Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataatgtctccaatcattaattcattcaaaagtaattaatgctaaaacaaaaagagactaatagatatgtcactgtccattctatatattcagTATTGGGGAATCACGACTATAGAGGAGATGTTGAGGCACAATTGAGTCCTATCCTCAGATCTATGGATAGCCGTTGGATTTGCATGAGATCCTTCATCGT

Basic information

species Arabidopsis thaliana
transcript AT1G25230.1
intron # 2
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|86018671|gb|DR314417.1|DR314417
EST:     CTTTAGTAATATCTACACTTCTCCTAGCCTGCAAAAGCCTTGGTAMCTTG                         TATTGGGGAATCACGACTATAGAGGAGATGTTGAGGCACAATTGAGTCCTA
genomic: CTTTAGTAATATCTACACTTCTCCTAGCCTGCAAAAGCCTTGGTACCTTGgtaataatgt ... atatattcagTATTGGGGAATCACGACTATAGAGGAGATGTTGAGGCACAATTGAGTCCTA
EST: gi|125296033|gb|EL310118.1|EL310118
EST:     CTTTAGTAATATCTACACCTCTCCTAGCCTGCAAAAGCCTTGGTACCTTG                         TATTGGGGAATCACGACTATA
genomic: CTTTAGTAATATCTACACTTCTCCTAGCCTGCAAAAGCCTTGGTACCTTGgtaataatgt ... atatattcagTATTGGGGAATCACGACTATA
EST: gi|124734441|gb|EH825843.1|EH825843
EST:     CTTTAGTAATATCTACACTTCTCCTAGCCTGCAAAAGCCTTGGTACCTTG                         TATTGGGGAATCACGACTATAGAGG
genomic: CTTTAGTAATATCTACACTTCTCCTAGCCTGCAAAAGCCTTGGTACCTTGgtaataatgt ... atatattcagTATTGGGGAATCACGACTATAGAGG
EST: gi|86018676|gb|DR314422.1|DR314422
EST:     CTTTAGTAATATCTACACTTCTCCTAGCCTGCAAAAGCCTTGGTACCTTG                         TATTGGGGAATCACGACTATAGAGGAGATGTTGAGGCACAATTGAGTCCTA
genomic: CTTTAGTAATATCTACACTTCTCCTAGCCTGCAAAAGCCTTGGTACCTTGgtaataatgt ... atatattcagTATTGGGGAATCACGACTATAGAGGAGATGTTGAGGCACAATTGAGTCCTA
EST: gi|125292970|gb|EL307055.1|EL307055
EST:     CCTAGCCTGCAAAAGCCTTGGTACCTTG                         TATTGGGGAATCACGACTATAGAGGAGATGTTGAGGCACAAT
genomic: CCTAGCCTGCAAAAGCCTTGGTACCTTGgtaataatgt ... atatattcagTATTGGGGAATCACGACTATAGAGGAGATGTTGAGGCACAAT
EST: gi|86018670|gb|DR314416.1|DR314416
EST:     CTTTAGTAATATCTACACTTCTCCTAGCCTGCAAAAGCCTTGGTACCTTG                         TATTGGGGAATCACGACTATAGAGGAGATGTTGAGGCACAATTGAGTCCTA
genomic: CTTTAGTAATATCTACACTTCTCCTAGCCTGCAAAAGCCTTGGTACCTTGgtaataatgt ... atatattcagTATTGGGGAATCACGACTATAGAGGAGATGTTGAGGCACAATTGAGTCCTA
EST: gi|125026543|gb|EL098812.1|EL098812
EST:     CCTGCAAAAGCCTTGGTACCTTG                         TATTGGGGAATCACGACTATAGAGGAGATGTTGAGGCACAATTGAGTCCTA
genomic: CCTGCAAAAGCCTTGGTACCTTGgtaataatgt ... atatattcagTATTGGGGAATCACGACTATAGAGGAGATGTTGAGGCACAATTGAGTCCTA
EST: gi|124904981|gb|EH979061.1|EH979061
EST:     GCCTGCAAAAGCCTTGGTACCTTG                         TATTGGGGAATCACGACTATAGAGGAGATGTTGAGGCACAATTGAGTCCTA
genomic: GCCTGCAAAAGCCTTGGTACCTTGgtaataatgt ... atatattcagTATTGGGGAATCACGACTATAGAGGAGATGTTGAGGCACAATTGAGTCCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgctaaaacaaaaagagactaatagatatgtcactgtccattctatatattcagTATTGGGGAATCACGACTATAGAGGAGATGTTGAGGCACAATTGAGTCCTATCCTCAGATCTATGGATAGCCGTTGGATTTGCATGAGATCCTTCATCGT
                 gactaat  putative branch site (score: 2)
                                        attctatatattca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaataatgtctccaatcattaattcattcaaaagtaattaatgctaaaacaaaaagagactaatagatatgtcactgtccattctatatattcagTATTGGGGAATCACGACTATAGAGGAGATGTTGAGGCACAATTGAGTCCTATCCTCAGATCTATGGATAGCCGTTGGATTTGCATGAGATCCTTCATCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC