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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacatctctaaaccctaaatcactccttacgtgaatcaaatactgatttcaaaatgctgagtatactcaaactgtatataaaaaagctaatcttgtttctcgtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG

Basic information

species Arabidopsis thaliana
transcript AT5G41520.1
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|124750673|gb|EH840803.1|EH840803
EST:     CGCCTCCTTCTTCAATCTCATCGCAATCATG                         ATCATATCAGAGACTAACCGCCGTGAGATCTACCAAGTACCTCTTCAAAG
genomic: CGCCTCCTTCTTCAATCTCATCGCAATCATGgtaacatctc ... gtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCT-CCAAGTACCTCTTCAAAG
EST: gi|164219842|gb|EL985539.1|EL985539
EST:     AATCTCATCGCAATCATG                         ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG
genomic: AATCTCATCGCAATCATGgtaacatctc ... gtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG
EST: gi|116471696|gb|EG514288.1|EG514288
EST:     ACGCAGTCACCTTCTCTATCGCCTCCTTCTTCAATCTCATCGCAATCATG                         ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG
genomic: ACGCAGTCACCTTCTCTATCGCCTCCTTCTTCAATCTCATCGCAATCATGgtaacatctc ... gtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG
EST: gi|116471744|gb|EG514336.1|EG514336
EST:     ACGCAGTCACCTTCTCTATCGCCTCCTTCTTCAATCTCATCGCAATCATG                         ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG
genomic: ACGCAGTCACCTTCTCTATCGCCTCCTTCTTCAATCTCATCGCAATCATGgtaacatctc ... gtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG
EST: gi|124864864|gb|EH949301.1|EH949301
EST:     TCGCAATCATG                         ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG
genomic: TCGCAATCATGgtaacatctc ... gtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG
EST: gi|116406681|gb|EG449273.1|EG449273
EST:     ACGCAGTCACCTTCTCTATCGCCTCCTTCTTCAATCTCATCGCAATCATG                         ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG
genomic: ACGCAGTCACCTTCTCTATCGCCTCCTTCTTCAATCTCATCGCAATCATGgtaacatctc ... gtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG
EST: gi|116406665|gb|EG449257.1|EG449257
EST:     ACGCAGTCACCTTCTCTATCGCCTCCTTCTTCAATCTCATCGCAATCATG                         ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG
genomic: ACGCAGTCACCTTCTCTATCGCCTCCTTCTTCAATCTCATCGCAATCATGgtaacatctc ... gtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG
EST: gi|116471706|gb|EG514298.1|EG514298
EST:     ACGCAGTCACCTTCTCTATCGCCTCCTTCTTCAATCTCATCGCAATCATG                         ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG
genomic: ACGCAGTCACCTTCTCTATCGCCTCCTTCTTCAATCTCATCGCAATCATGgtaacatctc ... gtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG
EST: gi|124800384|gb|EH890049.1|EH890049
EST:     TCACCTTCTCTATCGCCTCCTTCTTCAATCTCATCGCAATCATG                         ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCA
genomic: TCACCTTCTCTATCGCCTCCTTCTTCAATCTCATCGCAATCATGgtaacatctc ... gtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCA
EST: gi|163976375|gb|EL979175.1|EL979175
EST:     TCGCAATCATG                         ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG
genomic: TCGCAATCATGgtaacatctc ... gtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG
EST: gi|164122362|gb|ES097121.1|ES097121
EST:     TCGCAATCATG                         ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG
genomic: TCGCAATCATGgtaacatctc ... gtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG
EST: gi|164199833|gb|ES002100.1|ES002100
EST:     TCGCCTCCTTCTTCAATCTCATCGCAATCATG                         ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG
genomic: TCGCCTCCTTCTTCAATCTCATCGCAATCATGgtaacatctc ... gtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG
EST: gi|124926737|gb|EL004535.1|EL004535
EST:     TCGCAATCATG                         ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG
genomic: TCGCAATCATGgtaacatctc ... gtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG
EST: gi|164022090|gb|ES194591.1|ES194591
EST:     TCGCAATCATG                         ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG
genomic: TCGCAATCATGgtaacatctc ... gtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG
EST: gi|124804253|gb|EH892168.1|EH892168
EST:     CTTCAATCTCATCGCAATCATG                         ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAGG
genomic: CTTCAATCTCATCGCAATCATGgtaacatctc ... gtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG
EST: gi|124738327|gb|EH829671.1|EH829671
EST:     ACGCAGTCACCTTCTCTATCGCCTCC-TCTTCAATCTCATCGCAATCATG                         ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACC
genomic: ACGCAGTCACCTTCTCTATCGCCTCCTTCTTCAATCTCATCGCAATCATGgtaacatctc ... gtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACC
EST: gi|116471734|gb|EG514326.1|EG514326
EST:     CTATCGCCTCCTTCTTCAATCTCATCGCAATCATG                         ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG
genomic: CTATCGCCTCCTTCTTCAATCTCATCGCAATCATGgtaacatctc ... gtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG
EST: gi|47831362|gb|CK121046.1|CK121046
EST:     ACGCAGTCACCTTCTCTGTCGCCTCCTTCTTCAATCTCATCGCAATCATG                         ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG
genomic: ACGCAGTCACCTTCTCTATCGCCTCCTTCTTCAATCTCATCGCAATCATGgtaacatctc ... gtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG
EST: gi|124793263|gb|EH882942.1|EH882942
EST:     ATCGCCTCCTTTCTTCAATCTCATCGCAATCATG                         ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAG
genomic: ATCGCCTCC-TTCTTCAATCTCATCGCAATCATGgtaacatctc ... gtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAG
EST: gi|116476370|gb|EG518962.1|EG518962
EST:     ACGCAGTCACCTTCTCTATCGCCTCCTTCTTCAATCTCATCGCAATCATG                         ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG
genomic: ACGCAGTCACCTTCTCTATCGCCTCCTTCTTCAATCTCATCGCAATCATGgtaacatctc ... gtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgagtatactcaaactgtatataaaaaagctaatcttgtttctcgtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG
                            agctaat  putative branch site (score: 3)
                                       tttctcgt  putative PPT
            aaactgtatataaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacatctctaaaccctaaatcactccttacgtgaatcaaatactgatttcaaaatgctgagtatactcaaactgtatataaaaaagctaatcttgtttctcgtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC