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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatctgtcggcgtacgaccatttatcgttagttttcgattttcttcgcttgttgctgttacgttaatatctcctgtttggttaatattgtcatttctcgcgatttttcgatgatggtatagcatctgaaaccttgtttttggtttgtgcagTCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTGTCAACTATTGCTGAGAAACAATGAAG

Basic information

species Physcomitrella patens
transcript PP1S201_115V6.3
intron # 10
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|37846632|gb|BJ604640.1|BJ604640
EST:     AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGG                         TCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
genomic: AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGGgtaagtatct ... gtttgtgcagTCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
EST: gi|208385376|gb|DC956616.1|DC956616
EST:     AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGG                         TCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
genomic: AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGGgtaagtatct ... gtttgtgcagTCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
EST: gi|22492293|gb|BU052216.1|BU052216
EST:     AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGG                         TCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAA
genomic: AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGGgtaagtatct ... gtttgtgcagTCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAA
EST: gi|37847154|gb|BJ605162.1|BJ605162
EST:     AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGG                         TCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
genomic: AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGGgtaagtatct ... gtttgtgcagTCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
EST: gi|37835612|gb|BJ593624.1|BJ593624
EST:     AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGG                         TCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
genomic: AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGGgtaagtatct ... gtttgtgcagTCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
EST: gi|22132035|gb|BQ826945.1|BQ826945
EST:     AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGG                         TCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
genomic: AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGGgtaagtatct ... gtttgtgcagTCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
EST: gi|37833789|gb|BJ591801.1|BJ591801
EST:     AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGG                         TCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
genomic: AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGGgtaagtatct ... gtttgtgcagTCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
EST: gi|208393949|gb|DC928729.1|DC928729
EST:     AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGG                         TCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
genomic: AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGGgtaagtatct ... gtttgtgcagTCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
EST: gi|37821752|gb|BJ579818.1|BJ579818
EST:     AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGG                         TCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
genomic: AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGGgtaagtatct ... gtttgtgcagTCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
EST: gi|37825580|gb|BJ583646.1|BJ583646
EST:     AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGG                         TCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
genomic: AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGGgtaagtatct ... gtttgtgcagTCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
EST: gi|208397894|gb|DC916649.1|DC916649
EST:     AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGG                         TCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
genomic: AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGGgtaagtatct ... gtttgtgcagTCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
EST: gi|208385667|gb|DC952828.1|DC952828
EST:     AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGG                         TCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
genomic: AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGGgtaagtatct ... gtttgtgcagTCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
EST: gi|208380848|gb|DC923330.1|DC923330
EST:     AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGG                         TCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
genomic: AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGGgtaagtatct ... gtttgtgcagTCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
EST: gi|208356156|gb|DC957316.1|DC957316
EST:     AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGG                         TCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
genomic: AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGGgtaagtatct ... gtttgtgcagTCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
EST: gi|67692042|gb|BJ952275.1|BJ952275
EST:     AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGG                         TCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
genomic: AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGGgtaagtatct ... gtttgtgcagTCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
EST: gi|37853039|gb|BJ611047.1|BJ611047
EST:     AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGG                         TCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
genomic: AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGGgtaagtatct ... gtttgtgcagTCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
EST: gi|208393538|gb|DC949700.1|DC949700
EST:     AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGG                         TCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
genomic: AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGGgtaagtatct ... gtttgtgcagTCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
EST: gi|37845884|gb|BJ603892.1|BJ603892
EST:     AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGG                         TCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
genomic: AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGGgtaagtatct ... gtttgtgcagTCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
EST: gi|67725662|gb|BJ975921.1|BJ975921
EST:     AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGG                         TCCGTCGACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
genomic: AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGGgtaagtatct ... gtttgtgcagTCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
EST: gi|208381758|gb|DC928421.1|DC928421
EST:     AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGG                         TCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
genomic: AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGGgtaagtatct ... gtttgtgcagTCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
EST: gi|37840656|gb|BJ598664.1|BJ598664
EST:     AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGG                         TCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
genomic: AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGGgtaagtatct ... gtttgtgcagTCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
EST: gi|208354258|gb|DC957450.1|DC957450
EST:     AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGG                         TCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
genomic: AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGGgtaagtatct ... gtttgtgcagTCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
EST: gi|67722506|gb|BJ972765.1|BJ972765
EST:     AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGG                         TCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
genomic: AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGGgtaagtatct ... gtttgtgcagTCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
EST: gi|208348693|gb|DC926368.1|DC926368
EST:     AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGG                         TCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG
genomic: AAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGGgtaagtatct ... gtttgtgcagTCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 35 (downstream exon)
Score: 31

GTACGCAAAAGTGTATTTGAAGGCTTTGAAGAGCATCATTGATAAAGGTGAAGGATATGCAAAGAAGGAAGCAGATAGACTCACTCGCATTTTGTCCGGGgtaagtatct ... gtttgtgcagTCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTGTCAACTATTGCTGAGAAACAATGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgcgatttttcgatgatggtatagcatctgaaaccttgtttttggtttgtgcagTCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTGTCAACTATTGCTGAGAAACAATGAAG
                                    ttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatctgtcggcgtacgaccatttatcgttagttttcgattttcttcgcttgttgctgttacgttaatatctcctgtttggttaatattgtcatttctcgcgatttttcgatgatggtatagcatctgaaaccttgtttttggtttgtgcagTCCGTCAACCCAAGCAAGGTGGACGAGTTTATAGTAAAGAAGAACATATTGTCAACTATTGCTGAGAAACAATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC