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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtttctttgtccttcttctggttgatgttagaattacttgaatgttatgactgactcggttcttatttgtctagGTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGGTCGTTCTGCAGAAGATGAACTCCGTTCTGGTATCTACAAAGTCTCCAAG

Basic information

species Arabidopsis thaliana
transcript AT1G25260.1
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|125029100|gb|EL101369.1|EL101369
EST:     AGAAATATCAAATTCAAGGAGTTTAGGCAGCAGTTTAGGCACAATGGAAA                         GTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGG
genomic: AGAAATATCAAATTCAAGGAGTTTAGGCAGCAGTTTAGGCACAATGGAAAgttagtttct ... atttgtctagGTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGG
EST: gi|124943568|gb|EL019741.1|EL019741
EST:     GAAATATCAAATTCAAGGAGTTTAGGCAGTCAGTTTAGGCACAATGGAAA                         GTTCTTCCT-GGTTCGAACAAAGTGATGCAGGTTGCT
genomic: GAAATATCAAATTCAAGGAGTTTAGGCAG-CAGTTTAGGCACAATGGAAAgttagtttct ... atttgtctagGTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCT
EST: gi|125287789|gb|EL301874.1|EL301874
EST:     CAGTTTAGGCACAATGGAAA                         GTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGGTCGTTCTGC
genomic: CAGTTTAGGCACAATGGAAAgttagtttct ... atttgtctagGTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGGTCGTTCTGC
EST: gi|86050076|gb|DR345831.1|DR345831
EST:     AGAAATATCAAATTCAAGGAGTTTAGGCAGCAGTTTAGGCACAATGGAAA                         GTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGGTCGTTCTGC
genomic: AGAAATATCAAATTCAAGGAGTTTAGGCAGCAGTTTAGGCACAATGGAAAgttagtttct ... atttgtctagGTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGGTCGTTCTGC
EST: gi|86050071|gb|DR345826.1|DR345826
EST:     AGAAATATCAAATTCAAGGAGTTTAGGCAGCAGTTTAGGCACAATGGAAA                         GTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGGTCGTTCTGC
genomic: AGAAATATCAAATTCAAGGAGTTTAGGCAGCAGTTTAGGCACAATGGAAAgttagtttct ... atttgtctagGTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGGTCGTTCTGC
EST: gi|86050072|gb|DR345827.1|DR345827
EST:     AGAAATATCAAATTCAAGGAGTTTAGGCAGCAGTTTAGGCACAATGGAAA                         GTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGGTCGTTCTGC
genomic: AGAAATATCAAATTCAAGGAGTTTAGGCAGCAGTTTAGGCACAATGGAAAgttagtttct ... atttgtctagGTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGGTCGTTCTGC
EST: gi|124866567|gb|EH951004.1|EH951004
EST:     GTTTAGGCACAATGGAAA                         GTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGGTCGTTCTGC
genomic: GTTTAGGCACAATGGAAAgttagtttct ... atttgtctagGTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGGTCGTTCTGC
EST: gi|86050070|gb|DR345825.1|DR345825
EST:     AGAAATATCAAATTCAAGGAGTTTAGGCAGCAGTTTAGGCACAATGGAAA                         GTTCTTCCTAGGTTCGAACAAAGTGANTGCAGGTTGCTCTTGGTCGTTCTG
genomic: AGAAATATCAAATTCAAGGAGTTTAGGCAGCAGTTTAGGCACAATGGAAAgttagtttct ... atttgtctagGTTCTTCCTAGGTTCGAACAAAGTGA-TGCAGGTTGCTCTTGGTCGTTCTG
EST: gi|86050065|gb|DR345820.1|DR345820
EST:     AGAAATATCAAATTCAAGGAGTTTAGGCAGCAGTTTAGGCACAATGGAAA                         GTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGGTCGTTCTGC
genomic: AGAAATATCAAATTCAAGGAGTTTAGGCAGCAGTTTAGGCACAATGGAAAgttagtttct ... atttgtctagGTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGGTCGTTCTGC
EST: gi|116470214|gb|EG512806.1|EG512806
EST:     AGAAATATCAAATTCAAGGAGTTTAGGCAGCAGTTTAGGCACAATGGAAA                         GTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGGTCGTTCTGC
genomic: AGAAATATCAAATTCAAGGAGTTTAGGCAGCAGTTTAGGCACAATGGAAAgttagtttct ... atttgtctagGTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGGTCGTTCTGC
EST: gi|86050077|gb|DR345832.1|DR345832
EST:     AGAAATATCAAATTCAAGGAGTTTAGGCAGCAGTTTAGGCACAATGGAAA                         GTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGGTCGTTCTGC
genomic: AGAAATATCAAATTCAAGGAGTTTAGGCAGCAGTTTAGGCACAATGGAAAgttagtttct ... atttgtctagGTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGGTCGTTCTGC
EST: gi|86050073|gb|DR345828.1|DR345828
EST:     AGAAATATCAAATTCAAGGAGTTTAGGCAGCAGTTTAGGCACAATGGAAA                         GTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGGTCGTTCTGC
genomic: AGAAATATCAAATTCAAGGAGTTTAGGCAGCAGTTTAGGCACAATGGAAAgttagtttct ... atttgtctagGTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGGTCGTTCTGC
EST: gi|124869633|gb|EH954070.1|EH954070
EST:     AGTTTAGGCAGCAGTTTAGGCACAATGGAAA                         GTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGGTCGTTCTGC
genomic: AGTTTAGGCAGCAGTTTAGGCACAATGGAAAgttagtttct ... atttgtctagGTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGGTCGTTCTGC
EST: gi|86050069|gb|DR345824.1|DR345824
EST:     AGAAATATCAAATTCAAGGAGTTTAGGCAGCAGTTTAGGCACAATGGAAA                         GTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGGTCGTTCTGC
genomic: AGAAATATCAAATTCAAGGAGTTTAGGCAGCAGTTTAGGCACAATGGAAAgttagtttct ... atttgtctagGTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGGTCGTTCTGC
EST: gi|86050075|gb|DR345830.1|DR345830
EST:     AGAAATATCAAATTCAAGGAGTTTAGGCAGCAGTTTAGGCACAATGGAAA                         GTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGGTCGTTCTGC
genomic: AGAAATATCAAATTCAAGGAGTTTAGGCAGCAGTTTAGGCACAATGGAAAgttagtttct ... atttgtctagGTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGGTCGTTCTGC
EST: gi|86050067|gb|DR345822.1|DR345822
EST:     AGAAATATCAAATTCAAGGAGTTTAGGCAGCAGTTTAGGCACAATGGAAA                         GTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGGTCGTTCTGC
genomic: AGAAATATCAAATTCAAGGAGTTTAGGCAGCAGTTTAGGCACAATGGAAAgttagtttct ... atttgtctagGTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGGTCGTTCTGC
EST: gi|125039590|gb|EL111859.1|EL111859
EST:     AGAAATATCAAATTCAAGGAGTTTAGGCAGCAGTTTAGGCACAATGGAAA                         GTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGGTCGTT
genomic: AGAAATATCAAATTCAAGGAGTTTAGGCAGCAGTTTAGGCACAATGGAAAgttagtttct ... atttgtctagGTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGGTCGTT
EST: gi|152034840|gb|BP837977.2|BP837977
EST:     AGAAATATCAAATTCAAGGAGTTTAGGCAGCAGTTTAGGCACAATGGAAA                         GTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGGTCGTTCTGC
genomic: AGAAATATCAAATTCAAGGAGTTTAGGCAGCAGTTTAGGCACAATGGAAAgttagtttct ... atttgtctagGTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGGTCGTTCTGC
EST: gi|86050074|gb|DR345829.1|DR345829
EST:     AGAAATATCAAATTCAAGGAGTTTAGGCAGCAGTTTAGGCACAATGGAAA                         GTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGGTCGTTCTGC
genomic: AGAAATATCAAATTCAAGGAGTTTAGGCAGCAGTTTAGGCACAATGGAAAgttagtttct ... atttgtctagGTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGGTCGTTCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttgatgttagaattacttgaatgttatgactgactcggttcttatttgtctagGTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGGTCGTTCTGCAGAAGATGAACTCCGTTCTGGTATCTACAAAGTCTCCAAG
                             gactgac  putative branch site (score: 2)
                                        ttcttattt  putative PPT
        ttagaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtttctttgtccttcttctggttgatgttagaattacttgaatgttatgactgactcggttcttatttgtctagGTTCTTCCTAGGTTCGAACAAAGTGATGCAGGTTGCTCTTGGTCGTTCTGCAGAAGATGAACTCCGTTCTGGTATCTACAAAGTCTCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG