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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaaactaactacctatttggcctttgtaatatctgagaaattttcaaagtttagagttaaccttgaacttggtggacctgtgggcctgagcttcttattgaatttccttacgatccatttgtgttgtgggttccttagctttaatctttcatttgaatgtattaatttcagATTGCTCTTTGGTTGGTTTTGTGGTGGAAGCCTGTTCACCTTATGGTAATCATTTCTAAGATGTTCTTTGCAG

Basic information

species Arabidopsis thaliana
transcript AT1G14530.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G14530.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G174286_T03 (Zea mays), 3'ss of exon 6
gtgaaactaactacctatttggcctttgtaatatctgagaaattttcaaagtttagagttaaccttgaacttggtggacctgtgggcctgagcttcttattgaatttccttacgatccatttgtgttgtgggttccttagctttaatctttcatttga-atgtattaatttcagATTGCTCTTTGGTTGGTTTTGTGGTGGAAGCCTGTTCACCTTATGGTAATCATTTCTAAGATGTTCTTTGCAG
                                                                   || | |    ||   ||||| ||   || | | || ||||   |  ||| ||  |    |  |       | | ||      | ||||||| |   || ||||||||||    || |||||||||||||||||||| || ||||   ||||||| ||| | || ||||||||||||||||
-------------------------------------------------------------------aaatagtcacac---tgggcttg---ttgtgaatgcatttttatttgatacacgtaaaataggaacattctggtttctggact-catttgacaccaatgaatttcagATAATCCTATGGTTGGTTTTGTGGTGGAAACCAGTTCGAATTATGGTCATCTTGTCAAAGATGTTCTTTGCAG
















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|116477218|gb|EG519810.1|EG519810
EST:     GACTGAGGCCAAGTTTCTTCACAATTAATGCAGTTGTATACGTAATTCAG                         ATTGCTCTTTGGTTGGTTTTGTGGTGGAAGCCTGTTCACCTTATGGTAATC
genomic: GACTGAGGCCAAGTTTCTTCACAATTAATGCAGTTGTATACGTAATTCAGgtgaaactaa ... ttaatttcagATTGCTCTTTGGTTGGTTTTGTGGTGGAAGCCTGTTCACCTTATGGTAATC
EST: gi|116477220|gb|EG519812.1|EG519812
EST:     GACTGAGGCCAAGTTTCTTCACAATTAATGCAGTTGTATACGTAATTCAG                         ATTGCTCTTTGGTTGGTTTTGTGGTGGAAGCCTGTTCACCTTATGGTAATC
genomic: GACTGAGGCCAAGTTTCTTCACAATTAATGCAGTTGTATACGTAATTCAGgtgaaactaa ... ttaatttcagATTGCTCTTTGGTTGGTTTTGTGGTGGAAGCCTGTTCACCTTATGGTAATC
EST: gi|86039847|gb|DR335602.1|DR335602
EST:     GACTGAGGCCAAGTTTCTTCACAATTAATGCAGTTGTATACGTAATTCAG                         ATTGCTCTTTGGTTGGTTTTGTGGTGGAAGCCTGT
genomic: GACTGAGGCCAAGTTTCTTCACAATTAATGCAGTTGTATACGTAATTCAGgtgaaactaa ... ttaatttcagATTGCTCTTTGGTTGGTTTTGTGGTGGAAGCCTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgtgttgtgggttccttagctttaatctttcatttgaatgtattaatttcagATTGCTCTTTGGTTGGTTTTGTGGTGGAAGCCTGTTCACCTTATGGTAATCATTTCTAAGATGTTCTTTGCAG
                                           tattaat  putative branch site (score: 2)
                       tttaatctttcatttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaaactaactacctatttggcctttgtaatatctgagaaattttcaaagtttagagttaaccttgaacttggtggacctgtgggcctgagcttcttattgaatttccttacgatccatttgtgttgtgggttccttagctttaatctttcatttgaatgtattaatttcagATTGCTCTTTGGTTGGTTTTGTGGTGGAAGCCTGTTCACCTTATGGTAATCATTTCTAAGATGTTCTTTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG