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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTATTCCGGTTAACCCGAAACCATTCTTGAACAACTTGACCGGCAAGACTGTTATCGTCAAGCTTAAATGGGGAATGGAATACAAAGgtatatttttcttcaaaatgcttttgatgataagtatccagagcttatatagctaacagtcttccttctacttcacag

Basic information

species Arabidopsis thaliana
transcript AT4G30220.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G30220.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os11g43620.1 (Oryza sativa), 5'ss of exon 2
ACTATTCCGGTTAACCCGAAACCATTCTTGAACAACTTGACCGGCAAGACTGTTATCGTCAAGCTTAAATGGGGAATGGAATACAAAGg-----tatattttt-cttcaaaatgcttt-----tgatgataagtat---ccagagcttatatagct---aacagtcttccttctacttcacag-----
||| |||| |||||||| ||||| |||||||||||| |||| || ||| |||| || ||||| ||||| ||||| ||||||||||||||     |||| |||| | |   | | |||      | || | | |  |   |||| ||||  | |  |   ||     |  ||   | ||||        
ACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctatacttttacctttcacttcttcttcacttattacatgcttaagccagtgcttgaaaatttcagaatgaaatctctgagatttcaggaaatcc

upper sequence: AT4G30220.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os02g08090.1 (Oryza sativa), 5'ss of exon 2
ACTATTCCGGTTAACCCGAAACCATTCTTGAACAACTTGACCGGCAAGACTGTTATCGTCAAGCTTAAATGGGGAATGGAATACAAAGg-----tatattttt---cttcaaaatgcttttgatgataagtat---ccagagcttatatagctaacagtcttccttctacttcacag-----------
||| | || ||||||||||| || |||||||||||| |||| || ||| |||| || ||||| ||||| ||||| ||||||||||||||     |||| ||||   | ||| | |   ||   ||||| |  |   | || | ||  |     |  |      ||   |  |  |||           
ACTGTGCCAGTTAACCCGAAGCCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctatacttttacccgtcacattttattcactgatatgcttaggctagtgattgaaatttcagaatgaaatctctgaggtttcaggaacattgaaa

upper sequence: AT4G30220.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv00s0220g00030.t01 (Vitis vinifera), 5'ss of exon 2
ACTATTCCGGTTAACCCGAAACCATTCTTGAACAACTTGACCGGCAAGACTGTTATCGTCAAGCTTAAATGGGGAATGGAATACAAAGgtatatttttcttcaaaatgcttttgat-gataagtatcca-gagcttatatagctaacagtcttccttctacttcacag
||  | ||  | ||||| || || |||||||| |||||||| || ||| |||| || ||||| || || ||||||||||| |||||||||| ||| | |  |      || | | |  ||    ||| | ||  || | |  || |   | ||| |     ||   ||
ACCGTACCACTGAACCCTAAGCCCTTCTTGAATAACTTGACTGGGAAGCCTGTCATTGTCAAACTCAAGTGGGGAATGGAGTACAAAGgtaaattctcccgctttcgtctgtggttcaattgaaatctatgattttttttttcttaacattttcttgggtttttttag

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|164148928|gb|ES032866.1|ES032866
EST:     GGGGAATGGAATACAAAG                         GTTTTCTCGCCTCTGTTGACTCCTACATGAACTTGCAG
genomic: GGGGAATGGAATACAAAGgtatattttt ... tacttcacagGTTTTCTCGCCTCTGTTGACTCCTACATGAACTTGCAG
EST: gi|164043348|gb|EL969191.1|EL969191
EST:     GACCGGCAAGACTGTTATCGTCAAGCTTAAATGGGGAATGGAATACAAAG                         GTTTTCTCGCCTCTGT
genomic: GACCGGCAAGACTGTTATCGTCAAGCTTAAATGGGGAATGGAATACAAAGgtatattttt ... tacttcacagGTTTTCTCGCCTCTGT
EST: gi|125309073|gb|EL323158.1|EL323158
EST:     GGGGAAGTGGAATACAAAG                         GTTTTCTCGCCTCTGTTGACTCCTACATGAACTTGCAG
genomic: GGGGAA-TGGAATACAAAGgtatattttt ... tacttcacagGTTTTCTCGCCTCTGTTGACTCCTACATGAACTTGCAG
EST: gi|19741076|gb|AU226429.1|AU226429
EST:     -ACCGGCAAGACTGTTATCGTCAAGCTTAAATGGGGAATGGAATACAAAG                         TTTTTCTCGCCTCTGTTGACTCCTACATGAACTTCCAG
genomic: GACCGGCAAGACTGTTATCGTCAAGCTTAAATGGGGAATGGAATACAAAGgtatattttt ... tacttcacagGTTTTCTCGCCTCTGTTGACTCCTACATGAACTTGCAG
EST: gi|19874858|gb|AU235689.1|AU235689
EST:     GACCGGCAAGACTGTTATCGTCAAGCTTAAATGGGGAATGGAATACAAAG                         GTTTTCTCGCCTCTGTTGACTCCTACATGAACTTGCAG
genomic: GACCGGCAAGACTGTTATCGTCAAGCTTAAATGGGGAATGGAATACAAAGgtatattttt ... tacttcacagGTTTTCTCGCCTCTGTTGACTCCTACATGAACTTGCAG
EST: gi|86080133|gb|DR375890.1|DR375890
EST:     GACCGGCAAGACTGTTATCGTCAAGCTTAAATGGGGAATGGAATACAAAG                         GTTTTCTCGCCTCTGTTGACTCCTACATGAACTTGCAG
genomic: GACCGGCAAGACTGTTATCGTCAAGCTTAAATGGGGAATGGAATACAAAGgtatattttt ... tacttcacagGTTTTCTCGCCTCTGTTGACTCCTACATGAACTTGCAG
EST: gi|164027104|gb|ES017576.1|ES017576
EST:     TATCGTCAAGCTTAAATGGGGAATGGAATACAAAG                         GTTTTCTCGCCTCTGTTGACTCCTACATGAACTTGCAG
genomic: TATCGTCAAGCTTAAATGGGGAATGGAATACAAAGgtatattttt ... tacttcacagGTTTTCTCGCCTCTGTTGACTCCTACATGAACTTGCAG
EST: gi|124848527|gb|EH932964.1|EH932964
EST:     CTTAAATGGGGAATGGAATACAAAG                         GTTTTCTCGCCTCTGTTGACTCCTACATGAACTTGCAG
genomic: CTTAAATGGGGAATGGAATACAAAGgtatattttt ... tacttcacagGTTTTCTCGCCTCTGTTGACTCCTACATGAACTTGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTATTCCGGTTAACCCGAAACCATTCTTGAACAACTTGACCGGCAAGACTGTTATCGTCAAGCTTAAATGGGGAATGGAATACAAAGgtatatttttcttcaaaatgcttttgatgataagtatccagagcttatatagctaacagtcttccttctacttcacag

- - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT