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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatctctaattccacactcactacatttatgtacttttttctgtatctatacgctttgtgtatgatgttttgtatattgttgcttctcttgctttacttgtttggtttgggatttcttctctgttttttcttggtgaattttgcgtttcgcttaaaaatgagtgaaattgatttggtgaaattagGTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAGCTCTTCAGCGACCTCTCATG

Basic information

species Arabidopsis thaliana
transcript AT4G39460.1
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|86037549|gb|DR333304.1|DR333304
EST:     ATCTCTCTCTTTCGTACACTTCGCGCTTCTCTTCCT                         GTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
genomic: ATCTCTCTCTTTCGTACACTTCGCGCTTCTCTTCCTgtaatctcta ... gtgaaattagGTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
EST: gi|86037542|gb|DR333297.1|DR333297
EST:     TTCGTACACTTCGCGCTTCTCTTCCT                         GTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
genomic: TTCGTACACTTCGCGCTTCTCTTCCTgtaatctcta ... gtgaaattagGTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
EST: gi|86037537|gb|DR333292.1|DR333292
EST:     TTCGTACACTTCGCGCTTCTCTTCCT                         GTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
genomic: TTCGTACACTTCGCGCTTCTCTTCCTgtaatctcta ... gtgaaattagGTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
EST: gi|86037552|gb|DR333307.1|DR333307
EST:     GTACACTTCGCGCTTCTCTTCCT                         GTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
genomic: GTACACTTCGCGCTTCTCTTCCTgtaatctcta ... gtgaaattagGTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
EST: gi|86037535|gb|DR333290.1|DR333290
EST:     TTCGTACACTTCGCGCTTCTCTTCCT                         GTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
genomic: TTCGTACACTTCGCGCTTCTCTTCCTgtaatctcta ... gtgaaattagGTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
EST: gi|152038462|gb|AV823633.2|AV823633
EST:     TTCGTACACTTCGCAGCTTCTCTTCCT                         GTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
genomic: TTCGTACACTTCGC-GCTTCTCTTCCTgtaatctcta ... gtgaaattagGTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
EST: gi|86037532|gb|DR333287.1|DR333287
EST:     GTACACTTCGCGCTTCTCTTCCT                         GTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
genomic: GTACACTTCGCGCTTCTCTTCCTgtaatctcta ... gtgaaattagGTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
EST: gi|86037548|gb|DR333303.1|DR333303
EST:     TTCGTACACTTCGCGCTTCTCTTCCT                         GTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
genomic: TTCGTACACTTCGCGCTTCTCTTCCTgtaatctcta ... gtgaaattagGTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
EST: gi|86037533|gb|DR333288.1|DR333288
EST:     TTCGTACACTTCGCGCTTCTCTTCCT                         GTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
genomic: TTCGTACACTTCGCGCTTCTCTTCCTgtaatctcta ... gtgaaattagGTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
EST: gi|86037553|gb|DR333308.1|DR333308
EST:     ATCTCTCTCTTTCGTACACTTCGCGCTTCTCTTCCT                         GTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
genomic: ATCTCTCTCTTTCGTACACTTCGCGCTTCTCTTCCTgtaatctcta ... gtgaaattagGTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
EST: gi|86037534|gb|DR333289.1|DR333289
EST:     ACACTTCGCGCTTCTCTTCCT                         GTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
genomic: ACACTTCGCGCTTCTCTTCCTgtaatctcta ... gtgaaattagGTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
EST: gi|86037555|gb|DR333310.1|DR333310
EST:     TTCGTACACTTCGCGCTTCTCTTCCT                         GTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
genomic: TTCGTACACTTCGCGCTTCTCTTCCTgtaatctcta ... gtgaaattagGTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
EST: gi|86037540|gb|DR333295.1|DR333295
EST:     TTCGTACACTTCGCGCTTCTCTTCCT                         GTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
genomic: TTCGTACACTTCGCGCTTCTCTTCCTgtaatctcta ... gtgaaattagGTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
EST: gi|86037541|gb|DR333296.1|DR333296
EST:     ATCTCTCTCTTTCGTACACTTCGCGCTTCTCTTCCT                         GTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
genomic: ATCTCTCTCTTTCGTACACTTCGCGCTTCTCTTCCTgtaatctcta ... gtgaaattagGTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
EST: gi|86037539|gb|DR333294.1|DR333294
EST:     TTCGTACACTTCGCGCTTCTCTTCCT                         GTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
genomic: TTCGTACACTTCGCGCTTCTCTTCCTgtaatctcta ... gtgaaattagGTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
EST: gi|86037546|gb|DR333301.1|DR333301
EST:     TTCGTACACTTCGCGCTTCTCTTCCT                         GTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
genomic: TTCGTACACTTCGCGCTTCTCTTCCTgtaatctcta ... gtgaaattagGTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
EST: gi|86037536|gb|DR333291.1|DR333291
EST:     TTCGTACACTTCGCGCTTCTCTTCCT                         GTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
genomic: TTCGTACACTTCGCGCTTCTCTTCCTgtaatctcta ... gtgaaattagGTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
EST: gi|86037551|gb|DR333306.1|DR333306
EST:     TTCGTACACTTCGCGCTTCTCTTCCT                         GTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
genomic: TTCGTACACTTCGCGCTTCTCTTCCTgtaatctcta ... gtgaaattagGTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
EST: gi|152033833|gb|BP817226.2|BP817226
EST:     TCTCTCTCTTTCGTACACTTCGCGCTTCTCTTCCT                         GTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
genomic: TCTCTCTCTTTCGTACACTTCGCGCTTCTCTTCCTgtaatctcta ... gtgaaattagGTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
EST: gi|86037554|gb|DR333309.1|DR333309
EST:     TTCGTACACTTCGCGCTTCTCTTCCT                         GTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
genomic: TTCGTACACTTCGCGCTTCTCTTCCTgtaatctcta ... gtgaaattagGTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
EST: gi|86037544|gb|DR333299.1|DR333299
EST:     TTCGTACACTTCGCGCTTCTCTTCCT                         GTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG
genomic: TTCGTACACTTCGCGCTTCTCTTCCTgtaatctcta ... gtgaaattagGTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggtgaattttgcgtttcgcttaaaaatgagtgaaattgatttggtgaaattagGTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAGCTCTTCAGCGACCTCTCATG
                                   aattgat  putative branch site (score: 4)
                     ttaaaaatga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatctctaattccacactcactacatttatgtacttttttctgtatctatacgctttgtgtatgatgttttgtatattgttgcttctcttgctttacttgtttggtttgggatttcttctctgttttttcttggtgaattttgcgtttcgcttaaaaatgagtgaaattgatttggtgaaattagGTCAGAGGCGTTTCTCATGGCTCCTCTTACTCTCTCCGTTGATGTGAAGAGCTCTTCAGCGACCTCTCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT