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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGATGGAGGTGACATGGGAGGACCAGCAGAACATTAATATCTTCAGCCGTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctcttttatgtatccttgattttttcttctacacgattctagggttttaagattaggttttattcatggattcaattcgctatgttgcatcgttt...

Basic information

species Arabidopsis thaliana
transcript AT1G08780.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G08780.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA20G36840.1 (Glycine max), 5'ss of exon 2
TGAGATGGAGGTGACATGGGAGGACCAGCAGAACATTAATATCTTCAGCCGTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctcttttatgtatc--cttgattttttcttctacacgattctagggttttaagattaggttttattca-tggattcaattcgctatgttgcatcgttt
 |||| ||| |||||||||||||||||||||||||| || |  ||| |  |  | || ||  |  | || || || || || || ||||||  ||| |||||  ||| ||  |    |    |  | ||    |||| |||   ||     | | |   ||  ||| | || | || |||     |   |  |   |   | |
GGAGACGGAAGTGACATGGGAGGACCAGCAGAACATCAACAAATTCGGAAGGTTGAATAATCGCTTTCACGAGCTTGAGGATGAGATCAAAATCGCTAAGgtaatctattcaactctttatttccacttcagtttctgcacctatc---attctcatccttgtgttgtgtttagtgtattatgcgcagaacatcaaaggttat

upper sequence: AT1G08780.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv14s0081g00080.t01 (Vitis vinifera), 5'ss of exon 2
TGAGATGGAGGTGACATGGGAGGACCAGCAGAACATTAATATCTTCAGCCGTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctcttttatgtatcc--ttgattttttcttctacacgattctagggttttaagattaggttttattcatg-gattcaattcgctatgttgcatcgttt
||| |  ||||||||||||||||| |||||||||||||| |  ||| |  | || ||||||||| | || || ||||| || || |||||    ||||||||  |       |   |      |  | | || | ||   |||| ||| | ||||  | | |  |||||   ||  | ||| | |   ||   ||  |  || 
TGAAACAGAGGTGACATGGGAGGATCAGCAGAACATTAACAAATTCGGAAGACTAAACAACAGATTTCACGAGCTCGAAGATGAGATCAAGATGGCCAAGgtaataaagaaaaaagaaaggacttttctgttttccttttcgat-ctatgattttt-gttaattttttaaaaatttggttctacttttta-actgtgttttta

upper sequence: AT1G08780.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S341_64V6.1 (Physcomitrella patens), 5'ss of exon 2
TGAGATGGAGGTGACATGGGAGGACCAGCAGAACATTAATATCTTCAGCCGTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctcttttatgtatccttgattttttcttctacacgattctagggttttaagattaggttttattcatggattcaattcgctatgttgcatcgttt-
 |||| ||| ||||||||||| ||||||||||| ||||||  |||| | |||||||| ||||   | ||||| || || ||||| || ||  |    |||||  |   | ||||  | || | |  | ||    ||    | || |   |    |  | |      | | |   |  |||   |    |||  |   ||  
AGAGACGGAAGTGACATGGGAAGACCAGCAGAATATTAATGCCTTCGGTCGTCTCAATAACAAGTTTCATGAACTTGAGGACGAGATTAAGGCGAAGAAGgtattgcttattattaaaccctaaaatgttaca-tattgtactcaacaatcacgaactcattagaaaattagtcaaacaacatggctggttctaattttgt

upper sequence: AT1G08780.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EFJ09419 (Selaginella moellendorffii), 5'ss of exon 1
TGAGATGGAGGTGACATGGGAGGACCAGCAGAACATTAATATCTTCAGCCGTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctcttttatgtatccttgattttttcttctacacgattctagggttttaagattaggttttattcatggattcaattcgctatgttgcatcgttt
    | |||||||||||||||||| ||||||||||| ||    ||  | || ||||||  ||   |||| |||||||| ||||| |||||  |    ||||           | ||| |  |   ||  |||  | | || || |  |                                                    
----ACGGAGGTGACATGGGAGGATCAGCAGAACATCAACGCGTTTGGGCGACTCAACGCCAAGTTCCACGACCTCGAGGACGAGATCAAGGCGAAAAAGGC----------ACgtaactcttgcttgctctcgt-cgcggttttgagag--------------------------------------------------

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|86026581|gb|DR322334.1|DR322334
EST:     TCTCAACAACAGCAGTCCATGACCTCGATGACGATATCAAATCCGCCAAG                         GAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
genomic: TCTCAACAACAG-AGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctctt ... atttatgcagGAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
EST: gi|86026588|gb|DR322341.1|DR322341
EST:     GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAG                         GAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
genomic: GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctctt ... atttatgcagGAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
EST: gi|19741078|gb|AU226431.1|AU226431
EST:     GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAG                         GAAAAGGTGTG-AAATCTAGAGGATGCAGGG-ACGAGTTGATCCTTGCTGA
genomic: GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctctt ... atttatgcagGAAAA-GTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGA
EST: gi|86026595|gb|DR322348.1|DR322348
EST:     GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAG                         GAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
genomic: GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctctt ... atttatgcagGAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
EST: gi|86026599|gb|DR322352.1|DR322352
EST:     GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAG                         GAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
genomic: GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctctt ... atttatgcagGAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
EST: gi|86026594|gb|DR322347.1|DR322347
EST:     GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAG                         GAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
genomic: GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctctt ... atttatgcagGAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
EST: gi|164206351|gb|ES192653.1|ES192653
EST:     TCAAATCCGCCAAG                         GAAAAGTGTG-AAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
genomic: TCAAATCCGCCAAGgttctctctt ... atttatgcagGAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
EST: gi|86026590|gb|DR322343.1|DR322343
EST:     GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAG                         GAAAAGTATGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
genomic: GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctctt ... atttatgcagGAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
EST: gi|86026577|gb|DR322330.1|DR322330
EST:     GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAG                         GAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
genomic: GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctctt ... atttatgcagGAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
EST: gi|86026584|gb|DR322337.1|DR322337
EST:     GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAG                         GAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
genomic: GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctctt ... atttatgcagGAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
EST: gi|86026597|gb|DR322350.1|DR322350
EST:     GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAG                         GAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
genomic: GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctctt ... atttatgcagGAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
EST: gi|86026574|gb|DR322327.1|DR322327
EST:     GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAG                         GAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
genomic: GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctctt ... atttatgcagGAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
EST: gi|86026585|gb|DR322338.1|DR322338
EST:     GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAG                         GAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
genomic: GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctctt ... atttatgcagGAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
EST: gi|86026582|gb|DR322335.1|DR322335
EST:     GTCTCRACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAG                         GAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
genomic: GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctctt ... atttatgcagGAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
EST: gi|86026583|gb|DR322336.1|DR322336
EST:     GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAG                         GAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
genomic: GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctctt ... atttatgcagGAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
EST: gi|86026579|gb|DR322332.1|DR322332
EST:     GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAG                         GAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
genomic: GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctctt ... atttatgcagGAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
EST: gi|86026576|gb|DR322329.1|DR322329
EST:     GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAG                         GAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
genomic: GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctctt ... atttatgcagGAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
EST: gi|86026570|gb|DR322323.1|DR322323
EST:     GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAG                         GAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
genomic: GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctctt ... atttatgcagGAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
EST: gi|86026600|gb|DR322353.1|DR322353
EST:     GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAG                         GAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
genomic: GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctctt ... atttatgcagGAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
EST: gi|86026580|gb|DR322333.1|DR322333
EST:     GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAG                         GAAAAGTATGAAAATCTAGAGGATGCAGGGAAACGAGTTGATCCTTGCTGA
genomic: GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctctt ... atttatgcagGAAAAGTGTGAAAATCTAGAGGATGCAGGGAA-CGAGTTGATCCTTGCTGA
EST: gi|86026596|gb|DR322349.1|DR322349
EST:     GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAG                         GAAAAGTGTGAAAATCTAGAGGATNCAGGGAACGAGTTGATCCTTGCTGAT
genomic: GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctctt ... atttatgcagGAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
EST: gi|86026587|gb|DR322340.1|DR322340
EST:     GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAG                         GAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
genomic: GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctctt ... atttatgcagGAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
EST: gi|86026578|gb|DR322331.1|DR322331
EST:     GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAG                         GAAAAGTGTGAAAATCTAGAGGATG-AGGGAACGAGTTGATCCTTGCTGAT
genomic: GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctctt ... atttatgcagGAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
EST: gi|86026589|gb|DR322342.1|DR322342
EST:     GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAG                         GAAAAGTATGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
genomic: GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctctt ... atttatgcagGAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
EST: gi|86026586|gb|DR322339.1|DR322339
EST:     GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAG                         GAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
genomic: GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctctt ... atttatgcagGAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
EST: gi|86077415|gb|DR373172.1|DR373172
EST:     GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAG                         GAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
genomic: GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctctt ... atttatgcagGAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
EST: gi|86026575|gb|DR322328.1|DR322328
EST:     GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAG                         GAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
genomic: GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctctt ... atttatgcagGAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
EST: gi|86026593|gb|DR322346.1|DR322346
EST:     GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAG                         GAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
genomic: GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctctt ... atttatgcagGAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
EST: gi|86026571|gb|DR322324.1|DR322324
EST:     GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAG                         GAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
genomic: GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctctt ... atttatgcagGAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
EST: gi|86026592|gb|DR322345.1|DR322345
EST:     GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAG                         GAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
genomic: GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctctt ... atttatgcagGAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
EST: gi|86026572|gb|DR322325.1|DR322325
EST:     GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAG                         GAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
genomic: GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctctt ... atttatgcagGAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
EST: gi|86026601|gb|DR322354.1|DR322354
EST:     GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAG                         GAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT
genomic: GTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctctt ... atttatgcagGAAAAGTGTGAAAATCTAGAGGATGCAGGGAACGAGTTGATCCTTGCTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGATGGAGGTGACATGGGAGGACCAGCAGAACATTAATATCTTCAGCCGTCTCAACAACAGAGTCCATGACCTCGATGACGATATCAAATCCGCCAAGgttctctcttttatgtatccttgattttttcttctacacgattctagggttttaagattaggttttattcatggattcaattcgctatgttgcatcgttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctttta