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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaccaatttagaaagcaaagtttcctctatcaacagtaattcacaacatgtaattatgtgtgtgtttaacagGTGCCTTTGAACAACATGTTTGGCTACTCCACTTCTCTCCGGTCCATGACACAAGGCAAAGGAGAATTCACGATGGAATACAAAGAACATTCTGCTGTGT

Basic information

species Arabidopsis thaliana
transcript AT1G45332.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G45332.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA01G14800.1 (Glycine max), 3'ss of exon 14
gtaagaaccaatttagaaagcaaagtttcctctatcaacagtaattcaca----acatgtaattatgtgtgtgtttaacagGTGCCTTTGAACAA---------CATGTTTGGCTACTCC-ACTTCTCTCCGGTCCATGACACAAGGCAAAGGAG-AATTCACGATGGAATACAAAGAACATTCTGCTG-TGT
|| ||   || |  |      ||  |||| | | |      |||||   |       | |||||   ||  ||||    |    |    |  |||         ||   | |  |||    |    |  || ||   |  ||  | | | ||  | || | |  |     ||||| | | ||   |  | || 
gtgagtgtca-tgcactcgagaatatttcgtgttttgctgttaatttgtatttggtttttaatttcctggttgttctttaataactgcagGGCAAAGGTGAATTCACCATGGAATACAAGGAACATTTACCAGTTTCT--CATGATGTACAGACGCAACTGATAAACACGTACAAGGGAAATAAGGAAGGTG-
















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|164193948|gb|ES095374.1|ES095374
EST:     GGAAACGATCAAGAGGGTGACGATTCAGTAATCACTGCTAAT                         GTGCCTTTGAACAACATGTTTGGCTACTCC
genomic: GGAAACGATCAAGAGGGTGACGATTCAGTAATCACTGCTAATgtaagaacca ... tgtttaacagGTGCCTTTGAACAACATGTTTGGCTACTCC
EST: gi|125121697|gb|EL168738.1|EL168738
EST:     TAATCGTTGGAAACGATCAAGAGGGTGACGATTCAGTAATCACTGCTAAT                         GTGCCTTTGAACAACAT
genomic: TAATCGTTGGAAACGATCAAGAGGGTGACGATTCAGTAATCACTGCTAATgtaagaacca ... tgtttaacagGTGCCTTTGAACAACAT
EST: gi|125055324|gb|EL125604.1|EL125604
EST:     TAATCGTTGGAAACGATCAAGAGGGTGATGATTCAGTAATCACTGCTAAT                         GTGCCTTTGAACAACATGTT
genomic: TAATCGTTGGAAACGATCAAGAGGGTGACGATTCAGTAATCACTGCTAATgtaagaacca ... tgtttaacagGTGCCTTTGAACAACATGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtttcctctatcaacagtaattcacaacatgtaattatgtgtgtgtttaacagGTGCCTTTGAACAACATGTTTGGCTACTCCACTTCTCTCCGGTCCATGACACAAGGCAAAGGAGAATTCACGATGGAATACAAAGAACATTCTGCTGTGT
                              atgtaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaaccaatttagaaagcaaagtttcctctatcaacagtaattcacaacatgtaattatgtgtgtgtttaacagGTGCCTTTGAACAACATGTTTGGCTACTCCACTTCTCTCCGGTCCATGACACAAGGCAAAGGAGAATTCACGATGGAATACAAAGAACATTCTGCTGTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC