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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacaaggtgttattgaccacagactgtgtgaagttgaagcctttttctctgtatctcgttttataatatctgaacttacaagttgttgcgctgtccacagACATGATTGAAGAATTAATCAGCAGGGGACAACAGCTTGATGCTGTTCATTTTACTTATGAAGTTGGGCTTGTGGATAAGTTCCCTCCTGTTCCTTTGCT

Basic information

species Arabidopsis thaliana
transcript AT3G22440.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G22440.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G39330.1 (Glycine max), 3'ss of exon 1
tacaaggtgttattgaccac-agactgtgtgaagttgaagcctttttctctgtatctcgttttataatatctgaacttacaagttgttgcgctgtccacagACATGATTGAAGAATTAATCAGCAGGGGACAACAGCTTGATGCTGTTCATTTTACTTATGAAGTTGGGCTTGTGGATAAGTTCCCTCCTGTTCCTTTGCT
      || |  |  |     | | |   | || || ||  || |   | |  ||   ||  |  |       |  ||     |   ||   |||  | ||| ||||||||||| || |||||||  || || ||||||||||| ||||| ||||| |||||||| || |||||||| ||||||||||||||||| ||| |
------gtatagtcaatagtgataattaattaatttcaattctctgaatattgattctgtgcttcagctgaaaatgttgtgtttgtgtgaattgtttatagATATGATTGAAGAGTTGATCAGCAAAGGGCAGCAGCTTGATGCGGTTCACTTTACATATGAAGTGGGTCTTGTGGAAAAGTTCCCTCCTGTTCCCTTGTT

upper sequence: AT3G22440.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA20G28440.2 (Glycine max), 3'ss of exon 1
-tacaaggtgttattgaccacagactgtgtgaagttgaagcctttttctctgtatctcgttttataatatctgaacttacaagttgt-tgcgctgtccacagACATGATTGAAGAATTAATCAGCAGGGGACAACAGCTTGATGCTGTTCATTTTACTTATGAAGTTGGGCTTGTGGATAAGTTCCCTCCTGTTCCTTTGCT
 || |  |    ||| |  ||| | | | | || |||      |||| |   | | |  |||  | |  |   || ||     |||| ||   ||     ||| ||||||||||| || |||||||  || || ||||||||||| ||||| ||||| |||||||| || || ||||| ||||||||||||||||| ||| |
gtatagtg-acaattaattaca-attctcttaacttgg-----ttttgtggatttgttttttgttcagctgaaaattttgtgtttgtgtgaattgcttgtagATATGATTGAAGAGTTGATCAGCAAAGGGCAGCAGCTTGATGCGGTTCACTTTACCTATGAAGTGGGTCTGGTGGAAAAGTTCCCTCCTGTTCCCTTGTT

upper sequence: AT3G22440.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv05s0020g03470.t01 (Vitis vinifera), 3'ss of exon 1
--tacaaggtgt--tattgaccacagactgtgtgaagttgaagcctttttctctgtatctcgttttataatatctgaacttacaagttgttgcgctgtccacagACATGATTGAAGAATTAATCAGCAGGGGACAACAGCTTGATGCTGTTCATTTTACTTATGAAGTTGGGCTTGTGGATAAGTTCCCTCCTGTTCCTTTGCT
  |   |||| |   || |  |    ||||||     ||| | | | || |  ||||       | |   | |     |||  ||    ||  |   |   |||| ||||||||||||||| |||  |||||||||||  |||||||||| || ||||| || ||||||||||||||||| ||||| || ||||| || |||||
tttctgaggtatggcatggggcttttactgtgaattattgga-catgttccagtgtagtatagctga--gttttaatgcttgtaaaacttt-tgtcatatgcagATATGATTGAAGAATTAGTCAATAGGGGACAACAAGTTGATGCTGTGCACTTTACATACGAAGTTGGGCTTGTGGACAAGTTTCCCCCTGTACCCTTGCT

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|124706961|gb|EH798363.1|EH798363
EST:     CTTGCGGTTTCTGTTGGTTTGGGTGATCAAATGCCTG                         ACATGATTGAAGAATTAATCAGCAGGGGACAACAGCTTGATGCTGTTCATT
genomic: CTTGCGGTTTCTGTTGGTTTGGGTGATCAAATGCCTGgtaatcctct ... ctgtccacagACATGATTGAAGAATTAATCAGCAGGGGACAACAGCTTGATGCTGTTCATT
EST: gi|47828210|gb|CK117894.1|CK117894
EST:     ACAGATGCCTAAGCTTGCGGTTTCTGTTGGTTTGGGTGATCAAATGCCTG                         ACATGATTGAAGAATTAATCAGCAGGGGACAACAGCTTGATGCTGTTCATT
genomic: ACAGATGCCTAAGCTTGCGGTTTCTGTTGGTTTGGGTGATCAAATGCCTGgtaatcctct ... ctgtccacagACATGATTGAAGAATTAATCAGCAGGGGACAACAGCTTGATGCTGTTCATT
EST: gi|125302201|gb|EL316286.1|EL316286
EST:     CGGTTTCTGTTGGTTTGGGTGATCAAATGCCTG                         ACATGATTGAAGAATTAATCAGCAGGGGACAACAGCTTGATGCTGTTCATT
genomic: CGGTTTCTGTTGGTTTGGGTGATCAAATGCCTGgtaatcctct ... ctgtccacagACATGATTGAAGAATTAATCAGCAGGGGACAACAGCTTGATGCTGTTCATT
EST: gi|125104721|gb|EL158714.1|EL158714
EST:     ACAGATGCCTAAGCTTGCGGTTTCTGTTGGTTTGGGTGATCAAATGCCTG                         ACATGATTGAAGAATTAATCAGCAGG
genomic: ACAGATGCCTAAGCTTGCGGTTTCTGTTGGTTTGGGTGATCAAATGCCTGgtaatcctct ... ctgtccacagACATGATTGAAGAATTAATCAGCAGG
EST: gi|125256187|gb|EL270272.1|EL270272
EST:     ACAGATGCCTAAGCTTGCGGTTTCTGTTGGTTTGGGTGATCAAATGCCTG                         ACATGATTGAAGAATTAATCAGCAGGGGACAACAG
genomic: ACAGATGCCTAAGCTTGCGGTTTCTGTTGGTTTGGGTGATCAAATGCCTGgtaatcctct ... ctgtccacagACATGATTGAAGAATTAATCAGCAGGGGACAACAG
EST: gi|47832288|gb|CK121972.1|CK121972
EST:     ACAGATGCCTAAGCTTGCGGTTTCTGTTGGTTTGGGTGATCAAATGCCTG                         ACATGATTGAAGAATTAATCAGCAGGGGACAACAGCTTGATGCTGTTCATT
genomic: ACAGATGCCTAAGCTTGCGGTTTCTGTTGGTTTGGGTGATCAAATGCCTGgtaatcctct ... ctgtccacagACATGATTGAAGAATTAATCAGCAGGGGACAACAGCTTGATGCTGTTCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctgtatctcgttttataatatctgaacttacaagttgttgcgctgtccacagACATGATTGAAGAATTAATCAGCAGGGGACAACAGCTTGATGCTGTTCATTTTACTTATGAAGTTGGGCTTGTGGATAAGTTCCCTCCTGTTCCTTTGCT
                           aacttac  putative branch site (score: 2)
             ttttataatatctgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacaaggtgttattgaccacagactgtgtgaagttgaagcctttttctctgtatctcgttttataatatctgaacttacaagttgttgcgctgtccacagACATGATTGAAGAATTAATCAGCAGGGGACAACAGCTTGATGCTGTTCATTTTACTTATGAAGTTGGGCTTGTGGATAAGTTCCCTCCTGTTCCTTTGCT

- - - - - - - - -cacagac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acttaca