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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacatctctaaaccctaaatcactccttacgtgaatcaaatactgatttcaaaatgctgagtatactcaaactgtatataaaaaagctaatcttgtttctcgtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG

Basic information

species Arabidopsis thaliana
transcript AT5G41520.2
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|47831362|gb|CK121046.1|CK121046
EST:     ACGCAGTCACCTTCTCTGTCGCCTCCTTCTTCAATCTCATCGCAATCATG                         ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGAG
genomic: ACGCAGTCACCTTCTCTATCGCCTCCTTCTTCAATCTCATCGCAATCATGgtaacatctc ... gtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTC-AA-AG
EST: gi|116471696|gb|EG514288.1|EG514288
EST:     ACGCAGTCACCTTCTCTATCGCCTCCTTCTTCAATCTCATCGCAATCATG                         ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGAG
genomic: ACGCAGTCACCTTCTCTATCGCCTCCTTCTTCAATCTCATCGCAATCATGgtaacatctc ... gtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTC-AA-AG
EST: gi|116406681|gb|EG449273.1|EG449273
EST:     ACGCAGTCACCTTCTCTATCGCCTCCTTCTTCAATCTCATCGCAATCATG                         ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGAG
genomic: ACGCAGTCACCTTCTCTATCGCCTCCTTCTTCAATCTCATCGCAATCATGgtaacatctc ... gtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTC-AA-AG
EST: gi|163976375|gb|EL979175.1|EL979175
EST:     TCGCAATCATG                         ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG
genomic: TCGCAATCATGgtaacatctc ... gtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG
EST: gi|124800384|gb|EH890049.1|EH890049
EST:     TCACCTTCTCTATCGCCTCCTTCTTCAATCTCATCGCAATCATG                         ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCA
genomic: TCACCTTCTCTATCGCCTCCTTCTTCAATCTCATCGCAATCATGgtaacatctc ... gtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCA
EST: gi|116471706|gb|EG514298.1|EG514298
EST:     ACGCAGTCACCTTCTCTATCGCCTCCTTCTTCAATCTCATCGCAATCATG                         ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGAG
genomic: ACGCAGTCACCTTCTCTATCGCCTCCTTCTTCAATCTCATCGCAATCATGgtaacatctc ... gtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTC-AA-AG
EST: gi|124804253|gb|EH892168.1|EH892168
EST:     CTTCAATCTCATCGCAATCATG                         ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAGGAG
genomic: CTTCAATCTCATCGCAATCATGgtaacatctc ... gtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAA--AG
EST: gi|116476370|gb|EG518962.1|EG518962
EST:     ACGCAGTCACCTTCTCTATCGCCTCCTTCTTCAATCTCATCGCAATCATG                         ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGAG
genomic: ACGCAGTCACCTTCTCTATCGCCTCCTTCTTCAATCTCATCGCAATCATGgtaacatctc ... gtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTC-AA-AG
EST: gi|124738327|gb|EH829671.1|EH829671
EST:     ACGCAGTCACCTTCTCTATCGCCTCC-TCTTCAATCTCATCGCAATCATG                         ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACC
genomic: ACGCAGTCACCTTCTCTATCGCCTCCTTCTTCAATCTCATCGCAATCATGgtaacatctc ... gtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACC
EST: gi|116406665|gb|EG449257.1|EG449257
EST:     ACGCAGTCACCTTCTCTATCGCCTCCTTCTTCAATCTCATCGCAATCATG                         ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGAG
genomic: ACGCAGTCACCTTCTCTATCGCCTCCTTCTTCAATCTCATCGCAATCATGgtaacatctc ... gtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTC-AA-AG
EST: gi|116471734|gb|EG514326.1|EG514326
EST:     CTATCGCCTCCTTCTTCAATCTCATCGCAATCATG                         ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGAG
genomic: CTATCGCCTCCTTCTTCAATCTCATCGCAATCATGgtaacatctc ... gtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTC-AA-AG
EST: gi|124793263|gb|EH882942.1|EH882942
EST:     ATCGCCTCCTTTCTTCAATCTCATCGCAATCATG                         ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAG
genomic: ATCGCCTCC-TTCTTCAATCTCATCGCAATCATGgtaacatctc ... gtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAG
EST: gi|116471744|gb|EG514336.1|EG514336
EST:     ACGCAGTCACCTTCTCTATCGCCTCCTTCTTCAATCTCATCGCAATCATG                         ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGAG
genomic: ACGCAGTCACCTTCTCTATCGCCTCCTTCTTCAATCTCATCGCAATCATGgtaacatctc ... gtatttgcagATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTC-AA-AG


 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