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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtcaccacttctgctgtacaagatctaagcgtaatgcatgtgtcaagttcaatcagatgcttaaatttctcttttcgtacctctacgcactgaccatgaggcaacgcatcgaattgataagcattctattttttttgaatatatgtgaatgtcaatatgtgatcagGTTGATGGAGGGCTGATTTCCCCAGACGCTTGCATAAAACTTGAAATATCTTCCAAGGGCAGCCCTCCGACTGCTTCAACATTCGGTGCGAAGAAGCGAA

Basic information

species Physcomitrella patens
transcript PP1S48_101V6.2
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|162232026|gb|FC409100.1|FC409100
EST:     CTGGGGAACTCAGTGAAGGCAAAGATGTAAACTCTGGCATCTGTCACATG                         GTTGATGGAGGGCTGATTTCCCCAGACGCTTGCATAAAACTTGAAATATCT
genomic: CTGGGGAACTCAGTGAAGGCAAAGATGTAAACTCTGGCATCTGTCACATGgtcagtcacc ... atgtgatcagGTTGATGGAGGGCTGATTTCCCCAGACGCTTGCATAAAACTTGAAATATCT
EST: gi|208379608|gb|DC927105.1|DC927105
EST:     CTGGGGAACTCAGTGAAGGCAAAGATGTAAACTCTGGCATCTGTCACATG                         GTTGATGGAGGGCTGATTTCCCCAGACGCTTGCATAAAACTTGAAATATCT
genomic: CTGGGGAACTCAGTGAAGGCAAAGATGTAAACTCTGGCATCTGTCACATGgtcagtcacc ... atgtgatcagGTTGATGGAGGGCTGATTTCCCCAGACGCTTGCATAAAACTTGAAATATCT
EST: gi|208345923|gb|DC921094.1|DC921094
EST:     CTGGGGAACTCAGTGAAGGCAAAGATGTAAACTCTGGCATCTGTCACATG                         GTTGATGGAGGGCTGATTTCCCCAGACGCTTGCATAAAACTTGAAATATCT
genomic: CTGGGGAACTCAGTGAAGGCAAAGATGTAAACTCTGGCATCTGTCACATGgtcagtcacc ... atgtgatcagGTTGATGGAGGGCTGATTTCCCCAGACGCTTGCATAAAACTTGAAATATCT
EST: gi|208361173|gb|DC954279.1|DC954279
EST:     CTGGGGAACTCAGTGAAGGCAAAGATGTAAACTCTGGCATCTGTCACATG                         GTTGATGGAGGGCTGATTTCCCCAGACGCTTGCATAAAACTTGAAATATCT
genomic: CTGGGGAACTCAGTGAAGGCAAAGATGTAAACTCTGGCATCTGTCACATGgtcagtcacc ... atgtgatcagGTTGATGGAGGGCTGATTTCCCCAGACGCTTGCATAAAACTTGAAATATCT
EST: gi|162177488|gb|FC353749.1|FC353749
EST:     CTGGGGAACTCAGTGAAGGCAAAGATGTAAACTCTGGCATCTGTCACATG                         GTTGATGGAGGGCTGATTTCCCCAGACGCTTGCATAAAACTTGAAATATCT
genomic: CTGGGGAACTCAGTGAAGGCAAAGATGTAAACTCTGGCATCTGTCACATGgtcagtcacc ... atgtgatcagGTTGATGGAGGGCTGATTTCCCCAGACGCTTGCATAAAACTTGAAATATCT
EST: gi|37851284|gb|BJ609292.1|BJ609292
EST:     CTGGGGAACTCAGTGAAGGCAAAGATGTAAACTCTGGCATCTGTCACATG                         GTTGATGGAGGGCTGATTTCCCCAGACGCTTGCATAAAACTTGAAATATCT
genomic: CTGGGGAACTCAGTGAAGGCAAAGATGTAAACTCTGGCATCTGTCACATGgtcagtcacc ... atgtgatcagGTTGATGGAGGGCTGATTTCCCCAGACGCTTGCATAAAACTTGAAATATCT
EST: gi|162273040|gb|FC449171.1|FC449171
EST:     CTGGGGAACTCAGTGAAGGCAAAGATGTAAACTCTGGCATCTGTCACATG                         GTTGATGGAGGGCTGATTTCCCCAGACGCTTGCATAAAACTTGAAATATCT
genomic: CTGGGGAACTCAGTGAAGGCAAAGATGTAAACTCTGGCATCTGTCACATGgtcagtcacc ... atgtgatcagGTTGATGGAGGGCTGATTTCCCCAGACGCTTGCATAAAACTTGAAATATCT
EST: gi|162273041|gb|FC449172.1|FC449172
EST:     CTGGGGAACTCAGTGAAGGCAAAGATGTAAACTCTGGCATCTGTCACATG                         GTTGATGGAGGGCTGATTTCCCCAGACGCTTGCATAAAACTTGAAATATCT
genomic: CTGGGGAACTCAGTGAAGGCAAAGATGTAAACTCTGGCATCTGTCACATGgtcagtcacc ... atgtgatcagGTTGATGGAGGGCTGATTTCCCCAGACGCTTGCATAAAACTTGAAATATCT
EST: gi|162280175|gb|FC455984.1|FC455984
EST:     CTGGGGAACTCAGTGAAGGCAAAGATGTAAACTCTGGCATCTGTCACATG                         GTTGATGGAGGGCTGATTTCCCCAGACGCTTGCATAAAACTTGAAATATCT
genomic: CTGGGGAACTCAGTGAAGGCAAAGATGTAAACTCTGGCATCTGTCACATGgtcagtcacc ... atgtgatcagGTTGATGGAGGGCTGATTTCCCCAGACGCTTGCATAAAACTTGAAATATCT
EST: gi|18336887|gb|BJ168910.1|BJ168910
EST:     CTGGGGAACTCAGTGAAGGCAAAGATGTAAACTCTGGCATCTGTCACATG                         GTTGATGGAGGGCTGATTTCCCCAGACGCTTGCATAAAACTTGAAATATCT
genomic: CTGGGGAACTCAGTGAAGGCAAAGATGTAAACTCTGGCATCTGTCACATGgtcagtcacc ... atgtgatcagGTTGATGGAGGGCTGATTTCCCCAGACGCTTGCATAAAACTTGAAATATCT
EST: gi|162188134|gb|FC363900.1|FC363900
EST:     CTGGGGAACTCAGTGAAGGCAAAGATGTAAACTCTGGCATCTGTCACATG                         GTTGATGGAGGGCTGATTTCCCCAGACGCTTGCATAAAACTTGAAATATCT
genomic: CTGGGGAACTCAGTGAAGGCAAAGATGTAAACTCTGGCATCTGTCACATGgtcagtcacc ... atgtgatcagGTTGATGGAGGGCTGATTTCCCCAGACGCTTGCATAAAACTTGAAATATCT
EST: gi|162182407|gb|FC358006.1|FC358006
EST:     CTGGGGAACTCAGTGAAGGCAAAGATGTAAACTCTGGCATCTGTCACATG                         GTTGATGGAGGGCTGATTTCCCCAGACGCTTGCATAAAACTTGAAATATCT
genomic: CTGGGGAACTCAGTGAAGGCAAAGATGTAAACTCTGGCATCTGTCACATGgtcagtcacc ... atgtgatcagGTTGATGGAGGGCTGATTTCCCCAGACGCTTGCATAAAACTTGAAATATCT
EST: gi|208382944|gb|DC927694.1|DC927694
EST:     CTGGGGAACTCAGTGAAGGCAAAGATGTAAACTCTGGCATCTGTCACATG                         GTTGATGGAGGGCTGATTTCCCCAGACGCTTGCATAAAACTTGAAATATCT
genomic: CTGGGGAACTCAGTGAAGGCAAAGATGTAAACTCTGGCATCTGTCACATGgtcagtcacc ... atgtgatcagGTTGATGGAGGGCTGATTTCCCCAGACGCTTGCATAAAACTTGAAATATCT
EST: gi|162177489|gb|FC353750.1|FC353750
EST:     CTGGGGAACTCAGTGAAGGCAAAGATGTAAACTCTGGCATCTGTCACATG                         GTTGATGGAGGGCTGATTTCCCCAGACGCTTGCATAAAACTTGAAATATCT
genomic: CTGGGGAACTCAGTGAAGGCAAAGATGTAAACTCTGGCATCTGTCACATGgtcagtcacc ... atgtgatcagGTTGATGGAGGGCTGATTTCCCCAGACGCTTGCATAAAACTTGAAATATCT
EST: gi|162155773|gb|FC331802.1|FC331802
EST:     CTGGGGAACTCAGTGAAGGCAAAGATGTAAACTCTGGCATCTGTCACATG                         GTTGATGGAGGGCTGATTTCCCCAGACGCTTGCATAAAACTTGAAATATCT
genomic: CTGGGGAACTCAGTGAAGGCAAAGATGTAAACTCTGGCATCTGTCACATGgtcagtcacc ... atgtgatcagGTTGATGGAGGGCTGATTTCCCCAGACGCTTGCATAAAACTTGAAATATCT
EST: gi|37847539|gb|BJ605547.1|BJ605547
EST:     CTGGGGAACTCAGTGAAGGCAAAGATGTAAACTCTGGCATCTGTCACATG                         GTTGATGGAGGGCTGATTTCCCCAGACGCTTGCATAAAACTTGAAATATCT
genomic: CTGGGGAACTCAGTGAAGGCAAAGATGTAAACTCTGGCATCTGTCACATGgtcagtcacc ... atgtgatcagGTTGATGGAGGGCTGATTTCCCCAGACGCTTGCATAAAACTTGAAATATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattgataagcattctattttttttgaatatatgtgaatgtcaatatgtgatcagGTTGATGGAGGGCTGATTTCCCCAGACGCTTGCATAAAACTTGAAATATCTTCCAAGGGCAGCCCTCCGACTGCTTCAACATTCGGTGCGAAGAAGCGAA
 aattgat  putative branch site (score: 4)
     ataagcattctatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtcaccacttctgctgtacaagatctaagcgtaatgcatgtgtcaagttcaatcagatgcttaaatttctcttttcgtacctctacgcactgaccatgaggcaacgcatcgaattgataagcattctattttttttgaatatatgtgaatgtcaatatgtgatcagGTTGATGGAGGGCTGATTTCCCCAGACGCTTGCATAAAACTTGAAATATCTTCCAAGGGCAGCCCTCCGACTGCTTCAACATTCGGTGCGAAGAAGCGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC