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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gccatgttgagaagttttataactgataatgcaatgtggaaatttttgtgtttctgctttcttttcccagcgttaatggaaattttttgtggtattgcagGTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG

Basic information

species Arabidopsis thaliana
transcript AT1G54100.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G54100.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G130440_T01 (Zea mays), 3'ss of exon 6
--gccatgttgagaagttttataactgataatgcaatgtggaaatttttgtgtttctgctttcttttcccagcgttaatggaaattttttgtggtattgcagGTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
  ||    ||     | | | ||| || |    |||  |  |   | |  |  |      ||  |  ||  |  |   |  | | | |     ||  || ||||||||||||||| |||||| | ||||||||||| ||||| |||||
ttgctcatttctagtgctatgtaattgctgc--caacatttaccatataatcatgtaatcttaatagccatgaatacctcaataatctcccatgtcatgtagGTTGGAATGCTTGCATTGCTTTGGTCTGTGGAAATTGTGTCGTCTG
















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|116420799|gb|EG463391.1|EG463391
EST:     TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTG                         GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
genomic: TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTGgtaagtcttc ... ggtattgcagGTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
EST: gi|116420807|gb|EG463399.1|EG463399
EST:     TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTG                         GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
genomic: TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTGgtaagtcttc ... ggtattgcagGTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
EST: gi|116486592|gb|EG529184.1|EG529184
EST:     TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTG                         GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
genomic: TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTGgtaagtcttc ... ggtattgcagGTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
EST: gi|301501447|gb|HO206987.1|HO206987
EST:     TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTG                         GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
genomic: TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTGgtaagtcttc ... ggtattgcagGTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
EST: gi|116486594|gb|EG529186.1|EG529186
EST:     TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTG                         GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
genomic: TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTGgtaagtcttc ... ggtattgcagGTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
EST: gi|301501173|gb|HO206713.1|HO206713
EST:     TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTG                         GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
genomic: TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTGgtaagtcttc ... ggtattgcagGTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
EST: gi|116420806|gb|EG463398.1|EG463398
EST:     TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTG                         GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
genomic: TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTGgtaagtcttc ... ggtattgcagGTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
EST: gi|301502366|gb|HO207906.1|HO207906
EST:     GGCATTGTTGGTGTTATCACAGCCGTTTAATTTTCCCTGTGCAGTTCTTG                         GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
genomic: GGCATTGTTGGTGTTATCACAGC-GTTTAATTTTCCCTGTGCAGTTCTTGgtaagtcttc ... ggtattgcagGTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
EST: gi|116486590|gb|EG529182.1|EG529182
EST:     TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTG                         GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
genomic: TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTGgtaagtcttc ... ggtattgcagGTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
EST: gi|301502094|gb|HO207634.1|HO207634
EST:     TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTG                         GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTGGAAAG
genomic: TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTGgtaagtcttc ... ggtattgcagGTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTGGAAAG
EST: gi|116486591|gb|EG529183.1|EG529183
EST:     TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTG                         GTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
genomic: TGGCATTGTTGGTGTTATCACAGCGTTTAATTTTCCCTGTGCAGTTCTTGgtaagtcttc ... ggtattgcagGTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgtttctgctttcttttcccagcgttaatggaaattttttgtggtattgcagGTTGGAATGCTTGTATTGCTCTTGTCTGTGGAAACTGTGTAGTCTG
                         cgttaat  putative branch site (score: 4)
                           ttaatggaaatttttt  TA-rich tract