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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtctattctcttttacctacttcagattctttggggaatttgaaatatagttctaaagatatgagttttattacatgacaatggtggttctgtagaaattgtgtatcatttgtggttaatgatgttgttttagGTAAAAGGAACAGTGTTCAAGACTGATGCAAATGGTGCATTAGTTGACATTTCTGCAAAGTCATCGGCTTACTTGTCGGTAGAACAAGCGTGTATTCATA

Basic information

species Arabidopsis thaliana
transcript AT5G30510.1
intron # 1
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|125151962|gb|EL183835.1|EL183835
EST:     CTGCTATTGAACAATACGACTTCAATTCCGAAATCGGCACTAGG                         GTAAAAGGAACAGTGTTCAAGACTTGATGCAAATGGTGCATTAGTTGACAT
genomic: CTGCTATTGAACAATACGACTTCAATTCCGAAATCGGCACTAGGgtttgtctat ... gttgttttagGTAAAAGGAACAGTGTTCAAGACT-GATGCAAATGGTGCATTAGTTGACAT
EST: gi|125097855|gb|EL154180.1|EL154180
EST:     AATCGGCACTAGG                         GTAAAAGGAACAGTGTTCAAGACTGATGCAAATGGTGCATTAGTTGACATT
genomic: AATCGGCACTAGGgtttgtctat ... gttgttttagGTAAAAGGAACAGTGTTCAAGACTGATGCAAATGGTGCATTAGTTGACATT
EST: gi|47832014|gb|CK121698.1|CK121698
EST:     TCGCTGCTGCTATTGAACAATACGACTTCAATTCCGAAATCGGCACTAGG                         GTAAAAGGAACAGTGTTCAAGACTGATGCAAATGGTGCATTAGTTGACATT
genomic: TCGCTGCTGCTATTGAACAATACGACTTCAATTCCGAAATCGGCACTAGGgtttgtctat ... gttgttttagGTAAAAGGAACAGTGTTCAAGACTGATGCAAATGGTGCATTAGTTGACATT
EST: gi|124929948|gb|EL007443.1|EL007443
EST:     TCGCTGCTGCTATTGAACAATACGACTTCAATTCCGAAATCGGCACTAGG                         GTAAAAGGAACAGTGTTCAAGACTGATGCAAA
genomic: TCGCTGCTGCTATTGAACAATACGACTTCAATTCCGAAATCGGCACTAGGgtttgtctat ... gttgttttagGTAAAAGGAACAGTGTTCAAGACTGATGCAAA
EST: gi|124799271|gb|EH888950.1|EH888950
EST:     TCGCTGCTGCTATTGAACAATACGACTTCAATTCCGAAATCGGTACTAGG                         GTAAAAGGAACAGTGTTCAAGACTGATGCAAATGGTGCATTAGTTGACATT
genomic: TCGCTGCTGCTATTGAACAATACGACTTCAATTCCGAAATCGGCACTAGGgtttgtctat ... gttgttttagGTAAAAGGAACAGTGTTCAAGACTGATGCAAATGGTGCATTAGTTGACATT
EST: gi|124720603|gb|EH812005.1|EH812005
EST:     GCTGCTGCTATTGAACAATACGACTTCAATTCCGAAATCGGCACTAGG                         GTAAAAGGAACAGTGTTCAAGACTGATGCAAA
genomic: GCTGCTGCTATTGAACAATACGACTTCAATTCCGAAATCGGCACTAGGgtttgtctat ... gttgttttagGTAAAAGGAACAGTGTTCAAGACTGATGCAAA
EST: gi|124707134|gb|EH798536.1|EH798536
EST:     TCGGCACTAGG                         GTAAAAGGAACAGTGTTCAAGACTGATGCAAATGGTGCATTAGTTGACATT
genomic: TCGGCACTAGGgtttgtctat ... gttgttttagGTAAAAGGAACAGTGTTCAAGACTGATGCAAATGGTGCATTAGTTGACATT
EST: gi|125056548|gb|EL126242.1|EL126242
EST:     TCGCTGCTGCTATTGAACAATACGACTTCAATTCCGAAATCGGCACTAGG                         GTAAAAGGAACAGTGTTCAAGACTGATGCAAATGGTGCATTAG
genomic: TCGCTGCTGCTATTGAACAATACGACTTCAATTCCGAAATCGGCACTAGGgtttgtctat ... gttgttttagGTAAAAGGAACAGTGTTCAAGACTGATGCAAATGGTGCATTAG
EST: gi|125027460|gb|EL099729.1|EL099729
EST:     TCGCTGCTGCTATTGAACAATACGACTTCAATTCCGAAATCGGCACTAGG                         GTAAAAGGAACAGTGTTCAAGACTG
genomic: TCGCTGCTGCTATTGAACAATACGACTTCAATTCCGAAATCGGCACTAGGgtttgtctat ... gttgttttagGTAAAAGGAACAGTGTTCAAGACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatggtggttctgtagaaattgtgtatcatttgtggttaatgatgttgttttagGTAAAAGGAACAGTGTTCAAGACTGATGCAAATGGTGCATTAGTTGACATTTCTGCAAAGTCATCGGCTTACTTGTCGGTAGAACAAGCGTGTATTCATA
                                   ggttaat  putative branch site (score: 4)
                                              ttgtttt  putative PPT
              tagaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtctattctcttttacctacttcagattctttggggaatttgaaatatagttctaaagatatgagttttattacatgacaatggtggttctgtagaaattgtgtatcatttgtggttaatgatgttgttttagGTAAAAGGAACAGTGTTCAAGACTGATGCAAATGGTGCATTAGTTGACATTTCTGCAAAGTCATCGGCTTACTTGTCGGTAGAACAAGCGTGTATTCATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG