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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcaaaggtcttaaagtaatgtggatttacttttctagaaatcattggtatgttctgcgagtgattattacctgtgcagATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCATATGACCAGTTCGCCCGTGAAAG

Basic information

species Arabidopsis thaliana
transcript AT1G23310.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G23310.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os07g01760.1 (Oryza sativa), 3'ss of exon 8
--------------------------gtaagtcaaaggtcttaaagtaatgtggatttacttttctagaaatcattggtatgttctgcgagtgattattacctgtgcagATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCATATGACCAGTTCGCCCGTGAAAG
                           |     ||   |||| |||| ||||   ||| ||||   | |  | ||    ||| | |    || |||        | ||||||||||| |||||||| ||||| ||||||||||| || || |||    ||||  |   ||||||
tagttcctgaaacagtttagttgcaactgtactaattttcttgaagttatgttactttgctttaaca-agttaataaaaatggttttaatgtcatt--------tacagATGGGTTTAATGGTTAACCCTCCTAAGCCTGGAGATATCTCTTATCTGAAGTTTTCTGCTGAAAG

upper sequence: AT1G23310.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S215_28V6.1 (Physcomitrella patens), 3'ss of exon 9
-------------------------------------gtaagtcaaaggtc--ttaaagtaa-tgtggatttacttttctagaaatcattggtatgttct---gcgagt-----gattattacctgt-gcagATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCATATGACCAGTTCGCCCGTGAAAG
                                      ||| ||   ||||  |   | ||    |  | ||| ||   | |  |   |||    | ||    || ||      || |  ||  ||| |||||||||||||||||| | ||||||||| || ||||||||||| |||   | || |      |||||
gtatgtgttctaacccgatgaaaaatttatttgcattttaaatcgttggtccctcgcactaggcattaacttaattgcatggccaaggttgtaccgatcctaagcaagatactggacttctatgtgttgcagATGGGTTTGATGGTCAGTCCTCCAAAACCAGGAGACATTTCGTATCCTCTGTACAAGGCAGAAAG
















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|125096698|gb|EL153407.1|EL153407
EST:     AAGGTTGTTCATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTT                         ATGGGTTTGATGGTTAATCCTCCAAAG
genomic: AAGGTTG--CATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTTgtaagtcaaa ... acctgtgcagATGGGTTTGATGGTTAATCCTCCAAAG
EST: gi|125225261|gb|EL239346.1|EL239346
EST:     CCCTCAGCCCTAATGTCTCTGCGCAAATCTTT                         ATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCAATAATGACC
genomic: CCCTCAGCCCTAATGTCTCTGCGCAAATCTTTgtaagtcaaa ... acctgtgcagATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCA-TA-TGACC
EST: gi|124847314|gb|EH931751.1|EH931751
EST:     TGCGCAAATCTTT                         ATGGGTTTGATGGTTAATTCCTCCAAAGCCTGGAGACATTTCATATGACCA
genomic: TGCGCAAATCTTTgtaagtcaaa ... acctgtgcagATGGGTTTGATGGTTAA-TCCTCCAAAGCCTGGAGACATTTCATATGACCA
EST: gi|125192374|gb|EL207328.1|EL207328
EST:     ACAAGGTTGCATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTT                         ATGGGTTTGATGATTAATCCTCCAAAG
genomic: ACAAGGTTGCATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTTgtaagtcaaa ... acctgtgcagATGGGTTTGATGGTTAATCCTCCAAAG
EST: gi|124710790|gb|EH802192.1|EH802192
EST:     GTCTCTGCGCAAATCTTT                         ATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCATATGACCAG
genomic: GTCTCTGCGCAAATCTTTgtaagtcaaa ... acctgtgcagATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCATATGACCAG
EST: gi|125026180|gb|EL098449.1|EL098449
EST:     ACAAGGTTGCATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTT                         ATGGGTTTGATGGTTAA
genomic: ACAAGGTTGCATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTTgtaagtcaaa ... acctgtgcagATGGGTTTGATGGTTAA
EST: gi|125104424|gb|EL158503.1|EL158503
EST:     CGCAAATCTTT                         ATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCATATGACCAG
genomic: CGCAAATCTTTgtaagtcaaa ... acctgtgcagATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCATATGACCAG
EST: gi|124819787|gb|EH904653.1|EH904653
EST:     CTGCGCAAATCTTT                         ATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCATATGACCAG
genomic: CTGCGCAAATCTTTgtaagtcaaa ... acctgtgcagATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCATATGACCAG
EST: gi|125187658|gb|EL202612.1|EL202612
EST:     ACAAGGTTGCATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTT                         ATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCATATGA
genomic: ACAAGGTTGCATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTTgtaagtcaaa ... acctgtgcagATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCATATGA
EST: gi|125049958|gb|EL122227.1|EL122227
EST:     CATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTT                         ATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCATATGACCAG
genomic: CATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTTgtaagtcaaa ... acctgtgcagATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCATATGACCAG
EST: gi|124948016|gb|EL023811.1|EL023811
EST:     CGCAAATCTTT                         ATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCATATGACCAG
genomic: CGCAAATCTTTgtaagtcaaa ... acctgtgcagATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCATATGACCAG
EST: gi|125311118|gb|EL325203.1|EL325203
EST:     CTAATGTCTCTGCGCAAATCTTT                         ATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCATATGACCAG
genomic: CTAATGTCTCTGCGCAAATCTTTgtaagtcaaa ... acctgtgcagATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCATATGACCAG
EST: gi|125060829|gb|EL129506.1|EL129506
EST:     ACAAGGTTGCATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTT                         ATGGGGTTTGATGGTTAATCCT
genomic: ACAAGGTTGCATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTTgtaagtcaaa ... acctgtgcagATGGG-TTTGATGGTTAATCCT
EST: gi|125000948|gb|EL073217.1|EL073217
EST:     ACAAGGTTGCATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTT                         ATGGGTTTGATGGTTAATCCT
genomic: ACAAGGTTGCATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTTgtaagtcaaa ... acctgtgcagATGGGTTTGATGGTTAATCCT
EST: gi|124792413|gb|EH882092.1|EH882092
EST:     CCCTAATGTCTCTGCGCAAATCTTT                         ATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCATATGACCAA
genomic: CCCTAATGTCTCTGCGCAAATCTTTgtaagtcaaa ... acctgtgcagATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCATATGACCA-
EST: gi|124741575|gb|EH832737.1|EH832737
EST:     ACAAGGTTGCATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTT                         ATGGGTTTGATGGTTA
genomic: ACAAGGTTGCATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTTgtaagtcaaa ... acctgtgcagATGGGTTTGATGGTTA
EST: gi|86074126|gb|DR369883.1|DR369883
EST:     ACAAGGTTGCATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTT                         ATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCATATGACCAG
genomic: ACAAGGTTGCATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTTgtaagtcaaa ... acctgtgcagATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCATATGACCAG
EST: gi|86074135|gb|DR369892.1|DR369892
EST:     ACAAGGTTGCATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTT                         ATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCATATGACCAG
genomic: ACAAGGTTGCATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTTgtaagtcaaa ... acctgtgcagATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCATATGACCAG
EST: gi|124763447|gb|EH853577.1|EH853577
EST:     AGCCCTAATGTCTCTGCGCAAATCTTT                         ATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCATATGACCAG
genomic: AGCCCTAATGTCTCTGCGCAAATCTTTgtaagtcaaa ... acctgtgcagATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCATATGACCAG
EST: gi|125210753|gb|EL225707.1|EL225707
EST:     ACAAGGTTGCATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTT                         TATGGGTTTGA
genomic: ACAAGGTTGCATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTTgtaagtcaaa ... acctgtgcag-ATGGGTTTGA
EST: gi|125279070|gb|EL293155.1|EL293155
EST:     TTGCATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTT                         ATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCA
genomic: TTGCATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTTgtaagtcaaa ... acctgtgcagATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCA
EST: gi|124998412|gb|EL070681.1|EL070681
EST:     TTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTT                         ATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGAACATTTCATATGACCA
genomic: TTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTTgtaagtcaaa ... acctgtgcagATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGA-CATTTCATATGACCA
EST: gi|125274207|gb|EL288292.1|EL288292
EST:     TTGCATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTT                         ATGGGTTTGATGGTTAATCCTCC
genomic: TTGCATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTTgtaagtcaaa ... acctgtgcagATGGGTTTGATGGTTAATCCTCC
EST: gi|125245442|gb|EL259527.1|EL259527
EST:     ACAAGGTTGCATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTT                         ATGGGTTTGATGGTTAATCCTCCAAAGCCT
genomic: ACAAGGTTGCATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTTgtaagtcaaa ... acctgtgcagATGGGTTTGATGGTTAATCCTCCAAAGCCT
EST: gi|124712516|gb|EH803918.1|EH803918
EST:     ACAAGGTTGCATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTT                         ATAGGGTTTGATGGTTAATCCTCCAAAGCCTGGAG
genomic: ACAAGGTTGCATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTTgtaagtcaaa ... acctgtgcagAT-GGGTTTGATGGTTAATCCTCCAAAGCCTGGAG
EST: gi|125256988|gb|EL271073.1|EL271073
EST:     TTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTT                         ATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATT-CATATGACCAG
genomic: TTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTTgtaagtcaaa ... acctgtgcagATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCATATGACCAG
EST: gi|125269816|gb|EL283901.1|EL283901
EST:     ACAAGGTTGCATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTT                         ATGGGTTTGATGGTTAA
genomic: ACAAGGTTGCATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTTgtaagtcaaa ... acctgtgcagATGGGTTTGATGGTTAA
EST: gi|125194550|gb|EL209504.1|EL209504
EST:     CGCAAATCTTT                         ATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCATATGACCAG
genomic: CGCAAATCTTTgtaagtcaaa ... acctgtgcagATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCATATGACCAG
EST: gi|124948592|gb|EL024328.1|EL024328
EST:     CGCAAATCTTT                         ATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCATATGACCAG
genomic: CGCAAATCTTTgtaagtcaaa ... acctgtgcagATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCATATGACCAG
EST: gi|124755191|gb|EH845321.1|EH845321
EST:     ACAAGGTTGCATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTT                         ATGGGTTTGATGGTTAATCCTACCAAAGCCTGGAGACATTTCATATGAC
genomic: ACAAGGTTGCATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTTgtaagtcaaa ... acctgtgcagATGGGTTTGATGGTTAATCCT-CCAAAGCCTGGAGACATTTCATATGAC
EST: gi|125118774|gb|EL167323.1|EL167323
EST:     ACAAGGTTGCATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTT                         ATGGGTTTGATGGTTAATCCTCCAAAGCCTG
genomic: ACAAGGTTGCATCAATTGCCCTCAGCCCTAATGTCTCTGCGCAAATCTTTgtaagtcaaa ... acctgtgcagATGGGTTTGATGGTTAATCCTCCAAAGCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttacttttctagaaatcattggtatgttctgcgagtgattattacctgtgcagATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCATATGACCAGTTCGCCCGTGAAAG
                                     tgattatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcaaaggtcttaaagtaatgtggatttacttttctagaaatcattggtatgttctgcgagtgattattacctgtgcagATGGGTTTGATGGTTAATCCTCCAAAGCCTGGAGACATTTCATATGACCAGTTCGCCCGTGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA