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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctacgtggtattgtgcattaattaaaattttggtaaagtgggtactcgtgatttaatttggcccgctaagtctgaacatttgtgtatatgataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGCTATCGTGGAGCGTGCAGCCCAGTTGAACATTGCATTGACCAACGGAAGC

Basic information

species Physcomitrella patens
transcript PP1S98_19V6.1
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|18333387|gb|BJ165401.1|BJ165401
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|162232234|gb|FC408070.1|FC408070
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|18329113|gb|BJ161119.1|BJ161119
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|18359014|gb|BJ191074.1|BJ191074
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|18349181|gb|BJ181230.1|BJ181230
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|18332553|gb|BJ164566.1|BJ164566
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|208381398|gb|DC927834.1|DC927834
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|162217463|gb|FC393139.1|FC393139
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|67697693|gb|BJ957926.1|BJ957926
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|18336143|gb|BJ168165.1|BJ168165
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|162233982|gb|FC410300.1|FC410300
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|7648418|gb|AW739401.1|AW739401
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|162205354|gb|FC382063.1|FC382063
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|18349959|gb|BJ182010.1|BJ182010
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|162279864|gb|FC455148.1|FC455148
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|67696979|gb|BJ957212.1|BJ957212
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|67726861|gb|BJ977120.1|BJ977120
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|208353930|gb|DC914084.1|DC914084
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|162276296|gb|FC452104.1|FC452104
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|162230913|gb|FC406752.1|FC406752
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|18332458|gb|BJ164471.1|BJ164471
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|6102150|gb|AW126620.1|AW126620
EST:     TTTTTGGTTCACAATGTGAGGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATTAATGTATCCACCCTGAAGAGGAAG-
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACAT-AATGTATCCACCCTGAAGAGGAAGG
EST: gi|67574284|gb|BJ947108.1|BJ947108
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|37852413|gb|BJ610421.1|BJ610421
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|162279251|gb|FC455798.1|FC455798
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|18341795|gb|BJ173830.1|BJ173830
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|37828930|gb|BJ586942.1|BJ586942
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|67718387|gb|BJ968646.1|BJ968646
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|162227277|gb|FC402868.1|FC402868
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|162212773|gb|FC388573.1|FC388573
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|162232233|gb|FC408069.1|FC408069
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|18327908|gb|BJ159912.1|BJ159912
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|18325433|gb|BJ157429.1|BJ157429
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|37820943|gb|BJ579009.1|BJ579009
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|162205049|gb|FC381758.1|FC381758
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|18341873|gb|BJ173908.1|BJ173908
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|162279250|gb|FC455797.1|FC455797
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
EST: gi|67573594|gb|BJ946418.1|BJ946418
EST:     TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAG                         AAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC
genomic: TTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGC

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: 77

ACGGCTCAAACAAGAAGACGAGACATGTGCTCCCAAGTGGATTTGTGAAGTTTTTGGTTCACAATGTGAAGGACGTGGAGCTTCTGTTGATGCACAACAGgtaatcagtt ... gataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGCTATCGTGGAGCGTGCAGCCCAGTTGAACATTGCATTGACCAACGGAAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcgtgatttaatttggcccgctaagtctgaacatttgtgtatatgataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGCTATCGTGGAGCGTGCAGCCCAGTTGAACATTGCATTGACCAACGGAAGC
      atttaat  putative branch site (score: 77)
                                        tatatgataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctacgtggtattgtgcattaattaaaattttggtaaagtgggtactcgtgatttaatttggcccgctaagtctgaacatttgtgtatatgataatgcagAAAATACAGCGCTGAAATCGCACATAATGTATCCACCCTGAAGAGGAAGGCTATCGTGGAGCGTGCAGCCCAGTTGAACATTGCATTGACCAACGGAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgaaca