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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAGATGCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGCCAGgtaaagaaagaaccaactgtctgaacattatctttttcattttcttttggtctaacatatcttcttttcctctgcaccag

Basic information

species Arabidopsis thaliana
transcript AT1G64520.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G64520.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G121452_T01 (Zea mays), 5'ss of exon 3
ACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAGATGCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGCCAGgtaaagaaagaaccaactg-tctgaacattatctttttcattttcttttggtctaacatatctt--------cttttcctctgcaccag-----------
||||||||||||||||||||||| | || || |||   ||||| |||||||| |||||  | ||||||| ||||||||| ||||| ||  ||||| |  ||| |         || |   | ||   ||| | |||  | || |  ||| |  |   || | ||         |  |    |||  | |           
ACATTTATGAGCATGCTGTTGTTTTGAGTGTGAAACTTGAGGACCAAGATGCGTTTGAACGCGATTTCTGCCAGCTGAAGCCTTATTACATGGATACATGgttagttctttgtcacccaatttgtcgattttatttgcctttattattttgatttctattttttaggctgaattcatgtgatgcttcgggcaataaaaag

upper sequence: AT1G64520.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA05G25730.1 (Glycine max), 5'ss of exon 3
ACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAGATGCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGCCAGgtaaagaaa---gaaccaactgt------ctgaacattatctttttcattttcttttggtctaacatatcttcttttcctctgcaccag-----------
| || || |||||||||||||| || || || ||||  |||||||||||||||||||| || |||||||||||| |||| ||||| |||   |||||| |||||        |  ||   | |      ||||| |        |       |         ||   |  | || |   | | |||              
ATATATACGAGCATGCTGTTGTCCTTAGTGTGAAAAATGAGGATCAAGATGCTTTTGAAAGGGATTTCTTCCAGTTGAAGCCTTATTATACAGATGCCTGgtaacttttcttgtcccttttttttcactctgaagacagctgaatctgcaaccaaagcaaacaatggacatcctctgattgttcacttaacataaacctg

upper sequence: AT1G64520.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA08G08690.1 (Glycine max), 5'ss of exon 3
ACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAGATGCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGCCAGgtaaagaaa---gaaccaactgtctgaacat-tatctttttcattttcttttggtctaacatatcttcttttcctctgcac-cag---------------
| || ||||||||||||||||| || || || ||||  ||||||||||||||||| || || |||||||||||| |||| ||||| |||   |||||| |||||   |       ||   | | |  |||| ||  | | |  ||||  | ||    ||  |   |  |   ||   |||  |||               
ATATATATGAGCATGCTGTTGTCCTTAGTGTGAAAATTGAGGATCAAGATGCTTTCGAAAGGGATTTCTTCCAGTTGAAGCCTTATTATACAGATGCCTGgtaacttattcttgtcccttttttttcacatataaatatatatttttactctgaagaaagctgaatcttcaaccaaagcaaacagtggacatctcctgat

upper sequence: AT1G64520.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv02s0025g02010.t01 (Vitis vinifera), 5'ss of exon 3
ACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAGATGCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGCCAGgtaaagaaagaaccaactgtctgaacattatctt---tttcattttcttttggtc-taacatatcttcttttcctctgcaccag-----------------
| || ||||||||||||||||| ||||| ||||| || |||||||| ||||| |||||||| |||||||| ||| |||||||||| |||   ||| |  |||||         |  |||| | | |  ||| |    || ||||||   ||  |  ||| |  ||   |  | ||    |  ||                 
ATATATATGAGCATGCTGTTGTCCTAAGTGTCAAGACAGAGGATCAGGATGCGTTTGAGAGGGATTTCTTTCAGTTGAAACCTTATTATACAGATACAGGgtaattctttctgct-ctgtttaagccatatttgaagttgcattttaaattaataataataattcaggtactgctaattaaaagagttctgtacagctcct

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|116486366|gb|EG528958.1|EG528958
EST:     GCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGCCAG                         GAACCGTATTCCTCAGTCTCCACAGGAGAATCTTATCCTGGGTCTTAACCT
genomic: GCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGCCAGgtaaagaaag ... tctgcaccagGAACCGTATTCCTCAGTCTCCACAGGAGAATCTTATCCTGGGTCTTAACCT
EST: gi|116486373|gb|EG528965.1|EG528965
EST:     GCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGCCAG                         GAACCGTATTCCTCAGTCTCCACAGGAGAATCTTATCCTGGGTCTTAACCT
genomic: GCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGCCAGgtaaagaaag ... tctgcaccagGAACCGTATTCCTCAGTCTCCACAGGAGAATCTTATCCTGGGTCTTAACCT
EST: gi|116486364|gb|EG528956.1|EG528956
EST:     GCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGCCAG                         GAACCGTATTCCTCAGTCTCCACAGGAGAATCTTATCCTGGGTCTTAACCT
genomic: GCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGCCAGgtaaagaaag ... tctgcaccagGAACCGTATTCCTCAGTCTCCACAGGAGAATCTTATCCTGGGTCTTAACCT
EST: gi|164079332|gb|EL991568.1|EL991568
EST:     CTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTAATGTGGATGCCAG                         GAACCGTATTCCTCAG
genomic: CTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTA-TGTGGATGCCAGgtaaagaaag ... tctgcaccagGAACCGTATTCCTCAG
EST: gi|124950628|gb|EL026075.1|EL026075
EST:     ATTTCTTCCAGCTGAAACCTTACTATGTGGATGCCAG                         GAACCGTATTCCTCAGTCTCCACAGGAGAATCTTATCCTGGGTCTTAACCT
genomic: ATTTCTTCCAGCTGAAACCTTACTATGTGGATGCCAGgtaaagaaag ... tctgcaccagGAACCGTATTCCTCAGTCTCCACAGGAGAATCTTATCCTGGGTCTTAACCT
EST: gi|116486368|gb|EG528960.1|EG528960
EST:     GCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGCCAG                         GAACCGTATTCCTCAGTCTCCACAGGAGAATCTTATCCTGGGTCTTAACCT
genomic: GCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGCCAGgtaaagaaag ... tctgcaccagGAACCGTATTCCTCAGTCTCCACAGGAGAATCTTATCCTGGGTCTTAACCT
EST: gi|116486371|gb|EG528963.1|EG528963
EST:     GCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGCCAG                         GAACCGTATTCCTCAGTCTCCACAGGAGAATCTTATCCTGGGTCTTAACCT
genomic: GCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGCCAGgtaaagaaag ... tctgcaccagGAACCGTATTCCTCAGTCTCCACAGGAGAATCTTATCCTGGGTCTTAACCT
EST: gi|116486376|gb|EG528968.1|EG528968
EST:     GCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGCCAG                         GAACCGTATTCCTCAGTCTCCACAGGAGAATCTTATCCTGGGTCTTAACCT
genomic: GCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGCCAGgtaaagaaag ... tctgcaccagGAACCGTATTCCTCAGTCTCCACAGGAGAATCTTATCCTGGGTCTTAACCT
EST: gi|116486365|gb|EG528957.1|EG528957
EST:     GCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGCCAG                         GAACCGTATTCCTCAGTCTCCACAGGAGAATCTTATCCTGGGTCTTAACCT
genomic: GCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGCCAGgtaaagaaag ... tctgcaccagGAACCGTATTCCTCAGTCTCCACAGGAGAATCTTATCCTGGGTCTTAACCT
EST: gi|164010480|gb|EL967895.1|EL967895
EST:     CTTACTATGTGGATGCCAG                         GAACCGTATTCCTCAGTCTCCACAGGAGAATCTTATCCTGGGTCTTAACCT
genomic: CTTACTATGTGGATGCCAGgtaaagaaag ... tctgcaccagGAACCGTATTCCTCAGTCTCCACAGGAGAATCTTATCCTGGGTCTTAACCT
EST: gi|164000542|gb|ES142203.1|ES142203
EST:     TCTTCCAGCTGAAACCTTACTATGTGGATTGCCAG                         GAACCGTATTCCTCAGTCTCCACAGGAGAATCTTATCCTGGGTCTTAACC
genomic: TCTTCCAGCTGAAACCTTACTATGTGGA-TGCCAGgtaaagaaag ... tctgcaccagGAACCGTATTCCTCAGTCTCCACAGGAGAATCTTATCCTGGGTCTTAACC
EST: gi|125135557|gb|EL175814.1|EL175814
EST:     ATTTCTTCCAGCTGAAACCTTACTATGTGGATGCCAG                         GAACCGTATTCCTCAGTCTCCATAGGAGAATCTTATCCTGGGTCTTAACCT
genomic: ATTTCTTCCAGCTGAAACCTTACTATGTGGATGCCAGgtaaagaaag ... tctgcaccagGAACCGTATTCCTCAGTCTCCACAGGAGAATCTTATCCTGGGTCTTAACCT
EST: gi|116486359|gb|EG528951.1|EG528951
EST:     GCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGCCAG                         GAACCGTATTCCTCAGTCTCCACAGGAGAATCTTATCCTGGGTCTTAACCT
genomic: GCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGCCAGgtaaagaaag ... tctgcaccagGAACCGTATTCCTCAGTCTCCACAGGAGAATCTTATCCTGGGTCTTAACCT
EST: gi|124824740|gb|EH909606.1|EH909606
EST:     GCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGCCAG                         GA-CCGTATTCCTCAGTCTCCACAGGAGAAT
genomic: GCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGCCAGgtaaagaaag ... tctgcaccagGAACCGTATTCCTCAGTCTCCACAGGAGAAT
EST: gi|116486357|gb|EG528949.1|EG528949
EST:     GCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGCCAG                         GAACCGTATTCCTCAGTCTCCACAGGAGAATCTTATCCTGGGTCTTAACCT
genomic: GCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGCCAGgtaaagaaag ... tctgcaccagGAACCGTATTCCTCAGTCTCCACAGGAGAATCTTATCCTGGGTCTTAACCT
EST: gi|124834547|gb|EH918986.1|EH918986
EST:     GCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGCCAG                         GAACCGTATTCCTCAGTCTCCACAGGAGAAT
genomic: GCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGCCAGgtaaagaaag ... tctgcaccagGAACCGTATTCCTCAGTCTCCACAGGAGAAT
EST: gi|116486361|gb|EG528953.1|EG528953
EST:     GCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGCCAG                         GAACCGTATTCCTCAGTCTCCACAGGAGAATCTTATCCTGGGTCTTAACCT
genomic: GCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGCCAGgtaaagaaag ... tctgcaccagGAACCGTATTCCTCAGTCTCCACAGGAGAATCTTATCCTGGGTCTTAACCT
EST: gi|124820576|gb|EH905442.1|EH905442
EST:     AGCTGAAACCTTACTATGTGGATGCCAG                         GAACCGTATTCCTCAGTCTCCACAGGAGAATCTTATCCTGGGTCTTAACCT
genomic: AGCTGAAACCTTACTATGTGGATGCCAGgtaaagaaag ... tctgcaccagGAACCGTATTCCTCAGTCTCCACAGGAGAATCTTATCCTGGGTCTTAACCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACATTTATGAGCATGCTGTTGTTCTAAGCGTCAAAACCGAGGATCAAGATGCTTTTGAGAGAGATTTCTTCCAGCTGAAACCTTACTATGTGGATGCCAGgtaaagaaagaaccaactgtctgaacattatctttttcattttcttttggtctaacatatcttcttttcctctgcaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA