagctacagtc--tctgaaactttgattcttccttcttgatcag----------------

upper sequence: GLYMA16G13580.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv07s0005g06490.t01 (Vitis vinifera), 5'ss of exon 2
CAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAAGGTTTATGAGGGAATTCCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAAgtaagtgttcttttatcttttcctgaac--tgtttttaa---tggtaat----atttaatgtttaatctataaattatttgagt-tgttttttcctcttgtgaat-----attgaactaatcaatga--aaaatgaaatcag
| |||||||| | ||| || || || || ||||||| |||||||||||| ||||| |||||||| ||||| ||||| |||||  |||| ||||| || |||| ||| ||||| | ||| ||  | | |  ||| | | |   |  ||||     |||  | |  | |||||   || ||| |   ||| ||||  ||||||   |     |||||  | ||   ||    |||| |||| ||
CCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAAGGCTTATGAGGGAATCCCTCCACCATATGATAAGATGAAGAGGATGGTCATTCCTGATGCACTCAAgttagt-ttcttgtttctcttgattatcgttgtctctgaatttcttaattggggtttggtttcaagtctattgtttttttaatcatgtgttttaatcttgtttcttgctaattgatttgatggttggttgaaataaaattag

upper sequence: GLYMA16G13580.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv05s0029g00020.t01 (Vitis vinifera), 5'ss of exon 2
CAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAAGGTTTATGAGGGAATTCCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAAgtaagtgttcttttatcttttcctgaactgtttttaatggtaatatttaatgtttaatctataaattatttgagttgttttttcctcttgtgaatattgaactaatcaatgaaaaatgaaatcag
| |||||||| |  || || || ||  | ||||||| ||| ||||| ||||| ||||||||||| ||||| ||||| |||||| |||| || ||||| |||| |||  | | ||    |||  |    | ||||| ||  |    ||     | |||  | |   |  ||||||     |||    |||| || | |||    |||||                 
CTAAGCGTGGAGCCGCAGCGCTTGCCAGATTGAAGGCTTACGAGGGGATTCCACCTCCATATGATAAGATGAAGAGGATGGTTATTCCTGACGCTCTCAAgtgagttctgtatttgagttttattttttattttttattttttatttaggcctataaattcttgttggtttgaga---ctttaatgcttgagatttttgggaaaatcag----------------

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|298178143|gb|HO027526.1|HO027526
EST:     CCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAA                         GGTGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC
genomic: CCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAAgtaagtgttc ... atgaaatcagGGTGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC
EST: gi|193470062|gb|FK436843.1|FK436843
EST:     CCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAA                         GGTGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC
genomic: CCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAAgtaagtgttc ... atgaaatcagGGTGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC
EST: gi|298198649|gb|HO040188.1|HO040188
EST:     CCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAA                         GGTGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC
genomic: CCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAAgtaagtgttc ... atgaaatcagGGTGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC
EST: gi|151411210|gb|EV281021.1|EV281021
EST:     CCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAA                         GGTGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC
genomic: CCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAAgtaagtgttc ... atgaaatcagGGTGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC
EST: gi|192312241|gb|FK005698.1|FK005698
EST:     CCTCCTCCATATGGCAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAA                         GGTGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC
genomic: CCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAAgtaagtgttc ... atgaaatcagGGTGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC
EST: gi|193315341|gb|FK278943.1|FK278943
EST:     CCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAA                         GGTGTTGAGACTTCAGAAAGGACACA
genomic: CCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAAgtaagtgttc ... atgaaatcagGGTGTTGAGACTTCAGAAAGGACACA
EST: gi|298195471|gb|HO043862.1|HO043862
EST:     CCTCCTCCATATGACAAGATAAAGA-A-TGGTTGTTCCAGATGCTCTGAA                         GGTGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC
genomic: CCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAAgtaagtgttc ... atgaaatcagGGTGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC
EST: gi|209716349|gb|BW684793.1|BW684793
EST:     CCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAA                         GGTGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC
genomic: CCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAAgtaagtgttc ... atgaaatcagGGTGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC
EST: gi|51334831|gb|CO978697.1|CO978697
EST:     CCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAA                         GGTGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC
genomic: CCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAAgtaagtgttc ... atgaaatcagGGTGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC
EST: gi|58017414|gb|CX704156.1|CX704156
EST:     CCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAA                         GGTGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC
genomic: CCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAAgtaagtgttc ... atgaaatcagGGTGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC
EST: gi|193390501|gb|FK354993.1|FK354993
EST:     CCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAA                         GGTGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC
genomic: CCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAAgtaagtgttc ... atgaaatcagGGTGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC
EST: gi|17021875|gb|BM092909.1|BM092909
EST:     CCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAA                         GGTGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC
genomic: CCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAAgtaagtgttc ... atgaaatcagGGTGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC
EST: gi|22932124|gb|BU549263.1|BU549263
EST:     ATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAA                         GGTGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC
genomic: ATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAAgtaagtgttc ... atgaaatcagGGTGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC
EST: gi|18722168|gb|BM523389.1|BM523389
EST:     CCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAA                         GGTGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC
genomic: CCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAAgtaagtgttc ... atgaaatcagGGTGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC
EST: gi|192312242|gb|FK005699.1|FK005699
EST:     CCTCCTCCATATGGCAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAA                         GGTGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC
genomic: CCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAAgtaagtgttc ... atgaaatcagGGTGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC
EST: gi|298198972|gb|HO042335.1|HO042335
EST:     CCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAA                         GATGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC
genomic: CCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAAgtaagtgttc ... atgaaatcagGGTGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC
EST: gi|19052887|gb|BM731554.1|BM731554
EST:     CCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAA                         GGTGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC
genomic: CCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAAgtaagtgttc ... atgaaatcagGGTGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC
EST: gi|58017241|gb|CX703983.1|CX703983
EST:     CCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAA                         GGTGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC
genomic: CCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAAgtaagtgttc ... atgaaatcagGGTGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC
EST: gi|14259082|gb|BG881990.1|BG881990
EST:     CCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAA                         GGTGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC
genomic: CCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAAgtaagtgttc ... atgaaatcagGGTGTTGAGACTTCAGAAAGGACACAAGTACTGCATACTGGGCAGGTTGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAAGGTTTATGAGGGAATTCCTCCTCCATATGACAAGATAAAGAGAATGGTTGTTCCAGATGCTCTGAAgtaagtgttcttttatcttttcctgaactgtttttaatggtaatatttaatgtttaatctataaattatttgagttgttttttcctcttgtgaatattgaactaatcaatgaaaaatgaaatcag

- - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG