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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtatcttataacgacactataaagtttatgcgcagtaaactagtcatcgtgaagaaaactaactgttatgattcctttctcttctattggttttgtagCTAAGGTTGTCACAGACAGAGTATCAGGATATTCCAAAGGGTTTGGATTTGTTAGATATGCCACTTTAGAAGATTCTGCCAAAGGCATAGCTGGAATGGA

Basic information

species Arabidopsis thaliana
transcript AT5G54580.1
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|164038887|gb|ES122080.1|ES122080
EST:     TTCTGAAGGACTAAGGACTGCTTTTGCTCAGTTTGGAGAAGTTGCTGATG                         CTAAGGTTGTCACAGACAGAGTATCAGGATATTCCAAAGGGTTTG
genomic: TTCTGAAGGACTAAGGACTGCTTTTGCTCAGTTTGGAGAAGTTGCTGATGgtgcgtatct ... ggttttgtagCTAAGGTTGTCACAGACAGAGTATCAGGATATTCCAAAGGGTTTG
EST: gi|124805423|gb|EH892826.1|EH892826
EST:     TGCTTTTGTCTCAGTTTGGAGAAGTTGCTGATG                         CTAAGGTTGTCACAGACAGAGTATCAGGATATCCCAAAGGGTTTGGATTTG
genomic: TGCTTTTG-CTCAGTTTGGAGAAGTTGCTGATGgtgcgtatct ... ggttttgtagCTAAGGTTGTCACAGACAGAGTATCAGGATATTCCAAAGGGTTTGGATTTG
EST: gi|164161293|gb|ES084925.1|ES084925
EST:     TTCTGAAGGACTAAGGACTGCTTTTGCTCAGTTTGGAGAAGTTGCTGATG                         CTAAGGTTGTCACAGACAGAGTATCAGGATATTCCAAAGGGTTTGGA
genomic: TTCTGAAGGACTAAGGACTGCTTTTGCTCAGTTTGGAGAAGTTGCTGATGgtgcgtatct ... ggttttgtagCTAAGGTTGTCACAGACAGAGTATCAGGATATTCCAAAGGGTTTGGA
EST: gi|86076453|gb|DR372210.1|DR372210
EST:     TTCTGAAGGACTAAGGACTGCTTTTGCTCAGTTTGGAGAAGTTGCTGATG                         CTAAGGTTGTCACAGACAGAGTATCAGGATATTCCAAAGGGTTTGGATTTG
genomic: TTCTGAAGGACTAAGGACTGCTTTTGCTCAGTTTGGAGAAGTTGCTGATGgtgcgtatct ... ggttttgtagCTAAGGTTGTCACAGACAGAGTATCAGGATATTCCAAAGGGTTTGGATTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatcgtgaagaaaactaactgttatgattcctttctcttctattggttttgtagCTAAGGTTGTCACAGACAGAGTATCAGGATATTCCAAAGGGTTTGGATTTGTTAGATATGCCACTTTAGAAGATTCTGCCAAAGGCATAGCTGGAATGGA
             aactaac  putative branch site (score: 1)
                            ttcctttctcttctat  putative PPT
           aaaactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgtatcttataacgacactataaagtttatgcgcagtaaactagtcatcgtgaagaaaactaactgttatgattcctttctcttctattggttttgtagCTAAGGTTGTCACAGACAGAGTATCAGGATATTCCAAAGGGTTTGGATTTGTTAGATATGCCACTTTAGAAGATTCTGCCAAAGGCATAGCTGGAATGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA