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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acacatcttcaactcagaggttttatactgagggtttagtcgagtgtcagtttgatttcgttgcaaagtgtcccattaactgttattttcttttctgcagAATACCTTATTTCTCAACAACATCTTCAGATCAGAGCCATGTCGGGAGATCTAGCGGTTGTCGCGAAGGACAAGGAAGCTAGTTCCAAAGGCACCATGCA

Basic information

species Physcomitrella patens
transcript PP1S407_7V6.3
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|67717425|gb|BJ967684.1|BJ967684
EST:     GTGGGGAGTGTTCCGGCAGCGACTGAGACGTCTAGGTTTTGGTGCAAATG                         AATACCTTATTTCTCAACAACATCTTCAGATCAGAGCCATGTCGGGAGATC
genomic: GTGGGGAGTGTTCCGGCAGCGACTGAGACGTCTAGGTTTTGGTGCAAATGgttagtgcaa ... ttttctgcagAATACCTTATTTCTCAACAACATCTTCAGATCAGAGCCATGTCGGGAGATC
EST: gi|18327268|gb|BJ159270.1|BJ159270
EST:     GTGGGGAGTGTTCCGGCAGCGACTGAGACGTCTAGGTTTTGGTGCAAATG                         AATACCTTATTTCTCAACAACATCTTCAGATCAGAGCCATGTCGGGAGATC
genomic: GTGGGGAGTGTTCCGGCAGCGACTGAGACGTCTAGGTTTTGGTGCAAATGgttagtgcaa ... ttttctgcagAATACCTTATTTCTCAACAACATCTTCAGATCAGAGCCATGTCGGGAGATC
EST: gi|100388601|gb|BY970749.1|BY970749
EST:     GTGGGGAGTGTTCCGGCAGCGACTGAGACGTCTAGGTTTTGGTGCAAAGG                         AATACCTTATTTCTCAACAACATCTTCAGATCAGAGCCATGTCGGGAGATC
genomic: GTGGGGAGTGTTCCGGCAGCGACTGAGACGTCTAGGTTTTGGTGCAAATGgttagtgcaa ... ttttctgcagAATACCTTATTTCTCAACAACATCTTCAGATCAGAGCCATGTCGGGAGATC
EST: gi|162161524|gb|FC338731.1|FC338731
EST:     GTGGGGAGTGTTCCGGCAGCGACTGAGACGTCTAGGTTTTGGTGCAAATG                         AATACCTTATTTCTCAACAACATCTTCAGATCAGAGCCATGTCGGGAGATC
genomic: GTGGGGAGTGTTCCGGCAGCGACTGAGACGTCTAGGTTTTGGTGCAAATGgttagtgcaa ... ttttctgcagAATACCTTATTTCTCAACAACATCTTCAGATCAGAGCCATGTCGGGAGATC
EST: gi|18368288|gb|BJ200373.1|BJ200373
EST:     GTGGGGAGTGTTCCGGCAGCGACTGAGACGTCTAGGTTTTGGTGCAAATG                         AATACCTTATTTCTCAACAACATCTTCAGATCAGAGCCATGTCGGGAGATC
genomic: GTGGGGAGTGTTCCGGCAGCGACTGAGACGTCTAGGTTTTGGTGCAAATGgttagtgcaa ... ttttctgcagAATACCTTATTTCTCAACAACATCTTCAGATCAGAGCCATGTCGGGAGATC
EST: gi|18364681|gb|BJ196754.1|BJ196754
EST:     GTGGGGAGTGTTCCGGCAGCGACTGAGACGTCTAGGTTTTGGTGCAAATG                         AATACCTTATTTCTCAACAACATCTTCAGATCAGAGCCATGTCGGGAGATC
genomic: GTGGGGAGTGTTCCGGCAGCGACTGAGACGTCTAGGTTTTGGTGCAAATGgttagtgcaa ... ttttctgcagAATACCTTATTTCTCAACAACATCTTCAGATCAGAGCCATGTCGGGAGATC
EST: gi|18369465|gb|BJ201552.1|BJ201552
EST:     GTGGGGAGTGTTCCGGCAGCGACTGAGACGTCTAGGTTTTGGTGCAAATG                         AATACCTTATTTCTCAACAACATCTTCAGATCAGAGCCATGTCGGGAGATC
genomic: GTGGGGAGTGTTCCGGCAGCGACTGAGACGTCTAGGTTTTGGTGCAAATGgttagtgcaa ... ttttctgcagAATACCTTATTTCTCAACAACATCTTCAGATCAGAGCCATGTCGGGAGATC
EST: gi|18325312|gb|BJ157308.1|BJ157308
EST:     GTGGGGAGTGTTCCGGCAGCGACTGAGACGTCTAGGTTTTGGTGCAAATG                         AATACCTTATTTCTCAACAACATCTTCAGATCAGAGCCATGTCGGGAGATC
genomic: GTGGGGAGTGTTCCGGCAGCGACTGAGACGTCTAGGTTTTGGTGCAAATGgttagtgcaa ... ttttctgcagAATACCTTATTTCTCAACAACATCTTCAGATCAGAGCCATGTCGGGAGATC
EST: gi|67574848|gb|BJ947672.1|BJ947672
EST:     GTGGGGAGTGTTCCGGCAGCGACTGAGACGTCTAGGTTTTGGTGCAAATG                         AATACCTTATTTCTCAACAACATCTTCAGATCAGAGCCATGTCGGGAGATC
genomic: GTGGGGAGTGTTCCGGCAGCGACTGAGACGTCTAGGTTTTGGTGCAAATGgttagtgcaa ... ttttctgcagAATACCTTATTTCTCAACAACATCTTCAGATCAGAGCCATGTCGGGAGATC
EST: gi|18367201|gb|BJ199282.1|BJ199282
EST:     GTGGGGAGTGTTCCGGCAGCGACTGAGACGTCTAGGTTTTGGTGCAAATG                         AATACCTTATTTCTCAACAACATCTTCAGATCANAGCCATGTCNGGAGATC
genomic: GTGGGGAGTGTTCCGGCAGCGACTGAGACGTCTAGGTTTTGGTGCAAATGgttagtgcaa ... ttttctgcagAATACCTTATTTCTCAACAACATCTTCAGATCAGAGCCATGTCGGGAGATC
EST: gi|18345047|gb|BJ177088.1|BJ177088
EST:     GTGGGGAGTGTTCCGGCAGCGACTGAGACGTCTAGGTTTTGGTGCAAATG                         AATACCTTATTTCTCAACAACATCTTCAGATCAGAGCCATGTCGGGAGATC
genomic: GTGGGGAGTGTTCCGGCAGCGACTGAGACGTCTAGGTTTTGGTGCAAATGgttagtgcaa ... ttttctgcagAATACCTTATTTCTCAACAACATCTTCAGATCAGAGCCATGTCGGGAGATC
EST: gi|208346695|gb|DC913341.1|DC913341
EST:     GTTTTGGTGCAAATG                         AATACCTTATTTCTCAACAACATCTTCAGATCAGAGCCATGTCGGGAGATC
genomic: GTTTTGGTGCAAATGgttagtgcaa ... ttttctgcagAATACCTTATTTCTCAACAACATCTTCAGATCAGAGCCATGTCGGGAGATC
EST: gi|67577876|gb|BJ950043.1|BJ950043
EST:     GTGGGGAGTGTTCCGGCAGCGACTGAGACGTCTAGGTTTTGGTGCAAATG                         AATACCTTATTTCTCAACAACATCTTCAGATCAGAGCCATGTCGGGAGATC
genomic: GTGGGGAGTGTTCCGGCAGCGACTGAGACGTCTAGGTTTTGGTGCAAATGgttagtgcaa ... ttttctgcagAATACCTTATTTCTCAACAACATCTTCAGATCAGAGCCATGTCGGGAGATC
EST: gi|18351963|gb|BJ184015.1|BJ184015
EST:     GTGGGGAGTGTTCCGGCAGCGACTGAGACGTCTAGGTTTTGGTGCAAATG                         AATACCTTATTTCTCAACAACATCTTCAGATCAGAGCCATGTCGGGAGATC
genomic: GTGGGGAGTGTTCCGGCAGCGACTGAGACGTCTAGGTTTTGGTGCAAATGgttagtgcaa ... ttttctgcagAATACCTTATTTCTCAACAACATCTTCAGATCAGAGCCATGTCGGGAGATC
EST: gi|67712636|gb|BJ966085.1|BJ966085
EST:     GTGGGGAGTGTTCCGGCAGCGACTGAGACGTCTAGGTTTTGGTGCAAATG                         AATACCTTATTTCTCAACAACATCTTCAGATCAGAGCCATGTCGGGAGATC
genomic: GTGGGGAGTGTTCCGGCAGCGACTGAGACGTCTAGGTTTTGGTGCAAATGgttagtgcaa ... ttttctgcagAATACCTTATTTCTCAACAACATCTTCAGATCAGAGCCATGTCGGGAGATC

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: 30 (upstream exon), 35 (downstream exon)
Score: 9

CGTTCATGTTACTGAAAATGGTCTGCGTGCGGAATGCGAGGGCGAGGTCTGTGGGGAGTGTTCCGGCAGCGACTGAGACGTCTAGGTTTTGGTGCAAATGgttagtgcaa ... ttttctgcagAATACCTTATTTCTCAACAACATCTTCAGATCAGAGCCATGTCGGGAGATCTAGCGGTTGTCGCGAAGGACAAGGAAGCTAGTTCCAAAGGCACCATGCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcagtttgatttcgttgcaaagtgtcccattaactgttattttcttttctgcagAATACCTTATTTCTCAACAACATCTTCAGATCAGAGCCATGTCGGGAGATCTAGCGGTTGTCGCGAAGGACAAGGAAGCTAGTTCCAAAGGCACCATGCA
                            cattaac  putative branch site (score: 9)
                                  ctgttattttcttttc  CT-rich tract
                             attaactgttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acacatcttcaactcagaggttttatactgagggtttagtcgagtgtcagtttgatttcgttgcaaagtgtcccattaactgttattttcttttctgcagAATACCTTATTTCTCAACAACATCTTCAGATCAGAGCCATGTCGGGAGATCTAGCGGTTGTCGCGAAGGACAAGGAAGCTAGTTCCAAAGGCACCATGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA