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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccattttgatttgagcttatgaatctagttgtcttctacgttaatgggtttatgcatgatgattgattggttgattcaagagaattgtacttagaaatggttggaattggttctttttgtgtgcagAGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGATTGAGAGTGTTCCAAATCTGCAAGTTATCAAGTTGATGCAGAGTTTCAA

Basic information

species Arabidopsis thaliana
transcript AT5G41520.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G41520.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv02s0025g00310.t01 (Vitis vinifera), 3'ss of exon 2
gtaccattttgatttgagcttatgaatctagttgtcttctacgttaatgggtttatgcatgatgattgattggttgattcaagagaattgtacttagaaatggttggaattggttctttttgtgtgcagAGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGATTGAGAGTGTTCCAAATCTGCAAGTTATCAAGTTGATGCAGAGTTTCAA---
||| | |  | |||    |   | || |  | | |  | |   | | || ||| |||  |     ||  ||  ||||||        || ||                |||  ||||| ||   | ||||||| ||||  | ||| |||||||| | |||  |  |  |||||||    || ||   ||| || |||||||| |||||||||||||||||||| |||||   
gtatcttacttattctctcactttaaccacgatttgctgtgattcagtgtgttcatgtttttattttattttattgatt--------ttatat---------------attttttcttgtttgcttcagAGGGAGTTTGCTATGCGAAAAAGGACTACAATCTCGCGAAACATCCCGATATCGA---TGTCCCGAATCTGCAGGTTATCAAGTTGATGCAGAGCTTCAAGTC
















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:     ATCATATCAGAGACTAACCGCCGTGAGATCTACCAAGTACCTCTTCAAAG                         AGGGTGTTTTGTTTGCTAA
genomic: ATCATATCAGAGACTAACCGCCGTGAGATCT-CCAAGTACCTCTTCAAAGgtaccatttt ... ttgtgtgcagAGGGTGTTTTGTTTGCTAA
EST: gi|164219842|gb|EL985539.1|EL985539
EST:     ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG                         AGGGTGTTTTGTTTGCTAAAAAGGATTTCAA
genomic: ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGgtaccatttt ... ttgtgtgcagAGGGTGTTTTGTTTGCTAAAAAGGATTTCAA
EST: gi|163970478|gb|EL989863.1|EL989863
EST:     GTACCTCTTCAAAG                         AGGGTGTTTTGTTTGCTAAAAAAGGATTTCAACTTACCACAACATCCTTTG
genomic: GTACCTCTTCAAAGgtaccatttt ... ttgtgtgcagAGGGTGTTTTGTTTGCT-AAAAAGGATTTCAACTTACCACAACATCCTTTG
EST: gi|116471696|gb|EG514288.1|EG514288
EST:     ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG                         AGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGA
genomic: ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGgtaccatttt ... ttgtgtgcagAGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGA
EST: gi|116471744|gb|EG514336.1|EG514336
EST:     ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG                         AGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGA
genomic: ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGgtaccatttt ... ttgtgtgcagAGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGA
EST: gi|124864864|gb|EH949301.1|EH949301
EST:     ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG                         AGGGTAAGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACA
genomic: ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGgtaccatttt ... ttgtgtgcagAGGGT--GTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACA
EST: gi|164152199|gb|EL994072.1|EL994072
EST:     TCTCCAAGTACCTCTTCAAAG                         AGGGTGTTTTGTTTGCTAAAAAAGGATTTCAACTTACCACAACATCCTTTG
genomic: TCTCCAAGTACCTCTTCAAAGgtaccatttt ... ttgtgtgcagAGGGTGTTTTGTTTGCT-AAAAAGGATTTCAACTTACCACAACATCCTTTG
EST: gi|125023008|gb|EL095277.1|EL095277
EST:     AGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG                         AGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGA
genomic: AGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGgtaccatttt ... ttgtgtgcagAGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGA
EST: gi|116406681|gb|EG449273.1|EG449273
EST:     ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG                         AGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGA
genomic: ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGgtaccatttt ... ttgtgtgcagAGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGA
EST: gi|116406665|gb|EG449257.1|EG449257
EST:     ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG                         AGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGA
genomic: ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGgtaccatttt ... ttgtgtgcagAGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGA
EST: gi|116471706|gb|EG514298.1|EG514298
EST:     ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG                         AGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGA
genomic: ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGgtaccatttt ... ttgtgtgcagAGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGA
EST: gi|163976375|gb|EL979175.1|EL979175
EST:     ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG                         AGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACA
genomic: ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGgtaccatttt ... ttgtgtgcagAGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACA
EST: gi|164122362|gb|ES097121.1|ES097121
EST:     ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG                         AGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCA
genomic: ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGgtaccatttt ... ttgtgtgcagAGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCA
EST: gi|164199833|gb|ES002100.1|ES002100
EST:     ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG                         AGGGTGTTTTGTTTGC
genomic: ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGgtaccatttt ... ttgtgtgcagAGGGTGTTTTGTTTGC
EST: gi|47827937|gb|CK117621.1|CK117621
EST:     CCGCCGTGAGATCTCCAAGTACCTCTTCAAAG                         AGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGA
genomic: CCGCCGTGAGATCTCCAAGTACCTCTTCAAAGgtaccatttt ... ttgtgtgcagAGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGA
EST: gi|164107587|gb|ES170828.1|ES170828
EST:     TATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG                         AGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGA
genomic: TATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGgtaccatttt ... ttgtgtgcagAGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGA
EST: gi|164201321|gb|ES050450.1|ES050450
EST:     AGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG                         AGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCC
genomic: AGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGgtaccatttt ... ttgtgtgcagAGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCC
EST: gi|124926737|gb|EL004535.1|EL004535
EST:     ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG                         AGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTATCACAAC
genomic: ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGgtaccatttt ... ttgtgtgcagAGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAAC
EST: gi|164022090|gb|ES194591.1|ES194591
EST:     ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG                         AGGGTAGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACAT
genomic: ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGgtaccatttt ... ttgtgtgcagAGGGT-GTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACAT
EST: gi|124804253|gb|EH892168.1|EH892168
EST:     ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAGG                         AGGGTGTTTTGTTTGCTAAAAAGGATTTCAA
genomic: ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGgtaccatttt ... ttgtgtgcagAGGGTGTTTTGTTTGCTAAAAAGGATTTCAA
EST: gi|125013900|gb|EL086169.1|EL086169
EST:     GATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG                         AGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGA
genomic: GATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGgtaccatttt ... ttgtgtgcagAGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGA
EST: gi|116471734|gb|EG514326.1|EG514326
EST:     ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG                         AGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGA
genomic: ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGgtaccatttt ... ttgtgtgcagAGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGA
EST: gi|47831362|gb|CK121046.1|CK121046
EST:     ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG                         AGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGA
genomic: ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGgtaccatttt ... ttgtgtgcagAGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGA
EST: gi|124953707|gb|EL028864.1|EL028864
EST:     TATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG                         AGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGA
genomic: TATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGgtaccatttt ... ttgtgtgcagAGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGA
EST: gi|164215746|gb|ES118737.1|ES118737
EST:     CCGCCGTTGAGATCTCCAAGTTACCTCTTCAAAG                         AGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGA
genomic: CCGCCG-TGAGATCTCCAAG-TACCTCTTCAAAGgtaccatttt ... ttgtgtgcagAGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGA
EST: gi|116476370|gb|EG518962.1|EG518962
EST:     ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAG                         AGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGA
genomic: ATCATATCAGAGACTAACCGCCGTGAGATCTCCAAGTACCTCTTCAAAGgtaccatttt ... ttgtgtgcagAGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattcaagagaattgtacttagaaatggttggaattggttctttttgtgtgcagAGGGTGTTTTGTTTGCTAAAAAGGATTTCAACTTACCACAACATCCTTTGATTGAGAGTGTTCCAAATCTGCAAGTTATCAAGTTGATGCAGAGTTTCAA
 ggttgat  putative branch site (score: 5)
                                       ttctttttgt  putative PPT
                   ttagaaat  TA-rich tract