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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgctatagtttaatgtattatgatcatatttagaataagcttttaagtggttataggcatagaatgtattaggggatgtgattgaagcaacatgatttcttagttcattgcttttgtatctaatattttacatgttttcttgttttgtttggtaagTGCTGGTTCACTTAAGACCTTGAAGGTGCCAAGAAGTGGTCTGACTAATTCGGGTGTGGTAAACGTAGCTGAAAAGCTCTCGTCTCTCACTTTCTTGGAT

Basic information

species Arabidopsis thaliana
transcript AT4G08980.1
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|86056941|gb|DR352698.1|DR352698
EST:     TCCGTTACTGGCCTTCGAAATGACTCTATCTTCTCCTTCATTGCACAACA                         TGCTGGTTCACTTAAGACCTTGAAGGTGCCAAGAAGTGGTCTGACTAATT
genomic: TCCGTTACTGGCCTTCGAAATGACTCTATCTTCTCCTTCATTGCACAACAgtaagttgct ... gtttggtaagTGCTGGTTCACTTAAGACCTTGAAGGTGCCAAGAAGTGGTCTGACTAATT
EST: gi|163989115|gb|ES141450.1|ES141450
EST:     TCCGTTACTGGCCTTCGAAATGACTCTATCTTCTCCTTCATTGCACAACA                         TGCTGGTTCACTTAAGACCT
genomic: TCCGTTACTGGCCTTCGAAATGACTCTATCTTCTCCTTCATTGCACAACAgtaagttgct ... gtttggtaagTGCTGGTTCACTTAAGACCT
EST: gi|125306699|gb|EL320784.1|EL320784
EST:     TCCGTTACTGGCCTTCGAAATGACTCTATCTTCTCCTTCATTGCACAACA                         TGCTGGTTCACTTAAGACC
genomic: TCCGTTACTGGCCTTCGAAATGACTCTATCTTCTCCTTCATTGCACAACAgtaagttgct ... gtttggtaagTGCTGGTTCACTTAAGACC
EST: gi|86056935|gb|DR352692.1|DR352692
EST:     TCCGTTACTGGCCTTCGAAATGACTCTATCTTCTCCTTCATTGCACAACA                         TGCTGGTTCACTTAAGACCTTGAAGGTGCCAAGAAGTGGTCTGACTAATTC
genomic: TCCGTTACTGGCCTTCGAAATGACTCTATCTTCTCCTTCATTGCACAACAgtaagttgct ... gtttggtaagTGCTGGTTCACTTAAGACCTTGAAGGTGCCAAGAAGTGGTCTGACTAATTC
EST: gi|86056928|gb|DR352685.1|DR352685
EST:     TCCGTTACTGGCCTTCGAAATGACTCTATCTTCTCCTTCATTGCACAACA                         TGCTGGTTCACTTAAGACCTTGAAGGTGCCAAGAAGTGGTCTGACTAATTT
genomic: TCCGTTACTGGCCTTCGAAATGACTCTATCTTCTCCTTCATTGCACAACAgtaagttgct ... gtttggtaagTGCTGGTTCACTTAAGACCTTGAAGGTGCCAAGAAGTGGTCTGACTAATT-
EST: gi|86056918|gb|DR352675.1|DR352675
EST:     TCCGTTACTGGCCTTCGAAATGACTCTATCTTCTCCTTCATTGCACAACA                         TGCTGGTTCACTTAAGACCTTGAAGGTGCCAAGAAGTGGTCTGACTAATTC
genomic: TCCGTTACTGGCCTTCGAAATGACTCTATCTTCTCCTTCATTGCACAACAgtaagttgct ... gtttggtaagTGCTGGTTCACTTAAGACCTTGAAGGTGCCAAGAAGTGGTCTGACTAATTC
EST: gi|86056937|gb|DR352694.1|DR352694
EST:     TCCGTTACTGGCCTTCGAAATGACTCTATCTTCTCCTTCATTGCACAACA                         TGCTGGTTCACTTAAGACCTTGAAGGTGCCAAGAAGTGGTCTGACTAATTC
genomic: TCCGTTACTGGCCTTCGAAATGACTCTATCTTCTCCTTCATTGCACAACAgtaagttgct ... gtttggtaagTGCTGGTTCACTTAAGACCTTGAAGGTGCCAAGAAGTGGTCTGACTAATTC
EST: gi|86056921|gb|DR352678.1|DR352678
EST:     TCCGTTACTGGCCTTCGAAATGACTCTATCTTCTCCTTCATTGCACAACA                         TGCTGGTTCACTTAAGACCTTKAAGGTGCCAAGAAGTGGTCTGACTAATTC
genomic: TCCGTTACTGGCCTTCGAAATGACTCTATCTTCTCCTTCATTGCACAACAgtaagttgct ... gtttggtaagTGCTGGTTCACTTAAGACCTTGAAGGTGCCAAGAAGTGGTCTGACTAATTC
EST: gi|86056930|gb|DR352687.1|DR352687
EST:     TCCGTTACTGGCCTTCGAAATGACTCTATCTTCTCCTTCATTGCACAACA                         TGCTGGTTCACTTAAGACCTTGAAGGTGCCAAGAAGTGGTCTGACTAATTC
genomic: TCCGTTACTGGCCTTCGAAATGACTCTATCTTCTCCTTCATTGCACAACAgtaagttgct ... gtttggtaagTGCTGGTTCACTTAAGACCTTGAAGGTGCCAAGAAGTGGTCTGACTAATTC
EST: gi|86056939|gb|DR352696.1|DR352696
EST:     TCCGTTACTGGCCTTCGAAATGACTCTATCTTCTCCTTCATTGCACAACA                         TGCTGGTTCACTTAAGACCTTGAAGGTGCCAAGAAGTGGTCTGACTAATTC
genomic: TCCGTTACTGGCCTTCGAAATGACTCTATCTTCTCCTTCATTGCACAACAgtaagttgct ... gtttggtaagTGCTGGTTCACTTAAGACCTTGAAGGTGCCAAGAAGTGGTCTGACTAATTC
EST: gi|86056934|gb|DR352691.1|DR352691
EST:     TCCGTTACTGGCCTTCGAAATGACTCTATCTTCTCCTTCATTGCACAACA                         TGCTGGTTCACTTAAGACCTTGAAGGTGCCAAGAAGTGGTCTGACTAATTC
genomic: TCCGTTACTGGCCTTCGAAATGACTCTATCTTCTCCTTCATTGCACAACAgtaagttgct ... gtttggtaagTGCTGGTTCACTTAAGACCTTGAAGGTGCCAAGAAGTGGTCTGACTAATTC
EST: gi|86056924|gb|DR352681.1|DR352681
EST:     TCCGTTACTGGCCTTCGAAATGACTCTATCTTCTCCTTCATTGCACAACA                         TGCTGGTTCACTTAAGACCTTGAAGGTGCCAAGAAGTGGTCTGACTAATTC
genomic: TCCGTTACTGGCCTTCGAAATGACTCTATCTTCTCCTTCATTGCACAACAgtaagttgct ... gtttggtaagTGCTGGTTCACTTAAGACCTTGAAGGTGCCAAGAAGTGGTCTGACTAATTC
EST: gi|116458064|gb|EG500656.1|EG500656
EST:     TCCGTTACTGGCCTTCGAAATGACTCTATCTTCTCCTTCATTGCACAACA                         TGCTGGTTCACTTAAGACCTTGAAGGTGCCAAGAAGTGGTCTGACTAATTC
genomic: TCCGTTACTGGCCTTCGAAATGACTCTATCTTCTCCTTCATTGCACAACAgtaagttgct ... gtttggtaagTGCTGGTTCACTTAAGACCTTGAAGGTGCCAAGAAGTGGTCTGACTAATTC
EST: gi|86056945|gb|DR352702.1|DR352702
EST:     TCCGTTACTGGCCTTCGAAATGACTCTATCTTCTCCTTCATTGCACAACA                         TGCTGGTTCACTTAAGACCTTGAAGGTGCCAAGAAGTGGTCTGACTAATTC
genomic: TCCGTTACTGGCCTTCGAAATGACTCTATCTTCTCCTTCATTGCACAACAgtaagttgct ... gtttggtaagTGCTGGTTCACTTAAGACCTTGAAGGTGCCAAGAAGTGGTCTGACTAATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttcattgcttttgtatctaatattttacatgttttcttgttttgtttggtaagTGCTGGTTCACTTAAGACCTTGAAGGTGCCAAGAAGTGGTCTGACTAATTCGGGTGTGGTAAACGTAGCTGAAAAGCTCTCGTCTCTCACTTTCTTGGAT
                atctaat  putative branch site (score: 3)
                                 ttttcttgttttgttt  putative PPT
          ttttgtatctaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgctatagtttaatgtattatgatcatatttagaataagcttttaagtggttataggcatagaatgtattaggggatgtgattgaagcaacatgatttcttagttcattgcttttgtatctaatattttacatgttttcttgttttgtttggtaagTGCTGGTTCACTTAAGACCTTGAAGGTGCCAAGAAGTGGTCTGACTAATTCGGGTGTGGTAAACGTAGCTGAAAAGCTCTCGTCTCTCACTTTCTTGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA