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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caagaatttacgaggttacaacttaaggattgggttcagataactaataagctgttcaatttcgagtggagtatactaacgatgaccgaaatgaatgcagGGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTCTAGGCTCAGGTGGCACTGATTGCTTAGTTCTTAAGAGGTCGGACCCAGG

Basic information

species Physcomitrella patens
transcript PP1S9_381V6.1
intron # 11
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|162167394|gb|FC343097.1|FC343097
EST:     GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAG                         GGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
genomic: GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAGgtaagatagt ... atgaatgcagGGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
EST: gi|162221984|gb|FC398252.1|FC398252
EST:     CTACTTTTCATAATCGGGTTGCTAAGTTCACAG                         GGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
genomic: CTACTTTTCATAATCGGGTTGCTAAGTTCACAGgtaagatagt ... atgaatgcagGGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
EST: gi|162157673|gb|FC332995.1|FC332995
EST:     GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAG                         GGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
genomic: GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAGgtaagatagt ... atgaatgcagGGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
EST: gi|162249090|gb|FC420367.1|FC420367
EST:     GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAG                         GGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
genomic: GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAGgtaagatagt ... atgaatgcagGGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
EST: gi|162188292|gb|FC364786.1|FC364786
EST:     GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAG                         GGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
genomic: GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAGgtaagatagt ... atgaatgcagGGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
EST: gi|37840881|gb|BJ598889.1|BJ598889
EST:     GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAG                         GGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
genomic: GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAGgtaagatagt ... atgaatgcagGGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
EST: gi|162163548|gb|FC339458.1|FC339458
EST:     GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAG                         GGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
genomic: GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAGgtaagatagt ... atgaatgcagGGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
EST: gi|162156501|gb|FC332109.1|FC332109
EST:     GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAG                         GGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
genomic: GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAGgtaagatagt ... atgaatgcagGGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
EST: gi|19789265|gb|BQ041203.1|BQ041203
EST:     GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAG                         GGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
genomic: GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAGgtaagatagt ... atgaatgcagGGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
EST: gi|162169364|gb|FC346254.1|FC346254
EST:     GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAG                         GGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
genomic: GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAGgtaagatagt ... atgaatgcagGGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
EST: gi|162249089|gb|FC420366.1|FC420366
EST:     GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAG                         GGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
genomic: GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAGgtaagatagt ... atgaatgcagGGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
EST: gi|162185270|gb|FC361780.1|FC361780
EST:     GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAG                         GGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
genomic: GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAGgtaagatagt ... atgaatgcagGGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
EST: gi|162257436|gb|FC433310.1|FC433310
EST:     GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAG                         GGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
genomic: GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAGgtaagatagt ... atgaatgcagGGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
EST: gi|162221001|gb|FC398253.1|FC398253
EST:     CTACTTTTCATAATCGGGTTGCTAAGTT-ACAG                         GGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
genomic: CTACTTTTCATAATCGGGTTGCTAAGTTCACAGgtaagatagt ... atgaatgcagGGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
EST: gi|162181563|gb|FC357865.1|FC357865
EST:     GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAG                         GGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
genomic: GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAGgtaagatagt ... atgaatgcagGGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
EST: gi|162181564|gb|FC357866.1|FC357866
EST:     GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAG                         GGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
genomic: GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAGgtaagatagt ... atgaatgcagGGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
EST: gi|162247767|gb|FC421735.1|FC421735
EST:     GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAG                         GGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
genomic: GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAGgtaagatagt ... atgaatgcagGGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
EST: gi|162245446|gb|FC421348.1|FC421348
EST:     GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAG                         GGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
genomic: GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAGgtaagatagt ... atgaatgcagGGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
EST: gi|67579201|gb|BJ951346.1|BJ951346
EST:     GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAG                         GGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
genomic: GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAGgtaagatagt ... atgaatgcagGGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
EST: gi|162188291|gb|FC364785.1|FC364785
EST:     GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAG                         GGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC
genomic: GGTAATCCTACTTTTCATAATCGGGTTGCTAAGTTCACAGgtaagatagt ... atgaatgcagGGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aataagctgttcaatttcgagtggagtatactaacgatgaccgaaatgaatgcagGGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTCTAGGCTCAGGTGGCACTGATTGCTTAGTTCTTAAGAGGTCGGACCCAGG
                            tactaac  putative branch site (score: 0)
         ttcaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caagaatttacgaggttacaacttaaggattgggttcagataactaataagctgttcaatttcgagtggagtatactaacgatgaccgaaatgaatgcagGGGCAGTGGAAGTCCTGCAAGCCGTTGGCTTCACTGATGGAGGGAGTCCTCTAGGCTCAGGTGGCACTGATTGCTTAGTTCTTAAGAGGTCGGACCCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG