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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcacctctaaagccacgttcttgatacccctctttatgcattgtgtgtatgctcctttgtgtataatacctttatctgcttaattgtttcagCCGGTGATACTTGATTATCTTGCTAGCAAGTCAATTCCCTCAGAGGATTTGGTAGTGGTTTCTCCTGATGTTGGTGGAGTAGCCAGGGCCCGCGCTTTTG

Basic information

species Arabidopsis thaliana
transcript AT2G35390.3
intron # 3
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|116379575|gb|EG422167.1|EG422167
EST:     ACAGTCGGATGGGTTATTTTGACATTCCAGTCGACCATGTGTACTGCCAG                         CCGGTGATACTTGATTATCTTGCTAGCAAGTCA-TTCCCTCAGAGGAATTT
genomic: ACAGTCG-ATGGGTTATTTTGACATTCCAGTCGACCATGTGTACTGCCAGgttcacctct ... attgtttcagCCGGTGATACTTGATTATCTTGCTAGCAAGTCAATTCCCTCAGAGGA-TTT
EST: gi|116379978|gb|EG422570.1|EG422570
EST:     ACAGTCGAATGGGTTATTTTGACATTCCAGTCGACCATGTGTACTGCCAG                         CCGGTGATACTTGATTATCTTGCTAGCAAGTCA-TTCCCT
genomic: ACAGTCGA-TGGGTTATTTTGACATTCCAGTCGACCATGTGTACTGCCAGgttcacctct ... attgtttcagCCGGTGATACTTGATTATCTTGCTAGCAAGTCAATTCCCT
EST: gi|116379961|gb|EG422553.1|EG422553
EST:     GACAGTCGATGGGTTATTTTGACATTCCAGTCGACCATGTGTACTGCCAG                         CCGGTGATACTTGATTATCTTGCTAGCAAGT-AATTCCCTCAGAGGAATTT
genomic: GACAGTCGATGGGTTATTTTGACATTCCAGTCGACCATGTGTACTGCCAGgttcacctct ... attgtttcagCCGGTGATACTTGATTATCTTGCTAGCAAGTCAATTCCCTCAGAGGA-TTT
EST: gi|116379968|gb|EG422560.1|EG422560
EST:     GACAGTCGATGGGTTATTTTGACATTCCAGTCGACCATGTGTACTGCCAG                         CCGGTGATACTTGATTATCTTGCTAGCA-GTCAATTCCCTCAAAGGATTTG
genomic: GACAGTCGATGGGTTATTTTGACATTCCAGTCGACCATGTGTACTGCCAGgttcacctct ... attgtttcagCCGGTGATACTTGATTATCTTGCTAGCAAGTCAATTCCCTCAGAGGATTTG
EST: gi|116379973|gb|EG422565.1|EG422565
EST:     ACAGTCCGATGGGTTATTTTGACATTCCAGTCGACCATGTGTACTGCCAG                         CCGGTGATACTTGATTATCTTGCTAGCAAGTCA-TTCCCTCAGAG
genomic: ACAGTC-GATGGGTTATTTTGACATTCCAGTCGACCATGTGTACTGCCAGgttcacctct ... attgtttcagCCGGTGATACTTGATTATCTTGCTAGCAAGTCAATTCCCTCAGAG
EST: gi|116379979|gb|EG422571.1|EG422571
EST:     ACAGTCGAATGGGTTATTTTGACATTCCAGTCGACCATGTGTACTGCCAG                         CCGGTGATACTTGATTATCTTGCTAGCAAGTCAATTCCCTCAG
genomic: ACAGTCGA-TGGGTTATTTTGACATTCCAGTCGACCATGTGTACTGCCAGgttcacctct ... attgtttcagCCGGTGATACTTGATTATCTTGCTAGCAAGTCAATTCCCTCAG
EST: gi|116379976|gb|EG422568.1|EG422568
EST:     GACAGTCGATGGGTTATTTTGACATTCCAGTCGACCATGTGTACTGCCAG                         CCGGTGATACTTGATTATCTTGCTAGCAAGTCAATTCCCTCAGAGGATTTG
genomic: GACAGTCGATGGGTTATTTTGACATTCCAGTCGACCATGTGTACTGCCAGgttcacctct ... attgtttcagCCGGTGATACTTGATTATCTTGCTAGCAAGTCAATTCCCTCAGAGGATTTG
EST: gi|116379975|gb|EG422567.1|EG422567
EST:     ACAGTCGAATGGGTTATTTTGACATTCCAGTCGACCATGTGTACTGCCAG                         CCGGTGATACTTGATTATCTTGCTAGCAAGT-AATTCCCTC
genomic: ACAGTCGA-TGGGTTATTTTGACATTCCAGTCGACCATGTGTACTGCCAGgttcacctct ... attgtttcagCCGGTGATACTTGATTATCTTGCTAGCAAGTCAATTCCCTC
EST: gi|116379965|gb|EG422557.1|EG422557
EST:     GACAGTCGATGGGTTATTTTGACATTCCAGTCGACCATGTGTACTGCCAG                         CCGGTGATACTTGATTATCTTGCTAGCAAGTCAATTCCCTCAGAAGATTTT
genomic: GACAGTCGATGGGTTATTTTGACATTCCAGTCGACCATGTGTACTGCCAGgttcacctct ... attgtttcagCCGGTGATACTTGATTATCTTGCTAGCAAGTCAATTCCCTCAGAGGATTT-
EST: gi|116379954|gb|EG422546.1|EG422546
EST:     ACAGTCCGATGGGTTATTTTGACATTCCAGTCGACCATGTGTACTGCCAG                         CCGGTGATACTTGATTATCTTGCTAGCAAGTCA-TTCCCT
genomic: ACAGTC-GATGGGTTATTTTGACATTCCAGTCGACCATGTGTACTGCCAGgttcacctct ... attgtttcagCCGGTGATACTTGATTATCTTGCTAGCAAGTCAATTCCCT
EST: gi|116379955|gb|EG422547.1|EG422547
EST:     ACAGTCCGATGGGTTATTTTGACATTCCAGTCGACCATGTGTACTGCCAG                         CCGGTGATACTTGATTATCTTGCTAGCAAGTCA-TTCCCTCAG
genomic: ACAGTC-GATGGGTTATTTTGACATTCCAGTCGACCATGTGTACTGCCAGgttcacctct ... attgtttcagCCGGTGATACTTGATTATCTTGCTAGCAAGTCAATTCCCTCAG
EST: gi|116379969|gb|EG422561.1|EG422561
EST:     GACAGTCGATGGGTTATTTTGACATTCCAGTCGACCATGTGTACTGCCAG                         CCGGTGATACTTGATTATCTTGCTAGCAAGTCA-TTCCCTCAGAGGATTTG
genomic: GACAGTCGATGGGTTATTTTGACATTCCAGTCGACCATGTGTACTGCCAGgttcacctct ... attgtttcagCCGGTGATACTTGATTATCTTGCTAGCAAGTCAATTCCCTCAGAGGATTTG
EST: gi|116379981|gb|EG422573.1|EG422573
EST:     ACAGTCCGATGGGTTATTTTGACATTCCAGTCGACCATGTGTACTGCCAG                         CCGGTGATACTTGATTATCTTGCTAGCAAGTCA-TTCCCTCA
genomic: ACAGTC-GATGGGTTATTTTGACATTCCAGTCGACCATGTGTACTGCCAGgttcacctct ... attgtttcagCCGGTGATACTTGATTATCTTGCTAGCAAGTCAATTCCCTCA
EST: gi|116379958|gb|EG422550.1|EG422550
EST:     ACAGTCCGATGGGTTATTTTGACATTCCAGTCGACCATGTGTACTGCCAG                         CCGGTGATACTTGATTATCTTGCTAGCAAGTCA-TTCCCTCAGA
genomic: ACAGTC-GATGGGTTATTTTGACATTCCAGTCGACCATGTGTACTGCCAGgttcacctct ... attgtttcagCCGGTGATACTTGATTATCTTGCTAGCAAGTCAATTCCCTCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcattgtgtgtatgctcctttgtgtataatacctttatctgcttaattgtttcagCCGGTGATACTTGATTATCTTGCTAGCAAGTCAATTCCCTCAGAGGATTTGGTAGTGGTTTCTCCTGATGTTGGTGGAGTAGCCAGGGCCCGCGCTTTTG
                                        gcttaat  putative branch site (score: 4)
                                              ttgtttc  CT-rich tract
                        tataatacctttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcacctctaaagccacgttcttgatacccctctttatgcattgtgtgtatgctcctttgtgtataatacctttatctgcttaattgtttcagCCGGTGATACTTGATTATCTTGCTAGCAAGTCAATTCCCTCAGAGGATTTGGTAGTGGTTTCTCCTGATGTTGGTGGAGTAGCCAGGGCCCGCGCTTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG