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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgatgatttgtagttatcctcgagttcacctttcatgtaaccatataagcattgctcaaactacttgacactaatctggttttgggttttgctgctagGTCTCACTGAACCTTTGAAGATCATGACGAAAAAAGGATCGTCTCTTGTTTTTTTCTTAATTTTCAGCTTCATATGTCGAAATAAAGAGAACTGTGAAGA

Basic information

species Arabidopsis thaliana
transcript AT1G76200.1
intron # 3
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|125292888|gb|EL306973.1|EL306973
EST:     GGCACCCTTGGGATGGTCATGGTGATCACGGTCACGGAGATCATCACTAG                         GTCTCACTGAACCTTTGAAGATCATGACG
genomic: GGCACCCTTGGGATGGTCATGGTGATCACGGTCACGGAGATCATCACTAGgtaatgtctt ... ttgctgctagGTCTCACTGAACCTTTGAAGATCATGACG
EST: gi|86053204|gb|DR348961.1|DR348961
EST:     GGCACCCTTGGGATGGTCATGGTGATCACGGTCACGGAGATCATCACTAG                         GTCTCACTGAACCTTTGAAGATCATGACGAAAAAAGGATCGTCTCTTG
genomic: GGCACCCTTGGGATGGTCATGGTGATCACGGTCACGGAGATCATCACTAGgtaatgtctt ... ttgctgctagGTCTCACTGAACCTTTGAAGATCATGACGAAAAAAGGATCGTCTCTTG
EST: gi|164090318|gb|ES079268.1|ES079268
EST:     GGCACCCTTGGGATGGTCATGGTGATCACGGTCACGGAGATCATCACTAG                         GTCTCACTGAACCTTTGAAGATCACGACGAAAAAAGGA
genomic: GGCACCCTTGGGATGGTCATGGTGATCACGGTCACGGAGATCATCACTAGgtaatgtctt ... ttgctgctagGTCTCACTGAACCTTTGAAGATCATGACGAAAAAAGGA
EST: gi|124888508|gb|EH967410.1|EH967410
EST:     GGCACCCTTGGGATGGTCATGGTGATCACGGTCACGGAGATCATCACTAG                         GTCTCACTGAACCTTTGAAGATCATGACGAAAAAAGGATCGT
genomic: GGCACCCTTGGGATGGTCATGGTGATCACGGTCACGGAGATCATCACTAGgtaatgtctt ... ttgctgctagGTCTCACTGAACCTTTGAAGATCATGACGAAAAAAGGATCGT
EST: gi|86077411|gb|DR373168.1|DR373168
EST:     GGCACCCTTGGGATGGTCATGGTGATCACGGTCACGGAGATCATCACTAG                         GTCTCACTGAACCTTTGAAGATCATGA-GAAAAAAGGATCGTCTCTTGNNN
genomic: GGCACCCTTGGGATGGTCATGGTGATCACGGTCACGGAGATCATCACTAGgtaatgtctt ... ttgctgctagGTCTCACTGAACCTTTGAAGATCATGACGAAAAAAGGATCGTCTCTTGTTT
EST: gi|86053203|gb|DR348960.1|DR348960
EST:     GGCACCCTTGGGATGGTCATGGTGATCACGGTCACGGAGATCATCACTAG                         GTCTCACTGAACCTTTGAAGATCATGA-GAAAAAA
genomic: GGCACCCTTGGGATGGTCATGGTGATCACGGTCACGGAGATCATCACTAGgtaatgtctt ... ttgctgctagGTCTCACTGAACCTTTGAAGATCATGACGAAAAAA
EST: gi|124768710|gb|EH858840.1|EH858840
EST:     GGCACCCTTGGGATGGTCATGGTGATCACGGTCACGGAGATCATCACTAG                         GTCTCACTGAACCTTTGAAGATCATGACGAAAAAAGGAT
genomic: GGCACCCTTGGGATGGTCATGGTGATCACGGTCACGGAGATCATCACTAGgtaatgtctt ... ttgctgctagGTCTCACTGAACCTTTGAAGATCATGACGAAAAAAGGAT
EST: gi|116480564|gb|EG523156.1|EG523156
EST:     GGCACCCTTGGGATGGTCATGGTGATCACGGTCACGGAGATCATCACTAG                         GTCTCACTGAACCTTTGAAGATCATGACGAAAAAAGGATCGTCTCTTGNNN
genomic: GGCACCCTTGGGATGGTCATGGTGATCACGGTCACGGAGATCATCACTAGgtaatgtctt ... ttgctgctagGTCTCACTGAACCTTTGAAGATCATGACGAAAAAAGGATCGTCTCTTGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tataagcattgctcaaactacttgacactaatctggttttgggttttgctgctagGTCTCACTGAACCTTTGAAGATCATGACGAAAAAAGGATCGTCTCTTGTTTTTTTCTTAATTTTCAGCTTCATATGTCGAAATAAAGAGAACTGTGAAGA
                         cactaat  putative branch site (score: 2)
                                           ttttgct  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgatgatttgtagttatcctcgagttcacctttcatgtaaccatataagcattgctcaaactacttgacactaatctggttttgggttttgctgctagGTCTCACTGAACCTTTGAAGATCATGACGAAAAAAGGATCGTCTCTTGTTTTTTTCTTAATTTTCAGCTTCATATGTCGAAATAAAGAGAACTGTGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - gatttgt
- - - - - - - - - - - - - - - - - - - - aaccata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaacta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggttttg