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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgtcttttctctttttgcatgtgttcttgtttcagtttctttcttcacacatcaactgatcataattacgttttggtttagATCTTCCACAAAAGGATGCCCCCAGAAGCGATTGATTTTGCATCAAGGCTGCTTCAATACTCTCCAAGTCTAAGATGCACAGCG

Basic information

species Arabidopsis thaliana
transcript AT4G18710.1
intron # 8
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|124797430|gb|EH887109.1|EH887109
EST:     ATTACACAGATTTCAGGTTTCCACAGATAAAGGCACATCCCTGGCACAAG                         ATCTTCCACAAAAGGATGCCCCCAGAAGCGATTGATTTTGCA
genomic: ATTACACAGATTTCAGGTTTCCACAGATAAAGGCACATCCCTGGCACAAGgttagtgtct ... tttggtttagATCTTCCACAAAAGGATGCCCCCAGAAGCGATTGATTTTGCA
EST: gi|164204318|gb|ES012569.1|ES012569
EST:     GGTTTCCACAGATAAAGGCACATCCGTGGCACAAG                         ATCTTCCACAAAAGGATGCCCCCAGAAGCGATTGATTTTGCATCAAGGCTG
genomic: GGTTTCCACAGATAAAGGCACATCCCTGGCACAAGgttagtgtct ... tttggtttagATCTTCCACAAAAGGATGCCCCCAGAAGCGATTGATTTTGCATCAAGGCTG
EST: gi|116451981|gb|EG494573.1|EG494573
EST:     ATTACACAGATTTCAGGTTTCCACAGATAAAGGCACATCCCTGGCACAAG                         ATCTTCCACAAAAGGATGCCCCCAGAAGCGATTGATTTTGCATCAAGGCTG
genomic: ATTACACAGATTTCAGGTTTCCACAGATAAAGGCACATCCCTGGCACAAGgttagtgtct ... tttggtttagATCTTCCACAAAAGGATGCCCCCAGAAGCGATTGATTTTGCATCAAGGCTG
EST: gi|124752161|gb|EH842291.1|EH842291
EST:     ATTACACAGATTTCAGGTTTCCACAGATAAAGGCACATCCCTGGCACAAG                         ATCTTCCACAAAAGGATGCCCCCAGAAGCGATTGATTTTGCATCAAGG
genomic: ATTACACAGATTTCAGGTTTCCACAGATAAAGGCACATCCCTGGCACAAGgttagtgtct ... tttggtttagATCTTCCACAAAAGGATGCCCCCAGAAGCGATTGATTTTGCATCAAGG
EST: gi|86056749|gb|DR352506.1|DR352506
EST:     ACACAGATTTCAGGTTTCCACAGATAAAGGCACATCCCTGGCACAAG                         ATCTTCCACAAAAGGATGCCCCCAGAAGCGATTGATTTTGCATCAAGGCTG
genomic: ACACAGATTTCAGGTTTCCACAGATAAAGGCACATCCCTGGCACAAGgttagtgtct ... tttggtttagATCTTCCACAAAAGGATGCCCCCAGAAGCGATTGATTTTGCATCAAGGCTG
EST: gi|116452048|gb|EG494640.1|EG494640
EST:     ATTACACAGATTTCAGGTTTCCACAGATAAAGGCACATCCCTGGCACAAG                         ATCTTCCACAAAAGGATGCCCCCAGAAGCGATTGATTTTGCATCAAGGCTG
genomic: ATTACACAGATTTCAGGTTTCCACAGATAAAGGCACATCCCTGGCACAAGgttagtgtct ... tttggtttagATCTTCCACAAAAGGATGCCCCCAGAAGCGATTGATTTTGCATCAAGGCTG
EST: gi|125227216|gb|EL241301.1|EL241301
EST:     TACACAGATTTCAGGTTTTCCTACAGATAAAGGCACATCCCTGGCACAAG                         ATCTTCCACAAAAGGATGCCCCCAGAAGCGATTGATTTTG
genomic: TACACAGATTTCAGG-TTTCC-ACAGATAAAGGCACATCCCTGGCACAAGgttagtgtct ... tttggtttagATCTTCCACAAAAGGATGCCCCCAGAAGCGATTGATTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtttcagtttctttcttcacacatcaactgatcataattacgttttggtttagATCTTCCACAAAAGGATGCCCCCAGAAGCGATTGATTTTGCATCAAGGCTGCTTCAATACTCTCCAAGTCTAAGATGCACAGCG
                           aactgat  putative branch site (score: 3)
                                atcataatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtgtcttttctctttttgcatgtgttcttgtttcagtttctttcttcacacatcaactgatcataattacgttttggtttagATCTTCCACAAAAGGATGCCCCCAGAAGCGATTGATTTTGCATCAAGGCTGCTTCAATACTCTCCAAGTCTAAGATGCACAGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG