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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttgataattcccagttaattttaatttcggagacctcagctctattagtcttacgcatcaatggtttaatagtgactgaacgataaaattgattgatatttgtggcgatgcagATCTTCGAGTACAATGGAAGTGCTGTTGTTGCTATGGTAGGTAAGAATTGTTTCGCCATCGCCAGTGATCGGAGACTCGGTGTTCAGCTACAGACAATCG

Basic information

species Arabidopsis thaliana
transcript AT1G21720.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G21720.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S130_217V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------gtaagtttgataattcccagtta-attttaatttcggagacctcagctctattagtcttacgcatcaatggtttaatagtg-actgaacgataaaattgattgatatt----tgtggcgatgcagATCTTCGAGTACAATGGAAGTGCTGTTGTTGCTATGGTAGGTAAGAATTGTTTCGCCATCGCCAGTGATCGGAGACTCGGTGTTCAGCTACAGACAATCG
                  | |  |  |   |  | |  |||||  ||  |  |  |   |    || ||     |  | ||    |||    |    ||   |    ||||| ||  | ||    || ||      ||||       ||||||||||||||  |  |||| ||||| || |||||||| ||||||||||||||||| ||  | || |||||  |  | ||||| || |
gtacgtgttttccacttttctattcttcttcgatcatgttttacctttcgcaatttttaccgggttcgtgagctgatttaaaaaattagggttttggtgggagtctcaattgttttgtgttattttggggtatgatagATTACGAGCTACAATGGAAGTGCACTGATTGCCATGGTGGGCAAGAATTGCTTCGCCATCGCCAGTGACCGCCGTCTGGGTGTAAATTTCCAGACGATTG

upper sequence: AT1G21720.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S138_33V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------gtaagttt-gataat-----tcccagttaattttaatttcggagacctca-gctctattagtcttacgcatcaatggtttaat--agtgactgaacgataaaattgattgatatttgtggcgatgcagATCTTCGAGTACAATGGAAGTGCTGTTGTTGCTATGGTAGGTAAGAATTGTTTCGCCATCGCCAGTGATCGGAGACTCGGTGTTCAGCTACAGACAATCG
                       |||| || |||  |     || | || |||| | | ||  |   | |     |||  | || ||    || || |||||  |  ||    ||||   |    ||   | | ||| | ||   ||||||||  |   ||||||||||||||  |  |||| ||||| || ||| |||| ||||||||||||||||||||  | || |||||  |  | ||||| || |
gtatgtagtgccctgcagtcttctaagcttcgatcgtgcttttcgccgtcaattatgacttatgctgctttgtattcttgttgttttcattatgaaaggttttgtttaggatttgaagttttgggttttgtta-attgggggtattgcagATCACCAGCTACAATGGAAGTGCACTGATTGCCATGGTGGGCAAGGATTGCTTCGCCATCGCCAGTGATCGTCGTCTGGGTGTAAATTTCCAGACGATTG
















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|86039655|gb|DR335410.1|DR335410
EST:     CTCCAAATTCTACTCTGAAACCCTAAGTTTCCGATGTCG                         ATCTTCGAGTACAATGGAAGTGCTGTTGTTGCTATGGTAGGTAAGAATTGT
genomic: CTCCAAATTCTACTCTGAAACCCTAAGTTTCCGATGTCGgtaagtttga ... ggcgatgcagATCTTCGAGTACAATGGAAGTGCTGTTGTTGCTATGGTAGGTAAGAATTGT
EST: gi|86039666|gb|DR335421.1|DR335421
EST:     CTCCAAATTCTACTCTGAAACCCTAAGTTTCCGATGTCG                         ATCTTCGAGTACAATGGAAGTGCTGTTGTTGCTATGGTAGGTAAGAATTGT
genomic: CTCCAAATTCTACTCTGAAACCCTAAGTTTCCGATGTCGgtaagtttga ... ggcgatgcagATCTTCGAGTACAATGGAAGTGCTGTTGTTGCTATGGTAGGTAAGAATTGT
EST: gi|86039651|gb|DR335406.1|DR335406
EST:     TCTGNNNNNNNCTCCAAATTCTACTCTGAAACCCTAAGTTTCCGATGTCG                         ATCTTCGAGTACAATGGAAGTGCTGTTGTTGCTATGGTAGGTAAGAATTGT
genomic: TCTGAAAAAAACTCCAAATTCTACTCTGAAACCCTAAGTTTCCGATGTCGgtaagtttga ... ggcgatgcagATCTTCGAGTACAATGGAAGTGCTGTTGTTGCTATGGTAGGTAAGAATTGT
EST: gi|86039663|gb|DR335418.1|DR335418
EST:     CTCCAAATTCTACTCTGAAACCCTAAGTTTCCGATGTCG                         ATCTTCGAGTACAATGGAAGTGCTGTTGTTGCTATGGTAGGTAAGAATTGT
genomic: CTCCAAATTCTACTCTGAAACCCTAAGTTTCCGATGTCGgtaagtttga ... ggcgatgcagATCTTCGAGTACAATGGAAGTGCTGTTGTTGCTATGGTAGGTAAGAATTGT
EST: gi|86039667|gb|DR335422.1|DR335422
EST:     CTCCAAATTCTACTCTGAAACCCTAAGTTTCCGATGTCG                         ATCTTCGAGTACAATGGAAGTGCTGTTGTTGCTATGGTAGGTAAGAATTGT
genomic: CTCCAAATTCTACTCTGAAACCCTAAGTTTCCGATGTCGgtaagtttga ... ggcgatgcagATCTTCGAGTACAATGGAAGTGCTGTTGTTGCTATGGTAGGTAAGAATTGT
EST: gi|86039659|gb|DR335414.1|DR335414
EST:     CTCCAAATTCTACTCTGAAACCCTAAGTTTCCGATGTCG                         ATCTTCGAGTACAATGGAAGTGCTGTTGTTGCTATGGTAGGTAAGAATTGT
genomic: CTCCAAATTCTACTCTGAAACCCTAAGTTTCCGATGTCGgtaagtttga ... ggcgatgcagATCTTCGAGTACAATGGAAGTGCTGTTGTTGCTATGGTAGGTAAGAATTGT
EST: gi|86039656|gb|DR335411.1|DR335411
EST:     CTCCAAATTCTACTCTGAAACCCTAAGTTTCCGATGTCG                         ATCTTCGAGTACAATGGAAGTGCTGTTGTTGCTATGGTAGGTAAGAATTGT
genomic: CTCCAAATTCTACTCTGAAACCCTAAGTTTCCGATGTCGgtaagtttga ... ggcgatgcagATCTTCGAGTACAATGGAAGTGCTGTTGTTGCTATGGTAGGTAAGAATTGT
EST: gi|86039662|gb|DR335417.1|DR335417
EST:     TCTGAAAAAANCTCCAAATTCTACTCTGAAACCCTAAGTTTCCGATGTCG                         ATCTTCGAGTACAATGGAAGTGCTGTTGTTGCTATGGTAGGTAAGAATTGT
genomic: TCTGAAAAAAACTCCAAATTCTACTCTGAAACCCTAAGTTTCCGATGTCGgtaagtttga ... ggcgatgcagATCTTCGAGTACAATGGAAGTGCTGTTGTTGCTATGGTAGGTAAGAATTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatggtttaatagtgactgaacgataaaattgattgatatttgtggcgatgcagATCTTCGAGTACAATGGAAGTGCTGTTGTTGCTATGGTAGGTAAGAATTGTTTCGCCATCGCCAGTGATCGGAGACTCGGTGTTCAGCTACAGACAATCG
                                gattgat  putative branch site (score: 4)
                        ataaaattgattgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttgataattcccagttaattttaatttcggagacctcagctctattagtcttacgcatcaatggtttaatagtgactgaacgataaaattgattgatatttgtggcgatgcagATCTTCGAGTACAATGGAAGTGCTGTTGTTGCTATGGTAGGTAAGAATTGTTTCGCCATCGCCAGTGATCGGAGACTCGGTGTTCAGCTACAGACAATCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT