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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtttctgaattttcctgcctcaaattgtataaacaagtaacggctttagactggagtgtgacagattgattttccaattgtttcagATCGTGTTGGAGGCTGATGGTTATCAACCTTATCTCATATCTCCAGAGAAAGGGTTGAGATCGTTAATAAAAACCGTTCTTGAGTTGGCTAAAGACCCAG

Basic information

species Arabidopsis thaliana
transcript AT1G59610.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 9
gtgggtttctgaattttcctgcctcaaattgtataaacaagtaacggctttagactggagtgtgacagattgattttccaattgtttcagATCGTGTTGGAGGCTGATGGTTATCAACCTTATCTCATATCTCCAGAGAAAGGGTTGAGATCGTTAATAAAAACCGTTCTTGAGTTGGCTAAAGACCCAG
||  | ||        |         | |  ||  | || | |    |       |   |        |  |  ||  |     ||  |||| || ||||| || |||||||||||||| || || ||||||||||||||||||||||| || || ||||| |  ||  | ||  |||| || || ||| 
gtaagattggatccagtttcaggattagtgctactatcaggcattttcccatcttttatgaacactgaacagtattctctgacattctagATTGTCTTGGAAGCCGATGGTTATCAACCGTACCTGATATCTCCAGAGAAAGGGTTGAGGTCCTTGATAAAGATAGTATTGGATATGGCAAAGGAGCCAT

upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os02g50550.1 (Oryza sativa), 3'ss of exon 9
gtgggtttctgaattttcctgcctcaaattgtataaacaagtaacggctttagactggagtgtgacagattgattttccaattgtttcagATCGTGTTGGAGGCTGATGGTTATCAACCTTATCTCATATCTCCAGAGAAAGGGTTGAGATCGTTAATAAAAACCGTTCTTGAGTTGGCTAAAGACCCAG
||   ||    |    | ||      |||| ||  |    | |    ||||      ||   | || |     || ||    | ||  |||| ||  |||| || |||||||||||||| ||| | ||||||||||||||||| || | ||| |||||||||   || |||||  |||| || || ||| 
gtaaattcaaaagcccttctagaattaatttta-gagtgggcac--actttgcttatgatgattactg-----ttatctttatattctagATTGTCCTGGAAGCCGATGGTTATCAACCATATTTGATATCTCCAGAGAAAGGTTTAAAATCCTTAATAAAAGGAGTACTTGAAATGGCAAAGGAGCCAT

upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 9
gtgggtttctgaattttcctgcctcaaattgtataaacaagtaacggctttagactggagtgtgacagattgattttccaattgttt--cagATCGTGTTGGAGGCTGATGGTTATCAACCTTATCTCATATCTCCAGAGAAAGGGTTGAGATCGTTAATAAAAACCGTTCTTGAGTTGGCTAAAGACCCAG
             | |     | || |||| || |    ||    || |      | |    |||   |     ||||            |||| || ||||| || |||||||||||||| ||| | |||||||||||||||||||||||||| ||||||||||  || || ||  |||| || || ||| 
------------gtatgatcacttccaattttacat-tgagctctggttggcagttagcacatgattaaacacatttctctccacacaatagATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCAT

upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 9
gtgggtttctgaattttcctgcctcaaattgtataaacaagtaacggctt-----------tagac---tggagtg-tgacagattgattttccaattg--tttcagATCGTGTTGGAGGCTGATGGTTATCAACCTTATCTCATATCTCCAGAGAAAGGGTTGAGATCGTTAATAAAAACCGTTCTTGAGTTGGCTAAAGACCCAG
||   | |      ||   |   ||| ||||| ||   |    |  | |            | |||   ||| ||| |  |   |  ||| ||   |||  |||||||| ||  | || || ||||| |||||||||||||| || |||||||||||||| |||||||| ||||| |||  |||||||||  |||| || || ||| 
gtaaatcttctcccttgaatttgtcatattgtttaggtagaatatagttcatcttattctgttgacacttggggtgcttgcttctatattctcattttggctttcagATTGTCCTAGAAGCAGATGGATATCAACCTTATCTGATCTCTCCAGAGAAAGGTTTGAGATCCTTAATTAAAGGCGTTCTTGAACTGGCGAAGGAGCCAT

upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 9
--------------gtgggtttctgaattttcctgcctcaaattgtataaacaagtaacggctttagactggagtgtgacagattg-attttccaatt-------gtttcagATCGTGTTGGAGGCTGATGGTTATCAACCTTATCTCATATCTCCAGAGAAAGGGTTGAGATCGTTAATAAAAACCGTTCTTGAGTTGGCTAAAGACCCAG
               ||  ||| | |  ||   |   |  ||||   |  |    ||    ||| | ||| ||| |||   | ||  || |||| |||        |||||||| ||  | || || ||||| |||||||||||||| || |||||||||||||| |||||||| ||||| |||  |||||||||  |||| || || ||| 
gtaaaccttctcccttgaatttgtcatattgtttaggtagaatttagttcattt-tattctcttgacacttgag-gtgcttgcttctatattcccattttggcttatttcagATTGTCCTTGAAGCAGATGGATATCAACCTTATCTTATCTCTCCAGAGAAAGGTTTGAGATCCTTAATTAAAGGCGTTCTTGAACTGGCAAAGGAGCCAT

upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 9
gtgggtttctgaatt-ttcctgcctcaaattgtataa-----acaagtaacggctttagac---tggagtgtgacagattgattttccaattgtttcagATCGTGTTGGAGGCTGATGGTTATCAACCTTATCTCATATCTCCAGAGAAAGGGTTGAGATCGTTAATAAAAACCGTTCTTGAGTTGGCTAAAGACCCAG
||  | ||||   || |||      ||| || | |       | |  |   |   | || |   |   || ||  |  ||  ||||| | |  |  ||||| ||| | || || |||||||||||||||||||| ||||||||||| ||||| || || ||  |||||||||  || || ||| |||| ||||| ||| 
gtatggttctcttttattcacattccaacttttgtgccttttaaatatgttgttgtaaggcctttattgtttgcaatgttccttttcaattgataccagATTGTGCTAGAAGCAGATGGTTATCAACCTTATCTTATATCTCCAGAAAAAGGTTTAAGGTCTCTAATAAAAATTGTCCTGGAGCTGGCGAAAGAGCCAT

upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 9
--gtgggtttctgaattttcctgcctcaaattgtataaacaagtaacggctttagactggagtgtgaca-----gattgattttcca--att--gtttcagATCGTGTTGGAGGCTGATGGTTATCAACCTTATCTCATATCTCCAGAGAAAGGGTTGAGATCGTTAATAAAAACCGTTCTTGAGTTGGCTAAAGACCCAG
   |       ||  || | | | ||||| || ||||   |  |   || ||     ||  || | |       || |||||||||   |||  ||  ||||| ||||| || ||||||||||||||||| ||||| |||||||| |||||||| ||||||||||||||||||   ||  | ||| | || ||||| ||| 
gtatctaccattgtgttgttcggtctcaa-ttttatac-tatattttggattatttttgaggtctaattactttgagtgattttcccccatttggtcacagATTGTGTTAGAAGCTGATGGTTATCAACCATATCTTATATCTCCTGAGAAAGGTTTGAGATCGTTAATAAAAGGTGTCTTGGAGCTTGCAAAAGAGCCAT

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|125206571|gb|EL221525.1|EL221525
EST:     CCGTTGGATAGACATTTTGACTTGAACAATGTCAAAAGG                         ATCGTGTTGGAGGCTGATGGTTATCAACCTTATCTCATATCTCCAGAGAAA
genomic: CCGTTGGATAGACATTTTGACTTGAACAATGTCAAAAGGgtgggtttct ... attgtttcagATCGTGTTGGAGGCTGATGGTTATCAACCTTATCTCATATCTCCAGAGAAA
EST: gi|164125104|gb|EL988846.1|EL988846
EST:     CAAACAGCTTCCGTTGGATAGACATTTTGACTTGAACAATGTCAAAAGG                         ATCGTGTTGGAGGCTGATGGTTATCAACCTTATCTTATATCTCCAGAGAAA
genomic: CAAAAAGCTTCCGTTGGATAGACATTTTGACTTGAACAATGTCAAAAGGgtgggtttct ... attgtttcagATCGTGTTGGAGGCTGATGGTTATCAACCTTATCTCATATCTCCAGAGAAA
EST: gi|124724979|gb|EH816381.1|EH816381
EST:     CGTTGGATAGACATTTTGACTTGAACAATGTCAAAAGG                         ATCGTGTTGGAG
genomic: CGTTGGATAGACATTTTGACTTGAACAATGTCAAAAGGgtgggtttct ... attgtttcagATCGTGTTGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacaagtaacggctttagactggagtgtgacagattgattttccaattgtttcagATCGTGTTGGAGGCTGATGGTTATCAACCTTATCTCATATCTCCAGAGAAAGGGTTGAGATCGTTAATAAAAACCGTTCTTGAGTTGGCTAAAGACCCAG
                                              ttgtttc  CT-rich tract
                                 attgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggtttctgaattttcctgcctcaaattgtataaacaagtaacggctttagactggagtgtgacagattgattttccaattgtttcagATCGTGTTGGAGGCTGATGGTTATCAACCTTATCTCATATCTCCAGAGAAAGGGTTGAGATCGTTAATAAAAACCGTTCTTGAGTTGGCTAAAGACCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC