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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttttatccgaatcaacaatacatttttgttcaaagactctttggcaaagacaataactaatggtggttttgttgaaataaaaagGTGCATGTAGTGACCAAGTTATACTGGGGAGATGCAAGAGAGAAGCTTGTTGATGCTGTTAAAGATCTTAAACTCGATTCTATTGTCATGGGAAGCAGAG

Basic information

species Arabidopsis thaliana
transcript AT3G53990.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G53990.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G26300.1 (Glycine max), 3'ss of exon 2
---------------------------------------------------------------------------gtttttatccgaatcaacaatacatttt-tgttcaaag----actctttggcaaagacaataactaatggtggttttgttgaaataaaa-------agGTGCATGTAGTGACCAAGTTATACTGGGGAGATGCAAGAGAGAAGCTTGTTGATGCTGTTAAAGATCTTAAACTCGATTCTATTGTCATGGGAAGCAGAG
                                                                             ||| ||    | |||| ||   |||| ||| |   |    |   |||   |   |   |  || |   |  | ||| |   || ||        || | ||  | || || ||  |||| ||||| |||||||||||||||||| | |||||| || ||||||| || || |||||  | || ||||||||||| |
gtgtttttttttattagttttcttaaaaaaaacattgttttccttctctctttctacttagtttctacaaaatttaatttaatttaga-caacgattttttttgtgtgcggtgtgctatgttttactatgtattttgtctgaaattattattgctattattaatttttcttagATCCACATTGTTACAAAAATATATTGGGGGGATGCAAGAGAGAAGCTTTTGGATGCTATTGAAGATCTGAAGCTGGATTCGCTGGTTATGGGAAGCAGGG
















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|116402197|gb|EG444789.1|EG444789
EST:     CCGACATCGCATGTCTTGATATGCTCGACACTGGTTCGAGGCAGAAAGAG                         GTGCATGTAGTGACCAAGTTATACTGGGGAGATGCAAGAGAGAAGCTTGTT
genomic: CCGACATCGCATGTCTTGATATGCTCGACACTGGTTCGAGGCAGAAAGAGgtttttatcc ... aaataaaaagGTGCATGTAGTGACCAAGTTATACTGGGGAGATGCAAGAGAGAAGCTTGTT
EST: gi|124975387|gb|EL048889.1|EL048889
EST:     CCGACATCGCATGTCTTGATATGCTCGACACTGGTTCGAGGCAGAAAGAG                         GTGCATGTAGTGACCAAGTTATA
genomic: CCGACATCGCATGTCTTGATATGCTCGACACTGGTTCGAGGCAGAAAGAGgtttttatcc ... aaataaaaagGTGCATGTAGTGACCAAGTTATA
EST: gi|164208198|gb|EL975068.1|EL975068
EST:     CCGACATCGCATGTCTTGATATGCTCGACACTGGTTCGAGGCAGAAAGAG                         GTGCATGTAGT
genomic: CCGACATCGCATGTCTTGATATGCTCGACACTGGTTCGAGGCAGAAAGAGgtttttatcc ... aaataaaaagGTGCATGTAGT
EST: gi|116458737|gb|EG501329.1|EG501329
EST:     CCGACATCGCATGTCTTGATATGCTCGACACTGGTTCGAGGCAGAAAGAG                         GTGCATGTAGTGACCAAGTTATACTGGGGAGATGCAAGAGAGAAGCTTGTT
genomic: CCGACATCGCATGTCTTGATATGCTCGACACTGGTTCGAGGCAGAAAGAGgtttttatcc ... aaataaaaagGTGCATGTAGTGACCAAGTTATACTGGGGAGATGCAAGAGAGAAGCTTGTT
EST: gi|47828449|gb|CK118133.1|CK118133
EST:     CCGACATCGCATGTCTTGATATGCTCGACACTGGTTCGAGGCAGAAAGAG                         GTGCATGTAGTGACCAAGTTATACTGGGGAGATGCAAGAGAGAAGCTTGTT
genomic: CCGACATCGCATGTCTTGATATGCTCGACACTGGTTCGAGGCAGAAAGAGgtttttatcc ... aaataaaaagGTGCATGTAGTGACCAAGTTATACTGGGGAGATGCAAGAGAGAAGCTTGTT
EST: gi|124743491|gb|EH834653.1|EH834653
EST:     GACACTGGTTCGAGGCAGAAAGAG                         GTGCATGTAGTGACCAAGTTATACTGGGGAGATGCAAGAGAGAAGCTTGTT
genomic: GACACTGGTTCGAGGCAGAAAGAGgtttttatcc ... aaataaaaagGTGCATGTAGTGACCAAGTTATACTGGGGAGATGCAAGAGAGAAGCTTGTT
EST: gi|125216934|gb|EL231017.1|EL231017
EST:     GACACTGGTTCGAGGCAGAAAGAG                         GTGCATGTAGTGACCAAGTTATACTGGGGAGATGCAAGAGAGAAGCTTGTT
genomic: GACACTGGTTCGAGGCAGAAAGAGgtttttatcc ... aaataaaaagGTGCATGTAGTGACCAAGTTATACTGGGGAGATGCAAGAGAGAAGCTTGTT
EST: gi|164118276|gb|ES178796.1|ES178796
EST:     CGACACTGGTTCGAGGCAGAAAGAG                         GTGCATGTAGTGACCAAGTTATACTGGGGAGATGCAAGAGAGAAGCTTGTT
genomic: CGACACTGGTTCGAGGCAGAAAGAGgtttttatcc ... aaataaaaagGTGCATGTAGTGACCAAGTTATACTGGGGAGATGCAAGAGAGAAGCTTGTT
EST: gi|124706705|gb|EH798107.1|EH798107
EST:     CCGACATCGCATGTCTTGATATGCTCGACACTGGTTCGAGGCAGAAAGAG                         GTGCATGTAGTGACCAAGTTATACTGGGGAG
genomic: CCGACATCGCATGTCTTGATATGCTCGACACTGGTTCGAGGCAGAAAGAGgtttttatcc ... aaataaaaagGTGCATGTAGTGACCAAGTTATACTGGGGAG
EST: gi|124744552|gb|EH835714.1|EH835714
EST:     TTGATATGCTCGACACTGGTTCGAGGCAGAAAGAG                         GTGCATGTAGTGACCAAGTTATACTGGGGAGATGCAAGAGAGAAGCTTGTT
genomic: TTGATATGCTCGACACTGGTTCGAGGCAGAAAGAGgtttttatcc ... aaataaaaagGTGCATGTAGTGACCAAGTTATACTGGGGAGATGCAAGAGAGAAGCTTGTT
EST: gi|163970867|gb|ES095623.1|ES095623
EST:     CCGACATCGCATGTCTTGATATGCTCGACACTGGTTCGAGGCAGAAAGAG                         GTGCATGTAGTGACCAAGTTATACTGGGGAGATG
genomic: CCGACATCGCATGTCTTGATATGCTCGACACTGGTTCGAGGCAGAAAGAGgtttttatcc ... aaataaaaagGTGCATGTAGTGACCAAGTTATACTGGGGAGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaagactctttggcaaagacaataactaatggtggttttgttgaaataaaaagGTGCATGTAGTGACCAAGTTATACTGGGGAGATGCAAGAGAGAAGCTTGTTGATGCTGTTAAAGATCTTAAACTCGATTCTATTGTCATGGGAAGCAGAG
                         aactaat  putative branch site (score: 2)
                                     ttttgttgaaataaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttttatccgaatcaacaatacatttttgttcaaagactctttggcaaagacaataactaatggtggttttgttgaaataaaaagGTGCATGTAGTGACCAAGTTATACTGGGGAGATGCAAGAGAGAAGCTTGTTGATGCTGTTAAAGATCTTAAACTCGATTCTATTGTCATGGGAAGCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT