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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtattacttctctacttttgctcttatcgatgctttttactctctctttctatacttttcttactctctctttctatactttgtctcttgaattcaaagGTTATTGCTTACGATTTTGGAATCAAGCAAAACATCCTAAGACGCCTTTCATCTTACGGATGTCAAATCACTGTTGTTCCGTCCACATTTCCAGCTGCCG

Basic information

species Arabidopsis thaliana
transcript AT3G27740.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G27740.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA04G39390.1 (Glycine max), 3'ss of exon 7
gtgagtattacttctctacttttgctcttatcgatgctttttactctctctttctatacttttcttactctctctttctatactttgtctcttgaattcaaagGTTATTGCTTACGATTTTGGAATCAAGCAAAACATCCTAAGACGCCTTTCATCTTACGGATGTCAAATCACTGTTGTTCCGTCCACATTTCCAGCTGCCG
                           | |    |||     ||| | | ||   ||  ||   | | |   |  | | | |   ||     |||| |   ||||  ||||||| ||||||||||||||||| || || || || |||||  ||||||| || ||  ||||||||||||| || |  ||||   ||||  | |
--------------------------gtaagtagtgcaaaaaactttatgttg--attattggataattaattaatgccacatgctgatgaatgaaattgcagGTAGTTGCTTATGATTTTGGAATCAAGCATAATATACTTAGGCGCCTAGCATCTTATGGCTGCAAAATCACTGTTGTGCCATGTACATGGTCAGCATCAG
















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|116459030|gb|EG501622.1|EG501622
EST:     ACGCTGAATGGGATTTCAACACGAATTCACGAGATGGGAAATCCTACAAA                         GTTATTGCTTACGATTTTGGAATCAAGCAAAACATCCTAAGACGCCTTTCA
genomic: ACGCTGAATGGGATTTCAACACGAATTCACGAGATGGGAAATCCTACAAAgtgagtatta ... gaattcaaagGTTATTGCTTACGATTTTGGAATCAAGCAAAACATCCTAAGACGCCTTTCA
EST: gi|309381080|gb|HO850301.1|HO850301
EST:     ACGAGATGGGAAATCCTACAAA                         GTTATTGCTTACGATTTTGGAATCAAGCAAAACATCCTAAGACGCCTTTCA
genomic: ACGAGATGGGAAATCCTACAAAgtgagtatta ... gaattcaaagGTTATTGCTTACGATTTTGGAATCAAGCAAAACATCCTAAGACGCCTTTCA
EST: gi|125171903|gb|EL194465.1|EL194465
EST:     ACGCTGAATGGGATTTCAACACGAATTCACGAGATGGGAAATCCTACAAA                         GTTATTGCTTACGATTTTGGAATCAAG
genomic: ACGCTGAATGGGATTTCAACACGAATTCACGAGATGGGAAATCCTACAAAgtgagtatta ... gaattcaaagGTTATTGCTTACGATTTTGGAATCAAG
EST: gi|125000049|gb|EL072318.1|EL072318
EST:     CGCTGAATGGGATTTCAACACGAATTCACGAGATGGGAAATCCTAACAAA                         GTTATTGCTTACGATTTTGGAATCAAG
genomic: CGCTGAATGGGATTTCAACACGAATTCACGAGATGGGAAATCCTA-CAAAgtgagtatta ... gaattcaaagGTTATTGCTTACGATTTTGGAATCAAG
EST: gi|116459028|gb|EG501620.1|EG501620
EST:     ACGCTGAATGGGATTTCAACACGAATTCACGAGATGGGAAATCCTACAAA                         GTTATTGCTTACGATTTTGGAATCAAGCAAAACATCCTAAAGACGCCTTTC
genomic: ACGCTGAATGGGATTTCAACACGAATTCACGAGATGGGAAATCCTACAAAgtgagtatta ... gaattcaaagGTTATTGCTTACGATTTTGGAATCAAGCAAAACATCCTAA-GACGCCTTTC
EST: gi|47830985|gb|CK120669.1|CK120669
EST:     ACGCTGAATGGGATTTCAACACGAATTCACGAGATGGGAAATCCTACAAA                         GTTATTGCTTACGATTTTGGAATCAAGCAAAACATCCTAAGACGCCTTTCA
genomic: ACGCTGAATGGGATTTCAACACGAATTCACGAGATGGGAAATCCTACAAAgtgagtatta ... gaattcaaagGTTATTGCTTACGATTTTGGAATCAAGCAAAACATCCTAAGACGCCTTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttctatacttttcttactctctctttctatactttgtctcttgaattcaaagGTTATTGCTTACGATTTTGGAATCAAGCAAAACATCCTAAGACGCCTTTCATCTTACGGATGTCAAATCACTGTTGTTCCGTCCACATTTCCAGCTGCCG
             ttcttac  putative branch site (score: 2)
          cttttcttactctctc  CT-rich tract
      tatactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtattacttctctacttttgctcttatcgatgctttttactctctctttctatacttttcttactctctctttctatactttgtctcttgaattcaaagGTTATTGCTTACGATTTTGGAATCAAGCAAAACATCCTAAGACGCCTTTCATCTTACGGATGTCAAATCACTGTTGTTCCGTCCACATTTCCAGCTGCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC