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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcatccgattagttcaaccatctaagattagtttcattaagcgacttcttaagttttcaaggcttgcctgtacttaactagttatcgtttcaaattttagGCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATGGTAGCAGAGAAGTGGCTTGAATTGTCTTCGTTAATGGTCACTTCAGCTG

Basic information

species Arabidopsis thaliana
transcript AT3G02200.1
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|86045209|gb|DR340964.1|DR340964
EST:     CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAG                         GCAGCWGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
genomic: CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAGgtaacctcca ... caaattttagGCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
EST: gi|86045215|gb|DR340970.1|DR340970
EST:     CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAG                         GCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
genomic: CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAGgtaacctcca ... caaattttagGCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
EST: gi|86045211|gb|DR340966.1|DR340966
EST:     CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAG                         GCAGCAGAGCCAGAAATTACCAGGCTCTGT
genomic: CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAGgtaacctcca ... caaattttagGCAGCAGAGCCAGAAATTACCAGGCTCTGT
EST: gi|86045203|gb|DR340958.1|DR340958
EST:     CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAG                         GCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
genomic: CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAGgtaacctcca ... caaattttagGCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
EST: gi|86045207|gb|DR340962.1|DR340962
EST:     CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAG                         GCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
genomic: CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAGgtaacctcca ... caaattttagGCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
EST: gi|86045212|gb|DR340967.1|DR340967
EST:     CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAG                         GCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
genomic: CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAGgtaacctcca ... caaattttagGCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
EST: gi|86045200|gb|DR340955.1|DR340955
EST:     CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAG                         GCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
genomic: CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAGgtaacctcca ... caaattttagGCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
EST: gi|86045196|gb|DR340951.1|DR340951
EST:     CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAG                         GCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
genomic: CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAGgtaacctcca ... caaattttagGCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
EST: gi|86045199|gb|DR340954.1|DR340954
EST:     CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAG                         GCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
genomic: CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAGgtaacctcca ... caaattttagGCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
EST: gi|86045216|gb|DR340971.1|DR340971
EST:     CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAG                         GCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
genomic: CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAGgtaacctcca ... caaattttagGCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
EST: gi|86045193|gb|DR340948.1|DR340948
EST:     CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAG                         GCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
genomic: CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAGgtaacctcca ... caaattttagGCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
EST: gi|86045197|gb|DR340952.1|DR340952
EST:     CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAG                         GCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGASGCTGAGGAGTCAATG
genomic: CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAGgtaacctcca ... caaattttagGCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
EST: gi|86045195|gb|DR340950.1|DR340950
EST:     CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAG                         GCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
genomic: CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAGgtaacctcca ... caaattttagGCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
EST: gi|86045202|gb|DR340957.1|DR340957
EST:     ATGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAG                         GCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
genomic: CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAGgtaacctcca ... caaattttagGCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
EST: gi|86045208|gb|DR340963.1|DR340963
EST:     CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAG                         GCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
genomic: CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAGgtaacctcca ... caaattttagGCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
EST: gi|86045198|gb|DR340953.1|DR340953
EST:     CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAG                         GCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
genomic: CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAGgtaacctcca ... caaattttagGCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
EST: gi|86045201|gb|DR340956.1|DR340956
EST:     CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAG                         GCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
genomic: CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAGgtaacctcca ... caaattttagGCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
EST: gi|86045204|gb|DR340959.1|DR340959
EST:     CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAG                         GCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
genomic: CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAGgtaacctcca ... caaattttagGCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
EST: gi|86045205|gb|DR340960.1|DR340960
EST:     CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAG                         GCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
genomic: CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAGgtaacctcca ... caaattttagGCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
EST: gi|86045206|gb|DR340961.1|DR340961
EST:     CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAG                         GCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
genomic: CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAGgtaacctcca ... caaattttagGCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
EST: gi|86045210|gb|DR340965.1|DR340965
EST:     CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAG                         GCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG
genomic: CTGTTGTCCGATTCACTTCCCAGCTCGCCTGGGCCGATGCTGGTCCCGAGgtaacctcca ... caaattttagGCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttaagttttcaaggcttgcctgtacttaactagttatcgtttcaaattttagGCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATGGTAGCAGAGAAGTGGCTTGAATTGTCTTCGTTAATGGTCACTTCAGCTG
                          acttaac  putative branch site (score: 3)
                                       tcgtttc  putative PPT
                                          tttcaaatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatccgattagttcaaccatctaagattagtttcattaagcgacttcttaagttttcaaggcttgcctgtacttaactagttatcgtttcaaattttagGCAGCAGAGCCAGAAATTACCAGGCTCTGTAGGGAGGCTGAGGAGTCAATGGTAGCAGAGAAGTGGCTTGAATTGTCTTCGTTAATGGTCACTTCAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - -tcaacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acttaac