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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactcattttctttgattttgattatcagatttgcaataaaagatagagaattgatgatcatccattgttgtttgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTCAACCCAATCAGATGCTCCAACTGTGGCAAATGTTGCCCCAAG

Basic information

species Arabidopsis thaliana
transcript AT2G40510.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G40510.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA17G18200.1 (Glycine max), 3'ss of exon 1
-----gtactcattttctttgattttgattatcagatttgcaataaaagatagagaattgatgatcatccattgttgtttgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTCAACCCAATCAGATGCTCCAACTGTGGCAAATGTTGCCCCAAG
       |    || |  ||  | | |  |  |  | || ||  ||           ||  | ||| || |||||||||||| |||||||| |||||||| ||||| || ||  | ||||| |||  | | || ||||||||    ||| |||||||||||||||||||||| |||||||||
gttcgagatctgttgttcttattctcgccttccgtaattccag-aactttcttcttctttttcatcttctattgttgtttgt-ttgcagACATTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGTGGCCACGTCAAATTCATCCGATGCTCCAACTGTGGCAAATGCTGCCCCAAG
















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|47830262|gb|CK119946.1|CK119946
EST:     TAAACCCTAGCAGCAGACACAACACGAGTTCATCGAGAAGCAAGATG                         ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
genomic: TAAACCCTAGCAGCAGACACAACACGAGTTCATCGAGAAGCAAGATGgtactcattt ... tgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
EST: gi|86036211|gb|DR331964.1|DR331964
EST:     GCGTAAACCCTAGCAGCAGACACAACACGAGTTCATCGAGAAGCAAGATG                         ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
genomic: GCGTAAACCCTAGCAGCAGACACAACACGAGTTCATCGAGAAGCAAGATGgtactcattt ... tgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
EST: gi|86036204|gb|DR331957.1|DR331957
EST:     GCGTAAACCCTAGCAGCAGACACAACACGAGTTCATCGAGAAGCAAGATG                         ACTTTCAAGCGAAGGAACGGTGGGAGGWACAAGCACAACAGAGGACACGTC
genomic: GCGTAAACCCTAGCAGCAGACACAACACGAGTTCATCGAGAAGCAAGATGgtactcattt ... tgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
EST: gi|86036199|gb|DR331952.1|DR331952
EST:     ACGAGTTCATCGAGAAGCAAGATG                         ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
genomic: ACGAGTTCATCGAGAAGCAAGATGgtactcattt ... tgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
EST: gi|86036208|gb|DR331961.1|DR331961
EST:     GAGAAGCAAGATG                         ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
genomic: GAGAAGCAAGATGgtactcattt ... tgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
EST: gi|164132538|gb|EL998132.1|EL998132
EST:     AGACACAACACGAGTTCATCGAGAAGCAAGATG                         ACTTTCAAGCGAAGGAACGGTGGGAGG
genomic: AGACACAACACGAGTTCATCGAGAAGCAAGATGgtactcattt ... tgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGG
EST: gi|125073688|gb|EL137927.1|EL137927
EST:     CGTAAACCCTAGCAGCAGACACAACACGAGTTCATCGAGAAGCAAGAATG                         ACTTTCAAGCGAAGGAACGGTGGGAGGAACA
genomic: CGTAAACCCTAGCAGCAGACACAACACGAGTTCATCGAGAAGCAAGA-TGgtactcattt ... tgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACA
EST: gi|47828170|gb|CK117854.1|CK117854
EST:     TAAAACCTAGCAGCAGACACAACACGACTTCATCGAGAAGCAAGATG                         ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
genomic: TAAACCCTAGCAGCAGACACAACACGAGTTCATCGAGAAGCAAGATGgtactcattt ... tgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
EST: gi|86036202|gb|DR331955.1|DR331955
EST:     GCGTAAACCCTAGCAGCAGACACAACACGAGTTCATCGAGAAGCAAGATG                         ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
genomic: GCGTAAACCCTAGCAGCAGACACAACACGAGTTCATCGAGAAGCAAGATGgtactcattt ... tgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
EST: gi|47831156|gb|CK120840.1|CK120840
EST:     GCGTAAACCCTAGCAGCAGACACAACACGAGTTCATCGAGAAGCAAGATG                         ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
genomic: GCGTAAACCCTAGCAGCAGACACAACACGAGTTCATCGAGAAGCAAGATGgtactcattt ... tgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
EST: gi|86036210|gb|DR331963.1|DR331963
EST:     GCGTAAACCCTAGCAGCAGACACAACACGAGTTCATCGAGAAGCAAGATG                         ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
genomic: GCGTAAACCCTAGCAGCAGACACAACACGAGTTCATCGAGAAGCAAGATGgtactcattt ... tgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
EST: gi|86036200|gb|DR331953.1|DR331953
EST:     GCGTAAACCCTAGCAGCAGACACAACACGAGTTCATCGAGAAGCAAGATG                         ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
genomic: GCGTAAACCCTAGCAGCAGACACAACACGAGTTCATCGAGAAGCAAGATGgtactcattt ... tgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
EST: gi|86078577|gb|DR374334.1|DR374334
EST:     TAGCAGCAGACACAACACGAGTTCATCGAGAAGCAAGATG                         ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
genomic: TAGCAGCAGACACAACACGAGTTCATCGAGAAGCAAGATGgtactcattt ... tgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
EST: gi|47831171|gb|CK120855.1|CK120855
EST:     CTAGCAGCAGACACAACACGAGTTCATCGAGAAGCAAGATG                         ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
genomic: CTAGCAGCAGACACAACACGAGTTCATCGAGAAGCAAGATGgtactcattt ... tgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
EST: gi|86036209|gb|DR331962.1|DR331962
EST:     GCGTAAACCCTAGCAGCAGACACAACACGAGTTCATCGAGAAGCAAGATG                         ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
genomic: GCGTAAACCCTAGCAGCAGACACAACACGAGTTCATCGAGAAGCAAGATGgtactcattt ... tgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
EST: gi|86036201|gb|DR331954.1|DR331954
EST:     GCGTAAACCCTAGCAGCAGACACAACACGAGTTCATCGAGAAGCAAGATG                         ACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC
genomic: GCGTAAACCCTAGCAGCAGACACAACACGAGTTCATCGAGAAGCAAGATGgtactcattt ... tgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttgcaataaaagatagagaattgatgatcatccattgttgtttgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTCAACCCAATCAGATGCTCCAACTGTGGCAAATGTTGCCCCAAG
                     aattgat  putative branch site (score: 4)
       aataaaagata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactcattttctttgattttgattatcagatttgcaataaaagatagagaattgatgatcatccattgttgtttgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTCAACCCAATCAGATGCTCCAACTGTGGCAAATGTTGCCCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG