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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaatcacatttaaccatttttctttttggtattcgaatggagttcttcttgatatcctctgccattgttattttcagGTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAGTAGCTGAATACTTCGACAAAGCTGTGACAATAGCTCTCAAAGTCAAATC

Basic information

species Arabidopsis thaliana
transcript AT4G37930.1
intron # 13
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|116411252|gb|EG453844.1|EG453844
EST:     CACTGTTCCTGGAGATGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGG                         GTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
genomic: CACTGTTCCTGGAGATGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGGgtaaaaatca ... ttattttcagGTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
EST: gi|124776912|gb|EH866855.1|EH866855
EST:     CACTGTTCCTGGAGATGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGG                         GTACTCCTGCT
genomic: CACTGTTCCTGGAGATGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGGgtaaaaatca ... ttattttcagGTACTCCTGCT
EST: gi|86059292|gb|DR355049.1|DR355049
EST:     CACTGTTCCTGGAGATGTTTCTGCCATGGTTCCTGATGGAATCAGAATGG                         GTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
genomic: CACTGTTCCTGGAGATGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGGgtaaaaatca ... ttattttcagGTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
EST: gi|125173061|gb|EL194883.1|EL194883
EST:     TGGAATCAGAATGG                         GTA-TCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
genomic: TGGAATCAGAATGGgtaaaaatca ... ttattttcagGTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
EST: gi|124902592|gb|EH976672.1|EH976672
EST:     TTCCTGGTGGAATCAGAATGG                         GTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
genomic: TTCCTGGTGGAATCAGAATGGgtaaaaatca ... ttattttcagGTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
EST: gi|124866250|gb|EH950687.1|EH950687
EST:     CCTGGAGATGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGG                         GTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
genomic: CCTGGAGATGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGGgtaaaaatca ... ttattttcagGTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
EST: gi|125248580|gb|EL262665.1|EL262665
EST:     CACTGTTCCTGGAGATGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGG                         GTACTCCTGCTCTCACTTCCAGAGGCTTTGT
genomic: CACTGTTCCTGGAGATGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGGgtaaaaatca ... ttattttcagGTACTCCTGCTCTCACTTCCAGAGGCTTTGT
EST: gi|125239383|gb|EL253468.1|EL253468
EST:     ACTGTTCCTGGAGATGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGG                         GTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTT
genomic: ACTGTTCCTGGAGATGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGGgtaaaaatca ... ttattttcagGTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTT
EST: gi|125146826|gb|EL181353.1|EL181353
EST:     AATCAGAATGG                         GTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
genomic: AATCAGAATGGgtaaaaatca ... ttattttcagGTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
EST: gi|124783896|gb|EH873680.1|EH873680
EST:     CTGGAGATGTTTCTGCCATGGTTCCTTGGTGGAATCAGAATGG                         GTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
genomic: CTGGAGATGTTTCTGCCATGGTTCC-TGGTGGAATCAGAATGGgtaaaaatca ... ttattttcagGTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
EST: gi|125317715|gb|EL331800.1|EL331800
EST:     ACTGTTCCTTGGAGATGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGG                         GTACTCCTGCTCTCACTTCCAGAGGCTTT
genomic: ACTGTTCC-TGGAGATGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGGgtaaaaatca ... ttattttcagGTACTCCTGCTCTCACTTCCAGAGGCTTT
EST: gi|125146753|gb|EL181318.1|EL181318
EST:     TGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGG                         GTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGGGGAAGACTTTGCCAAAG
genomic: TGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGGgtaaaaatca ... ttattttcagGTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
EST: gi|125139889|gb|EL178427.1|EL178427
EST:     CACTGTTCCTGGAGATGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGG                         GTACTCCTGCTCTCACTTCCAGAGG
genomic: CACTGTTCCTGGAGATGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGGgtaaaaatca ... ttattttcagGTACTCCTGCTCTCACTTCCAGAGG
EST: gi|125062558|gb|EL130860.1|EL130860
EST:     AATCAGAATGG                         GTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
genomic: AATCAGAATGGgtaaaaatca ... ttattttcagGTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
EST: gi|125124297|gb|EL170328.1|EL170328
EST:     CCTGGAGATGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGG                         GTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
genomic: CCTGGAGATGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGGgtaaaaatca ... ttattttcagGTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
EST: gi|116443767|gb|EG486359.1|EG486359
EST:     CACTGTTCCTGGAGATGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGG                         GTACTCCTGCTCTCACTTCCAGAGGCTTCGTTGAGGAAGACTCTGCCAAAG
genomic: CACTGTTCCTGGAGATGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGGgtaaaaatca ... ttattttcagGTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
EST: gi|116484717|gb|EG527309.1|EG527309
EST:     CACTGTTCCTGGAGATGTTTTTGCCATGGTTCCTGGTGGAATCAGAATGG                         GTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
genomic: CACTGTTCCTGGAGATGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGGgtaaaaatca ... ttattttcagGTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
EST: gi|124918717|gb|EH992530.1|EH992530
EST:     ATGTTTCTGCCAT-GTTCCTGGTGGAATCAGAATGG                         GTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
genomic: ATGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGGgtaaaaatca ... ttattttcagGTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
EST: gi|125206407|gb|EL221361.1|EL221361
EST:     TTCCTGGTGGAATCAGAATGG                         GTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
genomic: TTCCTGGTGGAATCAGAATGGgtaaaaatca ... ttattttcagGTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
EST: gi|86079465|gb|DR375222.1|DR375222
EST:     CACTGTTCCTGGAGATGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGG                         GTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
genomic: CACTGTTCCTGGAGATGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGGgtaaaaatca ... ttattttcagGTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
EST: gi|124955691|gb|EL030683.1|EL030683
EST:     CACTGTTCCTGGAGATGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGG                         GTACTCCTGCTCTCAC
genomic: CACTGTTCCTGGAGATGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGGgtaaaaatca ... ttattttcagGTACTCCTGCTCTCAC
EST: gi|116484716|gb|EG527308.1|EG527308
EST:     CACTGTTCCTGGAGATGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGG                         GTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
genomic: CACTGTTCCTGGAGATGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGGgtaaaaatca ... ttattttcagGTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
EST: gi|124970157|gb|EL044006.1|EL044006
EST:     CTGGAGATGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGG                         GTACTCCTGCTCTCACTTCCAGAGG
genomic: CTGGAGATGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGGgtaaaaatca ... ttattttcagGTACTCCTGCTCTCACTTCCAGAGG
EST: gi|116484726|gb|EG527318.1|EG527318
EST:     CACTGTTCCTGGAGATGTTTTTGCCATGGTTCCTGGTGGAATCAGAATGG                         GTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
genomic: CACTGTTCCTGGAGATGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGGgtaaaaatca ... ttattttcagGTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
EST: gi|125262402|gb|EL276487.1|EL276487
EST:     TCCTGGTGGAATCAGAATGG                         GTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
genomic: TCCTGGTGGAATCAGAATGGgtaaaaatca ... ttattttcagGTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
EST: gi|125204289|gb|EL219243.1|EL219243
EST:     TTCCTGGAGATGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGG                         GTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
genomic: TTCCTGGAGATGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGGgtaaaaatca ... ttattttcagGTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
EST: gi|116484725|gb|EG527317.1|EG527317
EST:     CACTGTTCCTGGAGATGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGG                         GTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG
genomic: CACTGTTCCTGGAGATGTTTCTGCCATGGTTCCTGGTGGAATCAGAATGGgtaaaaatca ... ttattttcagGTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttggtattcgaatggagttcttcttgatatcctctgccattgttattttcagGTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAGTAGCTGAATACTTCGACAAAGCTGTGACAATAGCTCTCAAAGTCAAATC
                        tcttgat  putative branch site (score: 4)
                                             ttattttc  putative PPT
                                         attgttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaatcacatttaaccatttttctttttggtattcgaatggagttcttcttgatatcctctgccattgttattttcagGTACTCCTGCTCTCACTTCCAGAGGCTTTGTTGAGGAAGACTTTGCCAAAGTAGCTGAATACTTCGACAAAGCTGTGACAATAGCTCTCAAAGTCAAATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG