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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtccatacttcaacactttttgataatgaacacaacttcaatgtatgtgaccatgagaggctaatctgggttatgccctttagcaaaagctgatattgattgtgtaacttgttcacagGCATGGAATCTACACGAGAAAGGCCGTGAAGTTGAACTTATTGATCATCAGCTGACTGAATTCAACATGGAAGAAGGGAAACGCATGATTGGCATAGCCC

Basic information

species Arabidopsis thaliana
transcript AT1G56140.1
intron # 23
splice site 3'
intron type U2

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|124804876|gb|EH892411.1|EH892411
EST:     AGAACTTGGAGGATGAAAAAAGATATCTTCTTGAATGG                         GCATGGAATCTACACGAGAAAGGCCGTGAAGTTGAACTTAATTGATCATCA
genomic: AGAACTTGGAGGATGAAAAAAGATATCTTCTTGAATGGgtacgtccat ... ttgttcacagGCATGGAATCTACACGAGAAAGGCCGTGAAGTTGAACTTA-TTGATCATCA
EST: gi|125301281|gb|EL315366.1|EL315366
EST:     AACTTGGAGGATGAAAAAAGATATCTTCTTGAATGG                         GCATGGAATCTACACGAGAAAGGCCGTGAAGTTGAACTTATTGATCATCAG
genomic: AACTTGGAGGATGAAAAAAGATATCTTCTTGAATGGgtacgtccat ... ttgttcacagGCATGGAATCTACACGAGAAAGGCCGTGAAGTTGAACTTATTGATCATCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctgggttatgccctttagcaaaagctgatattgattgtgtaacttgttcacagGCATGGAATCTACACGAGAAAGGCCGTGAAGTTGAACTTATTGATCATCAGCTGACTGAATTCAACATGGAAGAAGGGAAACGCATGATTGGCATAGCCC
                                      gtgtaac  putative branch site (score: 3)
                                            cttgttc  CT-rich tract
                             atattgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtccatacttcaacactttttgataatgaacacaacttcaatgtatgtgaccatgagaggctaatctgggttatgccctttagcaaaagctgatattgattgtgtaacttgttcacagGCATGGAATCTACACGAGAAAGGCCGTGAAGTTGAACTTATTGATCATCAGCTGACTGAATTCAACATGGAAGAAGGGAAACGCATGATTGGCATAGCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG