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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacaaacaatcttctgtttggtatttagtcttttagtctctatgatgagaatcactcgtaattgatatatcactagatttttcgatgtttaccgaatctttgattttgatttgatgttaaggtgtcttctagagtctgatctcttatatgatgttgatataatcattagGTATTGGAGCTAGCTGGAAATGCAGCAAGAGATAACAAGAAGACACGTATCGTACCACGGCACATTCAGCTTGCAGTGAGGAACGATGAAGAGCTTAGTA

Basic information

species Arabidopsis thaliana
transcript AT1G54690.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G54690.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S452_4V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaacaaacaatcttctgtttggtatttagtcttttagtctctatgatgagaatcactcgtaattgatatatcactagatttttcgatgtttaccgaatctttgattttgatttgatgttaaggtgtcttctagagtctgatctcttatatgatgttgatataatcat-tagGTATTGGAGCTAGCTGGAAATGCAGCAAGAGATAACAAGAAGACACGTATCGTACCACGGCACATTCAGCTTGCAGTGAGGAACGATGAAGAGCTTAGTA
                                                                     | |  ||  | ||  |||     || |   ||   |    | |  |  |||   || | |||       || ||| ||    |   |  ||| | |  |  ||||| | ||  |||| |||||||| || ||||||||||||||||  || || ||||| || ||||| ||||| |||||||| ||||| || ||| | || |
------------------------------------------------------------------gcttctgtctccacttcgcgagcagcactgcgcctgaaaagcggctaagtggtttcagtttgttcg------tggtctgtttctggcgatccatacatttgtgcagGTACTTGAATTAGCAGGAAATGCCGCCAGAGATAACAAGAAGAATCGCATTGTACCCCGCCACATCCAGCTGGCAGTGAGAAACGACGAGGAGTTAAGCA

upper sequence: AT1G54690.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S188_35V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaacaaacaatcttctgtttggtatttagtcttttagtctctatgatgagaatcactcgtaattgatatatcactagatttttcgatgtttaccgaatctttgattttgatttgatgttaaggtgtcttctagagtctgatctcttatatgatgttgatataatcattagGTATTGGAGCTAGCTGGAAATGCAGCAAGAGATAACAAGAAGACACGTATCGTACCACGGCACATTCAGCTTGCAGTGAGGAACGATGAAGAGCTTAGTA
                                                         ||||   |     ||      || ||||  | | |   |||     |  |   | |||  |||||| |   |  ||  || ||      | ||  |  ||      ||   |||||  | ||||| ||||||||||| || ||||| ||||||||||  |||||||| || || ||||| ||||| || ||| | |||||||| ||||| ||||
--------------------------------------------------------ttcgtccctctccaattgaagtatatttcattctctg--gaa-----gggtgcaagttg--gttaagatcgttagtaacgtgtgcctaactttagaacatt------atgcgtagGTTCTTGAGCTGGCTGGAAATGCTGCGAGAGACAACAAGAAGAATCGTATCGTCCCTCGCCACATCCAGCTAGCGGTGCGAAACGATGAGGAGCTAAGTA
















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|86017303|gb|DR313049.1|DR313049
EST:     CCGGTGCTCCCGTTTATCTCTCCGCCGTTCTCGAATACCTCGCCGCTGAG                         GTATTGGAGCTAGCTGGAAATGCAGCAAGAGATAACAAGAAGACACGTATC
genomic: CCGGTGCTCCCGTTTATCTCTCCGCCGTTCTCGAATACCTCGCCGCTGAGgtaacaaaca ... taatcattagGTATTGGAGCTAGCTGGAAATGCAGCAAGAGATAACAAGAAGACACGTATC
EST: gi|86017291|gb|DR313037.1|DR313037
EST:     CCGGTGCTCCCGTTTATCTCTCCGCCGTTCTCGAATACCTCGCCGCTGAG                         GTATTGGAGCTAGCTGGAAATGCAGCAAGAGATAACAAGAAGACACGTATC
genomic: CCGGTGCTCCCGTTTATCTCTCCGCCGTTCTCGAATACCTCGCCGCTGAGgtaacaaaca ... taatcattagGTATTGGAGCTAGCTGGAAATGCAGCAAGAGATAACAAGAAGACACGTATC
EST: gi|86017294|gb|DR313040.1|DR313040
EST:     CCGGTGCTCCCGTTTATCTCTCCGCCGTTCTCGAATACCTCGCCGCTGAG                         GTATTGGAGCTAGCTGGAAATGCAGCAAGAGATAACAAGAAGACACGTATC
genomic: CCGGTGCTCCCGTTTATCTCTCCGCCGTTCTCGAATACCTCGCCGCTGAGgtaacaaaca ... taatcattagGTATTGGAGCTAGCTGGAAATGCAGCAAGAGATAACAAGAAGACACGTATC
EST: gi|125264375|gb|EL278460.1|EL278460
EST:     CCGGTGCTCCCGTTTATCTCTCCGCCGTTCTCGAATACCTCGCCGCTGAG                         GTATTGGAGCTAG
genomic: CCGGTGCTCCCGTTTATCTCTCCGCCGTTCTCGAATACCTCGCCGCTGAGgtaacaaaca ... taatcattagGTATTGGAGCTAG
EST: gi|86017290|gb|DR313036.1|DR313036
EST:     CCGGTGCTCCCGTTTATCTCTCCGCCGTTCTCGAATACCTCGCCGCTGAG                         GTATTGGAGCTAGCTGGAAATGCAGCAAGAGATAACAAGAAGACACGTATC
genomic: CCGGTGCTCCCGTTTATCTCTCCGCCGTTCTCGAATACCTCGCCGCTGAGgtaacaaaca ... taatcattagGTATTGGAGCTAGCTGGAAATGCAGCAAGAGATAACAAGAAGACACGTATC
EST: gi|86017302|gb|DR313048.1|DR313048
EST:     CCGGTGCTCCCGTTTATCTCTCCGCCGTTCTCGAATACCTCGCCGCTGAG                         GTATTGGAGCTAGCTGGAAATGCANCAAGAGATAACAAGAAGACACGTATC
genomic: CCGGTGCTCCCGTTTATCTCTCCGCCGTTCTCGAATACCTCGCCGCTGAGgtaacaaaca ... taatcattagGTATTGGAGCTAGCTGGAAATGCAGCAAGAGATAACAAGAAGACACGTATC
EST: gi|86017296|gb|DR313042.1|DR313042
EST:     CCGGTGCTCCCGTTTATCTCTCCGCCGTTCTCGAATACCTCGCCGCTGAG                         GTATTGGAGCTAGCTGGAAATGCAGCAAGAGATAACARGAAGACACGTATC
genomic: CCGGTGCTCCCGTTTATCTCTCCGCCGTTCTCGAATACCTCGCCGCTGAGgtaacaaaca ... taatcattagGTATTGGAGCTAGCTGGAAATGCAGCAAGAGATAACAAGAAGACACGTATC
EST: gi|86017292|gb|DR313038.1|DR313038
EST:     CCGGTGCTCCCGTTTATCTCTCCGCCGTTCTCGAATACCTCGCCGCTGAG                         GTATTGGAGCTAGCTGGAAATGCASCAAGAGATAACAAGAAGACACGTATC
genomic: CCGGTGCTCCCGTTTATCTCTCCGCCGTTCTCGAATACCTCGCCGCTGAGgtaacaaaca ... taatcattagGTATTGGAGCTAGCTGGAAATGCAGCAAGAGATAACAAGAAGACACGTATC
EST: gi|86017297|gb|DR313043.1|DR313043
EST:     CCGGTGCTCCCGTTTATCTCTCCGCCGTTCTCGAATACCTCGCCGCTGAG                         GTATTGGAGCTAGCTGGAAATGCAGCAAGAGATAACAAGAAGACACGTATC
genomic: CCGGTGCTCCCGTTTATCTCTCCGCCGTTCTCGAATACCTCGCCGCTGAGgtaacaaaca ... taatcattagGTATTGGAGCTAGCTGGAAATGCAGCAAGAGATAACAAGAAGACACGTATC
EST: gi|86017299|gb|DR313045.1|DR313045
EST:     CCGGTGCTCCCGTTTATCTCTCCGCCGTTCTCGAATACCTCGCCGCTGAG                         GTATTGGAGCTAGCTGGAAATGCAGCAAGAGATAACAAGAAGACACGTATC
genomic: CCGGTGCTCCCGTTTATCTCTCCGCCGTTCTCGAATACCTCGCCGCTGAGgtaacaaaca ... taatcattagGTATTGGAGCTAGCTGGAAATGCAGCAAGAGATAACAAGAAGACACGTATC
EST: gi|86017300|gb|DR313046.1|DR313046
EST:     CCGGTGCTCCCGTTTATCTCTCCGCCGTTCTCGAATACCTCGCCGCTGAG                         GTATTGGAGCTAGCTGGAAATGCAGCAAGAGATAACAAGAAGACACGTATC
genomic: CCGGTGCTCCCGTTTATCTCTCCGCCGTTCTCGAATACCTCGCCGCTGAGgtaacaaaca ... taatcattagGTATTGGAGCTAGCTGGAAATGCAGCAAGAGATAACAAGAAGACACGTATC
EST: gi|86017298|gb|DR313044.1|DR313044
EST:     CCGGTGCTCCCGTTTATCTCTCCGCCGTTCTCGAATACCTCGCCGCTGAG                         GTATTGGAGCTAGCTGGAAATGCAGCAAGAGATAACAAGAAGACACGTATC
genomic: CCGGTGCTCCCGTTTATCTCTCCGCCGTTCTCGAATACCTCGCCGCTGAGgtaacaaaca ... taatcattagGTATTGGAGCTAGCTGGAAATGCAGCAAGAGATAACAAGAAGACACGTATC
EST: gi|86017295|gb|DR313041.1|DR313041
EST:     CCGGTGCTCCCGTTTATCTCTCCGCCGTTCTCGAATACCTCGCCGCTGAG                         GTATTGGAGCTAGCTGGAAATGCAGCAAGAGATAACAAGAAGACACGTATC
genomic: CCGGTGCTCCCGTTTATCTCTCCGCCGTTCTCGAATACCTCGCCGCTGAGgtaacaaaca ... taatcattagGTATTGGAGCTAGCTGGAAATGCAGCAAGAGATAACAAGAAGACACGTATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttaaggtgtcttctagagtctgatctcttatatgatgttgatataatcattagGTATTGGAGCTAGCTGGAAATGCAGCAAGAGATAACAAGAAGACACGTATCGTACCACGGCACATTCAGCTTGCAGTGAGGAACGATGAAGAGCTTAGTA
                                     tgttgat  putative branch site (score: 4)
                                       ttgatataatcatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacaaacaatcttctgtttggtatttagtcttttagtctctatgatgagaatcactcgtaattgatatatcactagatttttcgatgtttaccgaatctttgattttgatttgatgttaaggtgtcttctagagtctgatctcttatatgatgttgatataatcattagGTATTGGAGCTAGCTGGAAATGCAGCAAGAGATAACAAGAAGACACGTATCGTACCACGGCACATTCAGCTTGCAGTGAGGAACGATGAAGAGCTTAGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT