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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAAGGAGTTGATCTCGTTGAAACGCGAGGCCAAGCTTAAGGGAGGTTTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGGgtatgttatactgttgttgtttgtcttataagcatttctaaagccagtgtctatgttgttgttcttatctgttgttctttttaatattgcag

Basic information

species Arabidopsis thaliana
transcript AT2G01250.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G01250.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA09G06860.1 (Glycine max), 5'ss of exon 3
GAGAAGGAGTTGATCTCGTTGAAACGCGAGGCCAAGCTTAAGGGAGGTTTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGGgtatgttatactgttgttgtttgtcttataagcatttctaaagccagtgtctatgttgttgttcttatctgttgttctttttaatattgcag---------
 | |||||||||||   |||||| || || ||||||||||||||||| || |||||||| ||||||||||||||||||||||||||| | |||||||||||  | ||    || ||  | || | ||||   | |   |    | ||||| | | ||| || || | | |  | ||   |   |||   |         
CAAAAGGAGTTGATTAGGTTGAAGCGTGAAGCCAAGCTTAAGGGAGGGTTTTATGTTGAACCTGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGGgtaattaattaatttattaat-gtatcataacattatgctagtatattgtctttttggttattgttgtttttattgctaaatggaatttatgtaatgtcag

upper sequence: AT2G01250.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA15G18170.2 (Glycine max), 5'ss of exon 3
GAGAAGGAGTTGATCTCGTTGAAACGCGAGGCCAAGCTTAAGGGAGGTTTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGGgtatgttat--------actgttgttgtttgtcttataagcatttctaaagccagtgtc--tatgttgttgttcttatc--tgttgttctttttaatattgcag---------------
 | |||||  ||||   |||||| || || ||||||||||||||||| || |||||||| || |||||||||||||||||||||||| | |||||||||||  | ||        |   |  || |||    | | |  || ||   |     | |   ||| ||||  || |  |   ||||||| || ||  || ||  |               
CAAAAGGAACTGATTAGGTTGAAGCGTGAAGCCAAGCTTAAGGGAGGGTTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGGgtaattaatcaataaatatattaattatttagtattttaatatatcatgacatcatattagtatattgtctttttggttattgttgtttttcttgctaatggcgtttctgtaacgtcag

upper sequence: AT2G01250.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA07G02270.1 (Glycine max), 5'ss of exon 3
GAGAAGGAGTTGATCTCGTTGAAACGCGAGGCCAAGCTTAAGGGAGGTTTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGGgtatgttatactgttgttgtttgtcttataagcatttctaaagccagtgtctatgttgttgttcttatctgttgttctttttaatattgcag
|||||||| |||||   ||||||||||||||||||||| || || ||||||||||| || || || |||||||| ||||| || || || || |||||||||||      |||  |  ||    |   ||  |||  ||      |||   | |   | |  | || ||  ||| |||| |         
GAGAAGGAATTGATTCGGTTGAAACGCGAGGCCAAGCTGAAAGGTGGTTTCTATGTGGATCCAGAGGCTAAGCTGTTGTTTATTATTCGCATTCGTGGgtatgt------gtttctacttagactg--agattttagaatattcatgttggtctaactatg-taatttgg-gtttttttcag--------

upper sequence: AT2G01250.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA08G23750.2 (Glycine max), 5'ss of exon 3
GAGAAGGAGTTGATCTCGTTGAAACGCGAGGCCAAGCTTAAGGGAGGTTTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGGgtatgttatactgttgttgtttgtcttataagcatttctaaagccag--tgtctatgttgttgttcttatctg-ttgttctttttaatattgcag
|||||||| |||||   ||||||||||||||||||||| || || || |||||||| || || || |||||||||||||| ||  | || || |||||||||||  | || |  || ||||  |      ||||    |    ||  | |  | |||| | |   ||| |  ||||  ||||| |        
GAGAAGGAATTGATTCGGTTGAAACGCGAGGCCAAGCTGAAAGGTGGATTCTATGTCGATCCAGAGGCTAAGCTCTTGTTTATTGTTCGCATTCGTGGgtatgtgtttctttgtttatttgcatctgcttcattagagattttagaatattcaggttggtctgactatgtaattgtgttttttcag-------

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|164004646|gb|EL970618.1|EL970618
EST:     CTTGTTCATCATCCGTATCCGTGG                         TATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTT
genomic: CTTGTTCATCATCCGTATCCGTGGgtatgttata ... aatattgcagTATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTT
EST: gi|124765001|gb|EH855131.1|EH855131
EST:     AAGCTAAGCTCTTGTTCATCATCCGTATCCGTGG                         TATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTT
genomic: AAGCTAAGCTCTTGTTCATCATCCGTATCCGTGGgtatgttata ... aatattgcagTATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTT
EST: gi|125083832|gb|EL144257.1|EL144257
EST:     TTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGG                         TATCAATGCCATTGACCCTAAGACTAAGAAG
genomic: TTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGGgtatgttata ... aatattgcagTATCAATGCCATTGACCCTAAGACTAAGAAG
EST: gi|164108926|gb|ES050871.1|ES050871
EST:     CTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGG                         TATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTT
genomic: CTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGGgtatgttata ... aatattgcagTATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTT
EST: gi|164160269|gb|ES170123.1|ES170123
EST:     AGCTAAGCTCTTGTTCATCATCCGTATCCGTGG                         TATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTT
genomic: AGCTAAGCTCTTGTTCATCATCCGTATCCGTGGgtatgttata ... aatattgcagTATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTT
EST: gi|125080290|gb|EL141947.1|EL141947
EST:     TAAGCTCTTGTTCATCATCCGTATCCGTGG                         TATCAATGCCATTGACCCTAAGACTAAAGAAGATTCTCCAGCTCTTGCGTT
genomic: TAAGCTCTTGTTCATCATCCGTATCCGTGGgtatgttata ... aatattgcagTATCAATGCCATTGACCCTAAGACTAA-GAAGATTCTCCAGCTCTTGCGTT
EST: gi|124949705|gb|EL025259.1|EL025259
EST:     TTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGG                         TATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCT
genomic: TTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGGgtatgttata ... aatattgcagTATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCT
EST: gi|124724499|gb|EH815901.1|EH815901
EST:     TAAGCTCTTGTTCATCATCCGTATCCGTGG                         TATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTT
genomic: TAAGCTCTTGTTCATCATCCGTATCCGTGGgtatgttata ... aatattgcagTATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTT
EST: gi|124775246|gb|EH865375.1|EH865375
EST:     TTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGG                         TATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCT
genomic: TTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGGgtatgttata ... aatattgcagTATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCT
EST: gi|164211690|gb|EL988985.1|EL988985
EST:     TTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGG                         TATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAG
genomic: TTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGGgtatgttata ... aatattgcagTATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAG
EST: gi|125325666|gb|EL339746.1|EL339746
EST:     TTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGG                         TATCAATGCCATTG
genomic: TTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGGgtatgttata ... aatattgcagTATCAATGCCATTG
EST: gi|152034121|gb|BP868106.2|BP868106
EST:     TTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGG                         TATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTT
genomic: TTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGGgtatgttata ... aatattgcagTATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTT
EST: gi|163985597|gb|EL967501.1|EL967501
EST:     CTTG-TCATCATCCGTATCCGTGG                         TATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTT
genomic: CTTGTTCATCATCCGTATCCGTGGgtatgttata ... aatattgcagTATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTT
EST: gi|152038370|gb|BP815237.2|BP815237
EST:     TTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGG                         TATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTT
genomic: TTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGGgtatgttata ... aatattgcagTATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTT
EST: gi|124915675|gb|EH989549.1|EH989549
EST:     TTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGG                         TATCAATGCCATTGACCCTAAGACTAAG
genomic: TTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGGgtatgttata ... aatattgcagTATCAATGCCATTGACCCTAAGACTAAG
EST: gi|86082419|gb|DR378178.1|DR378178
EST:     CTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGG                         TATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTT
genomic: CTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGGgtatgttata ... aatattgcagTATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTT
EST: gi|125144823|gb|EL180253.1|EL180253
EST:     TTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGG                         TATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCT
genomic: TTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGGgtatgttata ... aatattgcagTATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCT
EST: gi|164200246|gb|EL968786.1|EL968786
EST:     TTGTTCATCATCCGTATCCGTGG                         TATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTT
genomic: TTGTTCATCATCCGTATCCGTGGgtatgttata ... aatattgcagTATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTT
EST: gi|124964073|gb|EL038365.1|EL038365
EST:     TTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGG                         TATCAATGCCATTGACCCTAAGA
genomic: TTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGGgtatgttata ... aatattgcagTATCAATGCCATTGACCCTAAGA
EST: gi|164011254|gb|ES208951.1|ES208951
EST:     TTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGG                         TATCAATGCCATTGACCCTAAGAACTAAGAAGATTCTCCAG
genomic: TTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGGgtatgttata ... aatattgcagTATCAATGCCATTGACCCTAAGA-CTAAGAAGATTCTCCAG
EST: gi|164049079|gb|ES080861.1|ES080861
EST:     GCTCTTGTTCATCGTCCGTATCCGTGG                         TATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTT
genomic: GCTCTTGTTCATCATCCGTATCCGTGGgtatgttata ... aatattgcagTATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTT
EST: gi|124760594|gb|EH850724.1|EH850724
EST:     TTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGG                         TATCAATGCCA
genomic: TTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGGgtatgttata ... aatattgcagTATCAATGCCA
EST: gi|163978199|gb|ES156398.1|ES156398
EST:     TTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGG                         TATCAATGCCATTGACCCTAAAGACTAAGAAGATTCTCCAG
genomic: TTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGGgtatgttata ... aatattgcagTATCAATGCCATTGACCCTAA-GACTAAGAAGATTCTCCAG
EST: gi|86082295|gb|DR378054.1|DR378054
EST:     AGCT-AGCTCTTG-TCATCAT-CGTAT-CGT-G                         TATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTT
genomic: AGCTAAGCTCTTGTTCATCATCCGTATCCGTGGgtatgttata ... aatattgcagTATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTT
EST: gi|47828829|gb|CK118513.1|CK118513
EST:     TTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGG                         TATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTT
genomic: TTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGGgtatgttata ... aatattgcagTATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTT
EST: gi|124705769|gb|EH797171.1|EH797171
EST:     TCATCCGTATCCGTGG                         TATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTT
genomic: TCATCCGTATCCGTGGgtatgttata ... aatattgcagTATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTT
EST: gi|125274717|gb|EL288802.1|EL288802
EST:     TTCTATGTTGACCCTGAAGC-AAGCTCTTGTTCATCATCCGTATCCGTGG                         TATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAG
genomic: TTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGGgtatgttata ... aatattgcagTATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAG
EST: gi|125276746|gb|EL290831.1|EL290831
EST:     CCGTATCCGTGG                         TATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTT
genomic: CCGTATCCGTGGgtatgttata ... aatattgcagTATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGAAGGAGTTGATCTCGTTGAAACGCGAGGCCAAGCTTAAGGGAGGTTTCTATGTTGACCCTGAAGCTAAGCTCTTGTTCATCATCCGTATCCGTGGgtatgttatactgttgttgtttgtcttataagcatttctaaagccagtgtctatgttgttgttcttatctgttgttctttttaatattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC