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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattgttttcatctgcacaatgaaatagatttttgttgtagaaacaaacccagcttaggctttttggttctttatttttagTGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGG

Basic information

species Arabidopsis thaliana
transcript AT1G23310.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G23310.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G04320.2 (Glycine max), 3'ss of exon 5
--------------------------------------------------gtgattgttttcatctgcacaatgaaatagatttttgttgtag-aaacaaacccagcttaggctttttggttctttatttttagTGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGG
                                                   |  || |||  |   |     | |  |   ||| |  | |   |  ||||   |      |||| ||| | | |||     ||||| ||||| ||||| | |||||||||||| || |||||||| |||||||| || || |||  | | ||  | ||| | |  ||||||
gtatttatactctatacagtctctttctgttttctaatttatcttgtaaaatctttctttaaaagggagtcttaagcttagtttctaatttgttaggcaaatggattaattgcttcttgctccattac----agTGATCCAGAGCTCATATATCTCACTGATGGTGCAAGCAAAGGAGTGATGCAGATATTAAATACTATCATCAGGGGTCAAGACGATGGG

upper sequence: AT1G23310.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G03260.3 (Glycine max), 3'ss of exon 5
--------------------------------------------gtgattgttttcatctgcacaatgaaatagatttttgttgtagaaacaaacccagcttaggctttttggttctttatttttagTGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGG
                                            || |    |||| | |  |   |    ||  |||    | |   |   ||      | |    || | ||||   ||||  ||||| ||||||||||| | |||||||||||| || ||||| || |||||||| || || |||  | | ||  | ||| | |  ||||||
gtattatactctatacagtctcattctgttttctaatttatcttgtaaaatctttc-tttaaagggtctcttaagtttccaatttgttatgcaaatggattcattgcttcttgttcc--atttacagTGATCCAGAACTCATATATCTCACTGATGGTGCCAGCAAGGGGGTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGG

upper sequence: AT1G23310.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S215_28V6.1 (Physcomitrella patens), 3'ss of exon 4
------------------------gtgattgttttcatctgcacaatgaaatagatttt-tgttgtagaaacaaacccagcttaggctttttggttctttatttttagTGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGG
                         |||   |||  |    ||       || ||||     |  |   ||   |   | ||||      ||  || || |  |  || || || ||    ||||| ||||||||||||||||||||||||||    ||| | ||||||    | || |||| | |    ||||||
gtgaactttgcctttcaattcgccttgaaaatttgaagtctcaatggttcatggattccacatcttttgaatgga---aacttaaaaccgtt--ttattgaactgcagCGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGTGTAGCACAAGTTTTGAATGCCCTCATCCGCGATGAGAAGGATGGG

upper sequence: AT1G23310.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S341_73V6.2 (Physcomitrella patens), 3'ss of exon 4
------------------------------gtgattg-ttttcatctgcacaatgaaatagattttt-gttgtagaaacaaacccagcttaggctttttggttctttatttttagTGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGG
                              || |  | |||| | |   ||       |  ||| ||  | ||   || |    ||  | |   |||  |||     |  |  ||||| || ||    ||||| ||||||||||||||||||||||| ||    ||| | ||||||    | || || | | |   |||||| 
gtgaacatactttggctgttcaatcaaagcgtcagagattttgagcgatactgcttcttgaattcttcatcgtttgaagagtaacaaataaaagttt--ggtg---gaactgcagTGATCCGGAGAATATCTTCCTCACTGATGGAGCTAGCAAAGGGGTTGCACAAGTTTTGAATGCCCTCATCCGTGATGAAAAAGATGGA

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|86074112|gb|DR369869.1|DR369869
EST:     GTTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAG                         TGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCNNNNGTGTGATGCA
genomic: GTTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAGgtgattgttt ... ttatttttagTGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCA
EST: gi|86074113|gb|DR369870.1|DR369870
EST:     TTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTAATCCAAG                         TGACCCAGAACTCATC
genomic: TTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTA-TCCAAGgtgattgttt ... ttatttttagTGACCCAGAACTCATC
EST: gi|116482909|gb|EG525501.1|EG525501
EST:     GTTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAG                         TGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCA
genomic: GTTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAGgtgattgttt ... ttatttttagTGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCA
EST: gi|124887966|gb|EH966868.1|EH966868
EST:     GTTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAG                         TGACCCAGAACTCATCTTTCTCACTGA
genomic: GTTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAGgtgattgttt ... ttatttttagTGACCCAGAACTCATCTTTCTCACTGA
EST: gi|124981343|gb|EL054218.1|EL054218
EST:     GTGATGGGTATCCAAG                         TGACCCAGAACTCATCTTTCTCACTGATGGAGCTAG
genomic: GTGATGGGTATCCAAGgtgattgttt ... ttatttttagTGACCCAGAACTCATCTTTCTCACTGATGGAGCTAG
EST: gi|86074105|gb|DR369862.1|DR369862
EST:     GTTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAG                         TGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGNGTGATGCA
genomic: GTTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAGgtgattgttt ... ttatttttagTGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCA
EST: gi|116434550|gb|EG477142.1|EG477142
EST:     GTTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAG                         TGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCA
genomic: GTTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAGgtgattgttt ... ttatttttagTGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCA
EST: gi|86074145|gb|DR369902.1|DR369902
EST:     TTAGGAAAAAGGTTGCTGAGTTCATTCAACGGCGTGATGGGGTATC-AAG                         TGACCCAGAACTCATCTTTCTCAACTGATGGA
genomic: TTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGG-TATCCAAGgtgattgttt ... ttatttttagTGACCCAGAACTCATCTTTCTCA-CTGATGGA
EST: gi|125298419|gb|EL312504.1|EL312504
EST:     GTTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAG                         TGACCCAGAACTCATCTTTCACACTGATGGAGCTAGCAAAGGTGT
genomic: GTTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAGgtgattgttt ... ttatttttagTGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGT
EST: gi|124949349|gb|EL024966.1|EL024966
EST:     GTTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAG                         TGACCCAGAACTCATCTTT
genomic: GTTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAGgtgattgttt ... ttatttttagTGACCCAGAACTCATCTTT
EST: gi|116434562|gb|EG477154.1|EG477154
EST:     GTTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAG                         TGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCA
genomic: GTTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAGgtgattgttt ... ttatttttagTGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCA
EST: gi|125081352|gb|EL142607.1|EL142607
EST:     GTTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAG                         TGACCCAGAACTCATCTT
genomic: GTTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAGgtgattgttt ... ttatttttagTGACCCAGAACTCATCTT
EST: gi|124981356|gb|EL054230.1|EL054230
EST:     TTAGGTAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAG                         TGACCCAGAACTCATCTTT
genomic: TTAGG-AAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAGgtgattgttt ... ttatttttagTGACCCAGAACTCATCTTT
EST: gi|125202088|gb|EL217042.1|EL217042
EST:     AACGGCGTGATGGGTATCCAAG                         TGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTAGATGC
genomic: AACGGCGTGATGGGTATCCAAGgtgattgttt ... ttatttttagTGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGT-GATGC
EST: gi|116482910|gb|EG525502.1|EG525502
EST:     GTTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAG                         TGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCA
genomic: GTTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAGgtgattgttt ... ttatttttagTGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCA
EST: gi|116400460|gb|EG443052.1|EG443052
EST:     GTTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAG                         TGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCA
genomic: GTTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAGgtgattgttt ... ttatttttagTGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCA
EST: gi|86074107|gb|DR369864.1|DR369864
EST:     GTTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAG                         TGACCCAGAACTCATCTTTCTCCCTGATGGAGCTAGCAAAGGTGTGATGCA
genomic: GTTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAGgtgattgttt ... ttatttttagTGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCA
EST: gi|86074110|gb|DR369867.1|DR369867
EST:     GTTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAG                         TGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCA
genomic: GTTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAGgtgattgttt ... ttatttttagTGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCA
EST: gi|86074144|gb|DR369901.1|DR369901
EST:     TTAGGAAAGAGGTTGCTGAGTTTCATTCAACGGCGTGATGGGTATC-AAG                         TGGACC-AGA-CTCATCTT-CTCACTGATGGAGCTAGCA
genomic: TTAGGAAAGAGGTTGCTGAGTT-CATTCAACGGCGTGATGGGTATCCAAGgtgattgttt ... ttatttttagTG-ACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCA
EST: gi|86074123|gb|DR369880.1|DR369880
EST:     GTTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAG                         TGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCA
genomic: GTTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAGgtgattgttt ... ttatttttagTGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCA
EST: gi|86074134|gb|DR369891.1|DR369891
EST:     GTTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAG                         TGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCA
genomic: GTTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAGgtgattgttt ... ttatttttagTGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCA
EST: gi|86074106|gb|DR369863.1|DR369863
EST:     GTTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAG                         TGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCNNNGGTGTGATGCA
genomic: GTTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAGgtgattgttt ... ttatttttagTGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCA
EST: gi|125127001|gb|EL172068.1|EL172068
EST:     TTCATTCAACGGCGTGATGGGTATCCAAG                         TGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCA
genomic: TTCATTCAACGGCGTGATGGGTATCCAAGgtgattgttt ... ttatttttagTGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCA
EST: gi|152038525|gb|AV826916.2|AV826916
EST:     GTTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAG                         TAACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCA
genomic: GTTAGGAAAGAGGTTGCTGAGTTCATTCAACGGCGTGATGGGTATCCAAGgtgattgttt ... ttatttttagTGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatttttgttgtagaaacaaacccagcttaggctttttggttctttatttttagTGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGG
                                 ctttttggttcttt  CT-rich tract
                                         ttctttattttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgattgttttcatctgcacaatgaaatagatttttgttgtagaaacaaacccagcttaggctttttggttctttatttttagTGACCCAGAACTCATCTTTCTCACTGATGGAGCTAGCAAAGGTGTGATGCAAATCTTGAATTGTGTTATACGCGGTAATGGAGATGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG