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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tataatgtttaattatcctcagaacaacatgtatcttctctttggctgtgttgtttcgtcagataattctgttcttatgcaattaaactctctggaccagGTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAGTCTGCTCTTGCTGGTGATGTTACTCTGCCTAAATATCGAGGATTGTTGG

Basic information

species Arabidopsis thaliana
transcript AT3G54110.1
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|86059200|gb|DR354957.1|DR354957
EST:     CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAG                         GTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
genomic: CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAGgtaatcgccg ... tctggaccagGTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
EST: gi|86059190|gb|DR354947.1|DR354947
EST:     CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAG                         GTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
genomic: CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAGgtaatcgccg ... tctggaccagGTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
EST: gi|86059189|gb|DR354946.1|DR354946
EST:     CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAG                         GTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
genomic: CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAGgtaatcgccg ... tctggaccagGTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
EST: gi|86059197|gb|DR354954.1|DR354954
EST:     CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAG                         GTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
genomic: CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAGgtaatcgccg ... tctggaccagGTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
EST: gi|86059192|gb|DR354949.1|DR354949
EST:     CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAG                         GTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
genomic: CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAGgtaatcgccg ... tctggaccagGTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
EST: gi|86059195|gb|DR354952.1|DR354952
EST:     CCTTGCCCAAAACTTCCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAG                         GTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
genomic: CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAGgtaatcgccg ... tctggaccagGTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
EST: gi|86059193|gb|DR354950.1|DR354950
EST:     CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAG                         GTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
genomic: CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAGgtaatcgccg ... tctggaccagGTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
EST: gi|86059204|gb|DR354961.1|DR354961
EST:     CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAG                         GTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
genomic: CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAGgtaatcgccg ... tctggaccagGTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
EST: gi|86059186|gb|DR354943.1|DR354943
EST:     CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAG                         GTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
genomic: CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAGgtaatcgccg ... tctggaccagGTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
EST: gi|86059202|gb|DR354959.1|DR354959
EST:     CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAG                         GTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
genomic: CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAGgtaatcgccg ... tctggaccagGTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
EST: gi|86059205|gb|DR354962.1|DR354962
EST:     CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAG                         GTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
genomic: CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAGgtaatcgccg ... tctggaccagGTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
EST: gi|86059199|gb|DR354956.1|DR354956
EST:     CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAG                         GTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
genomic: CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAGgtaatcgccg ... tctggaccagGTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
EST: gi|86059196|gb|DR354953.1|DR354953
EST:     CCTTGCCCAAAACTTYCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAG                         GTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
genomic: CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAGgtaatcgccg ... tctggaccagGTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
EST: gi|86059203|gb|DR354960.1|DR354960
EST:     CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAG                         GTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
genomic: CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAGgtaatcgccg ... tctggaccagGTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
EST: gi|86059198|gb|DR354955.1|DR354955
EST:     CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAG                         GTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
genomic: CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAGgtaatcgccg ... tctggaccagGTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
EST: gi|86059194|gb|DR354951.1|DR354951
EST:     CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAG                         GTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
genomic: CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAGgtaatcgccg ... tctggaccagGTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
EST: gi|86059184|gb|DR354941.1|DR354941
EST:     CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAG                         GTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
genomic: CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAGgtaatcgccg ... tctggaccagGTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
EST: gi|86059201|gb|DR354958.1|DR354958
EST:     CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAG                         GTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
genomic: CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAGgtaatcgccg ... tctggaccagGTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
EST: gi|86059188|gb|DR354945.1|DR354945
EST:     CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAG                         GTATGCACAATTCCATTGGACACTGCTAAAGTTAGGSTTCAGCTCCAAAAG
genomic: CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAGgtaatcgccg ... tctggaccagGTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
EST: gi|86059207|gb|DR354964.1|DR354964
EST:     CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAG                         GTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
genomic: CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAGgtaatcgccg ... tctggaccagGTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
EST: gi|86059185|gb|DR354942.1|DR354942
EST:     CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAG                         GTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
genomic: CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAGgtaatcgccg ... tctggaccagGTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
EST: gi|86059187|gb|DR354944.1|DR354944
EST:     CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAG                         GTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG
genomic: CCTTGCCCAAAACTTTCGCCTGCAGTGCCTTCGCTGCTTGCGTCGGCGAGgtaatcgccg ... tctggaccagGTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtgttgtttcgtcagataattctgttcttatgcaattaaactctctggaccagGTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAGTCTGCTCTTGCTGGTGATGTTACTCTGCCTAAATATCGAGGATTGTTGG
                                          ctctct  CT-rich tract
                                   aattaaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tataatgtttaattatcctcagaacaacatgtatcttctctttggctgtgttgtttcgtcagataattctgttcttatgcaattaaactctctggaccagGTATGCACAATTCCATTGGACACTGCTAAAGTTAGGCTTCAGCTCCAAAAGTCTGCTCTTGCTGGTGATGTTACTCTGCCTAAATATCGAGGATTGTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - atcctca
- - - - - - - - - - - aacaaca
- - - - - - - - - - - - - - - - - cttctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taaactc