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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgattaataccctttccttcgcctgttgtcattttggtgaaatagcattagggttttcgtggatctttttagactgacatctgttgtctgtttcgttggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTACGTTGCAGAGGAAGCGCCGCAGAATCGCTATCAAGAAAGAACGAGTTGC

Basic information

species Physcomitrella patens
transcript PP1S311_33V6.1
intron # 5
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|208372979|gb|DC940610.1|DC940610
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
EST: gi|18339894|gb|BJ171921.1|BJ171921
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
EST: gi|67698486|gb|BJ958719.1|BJ958719
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
EST: gi|162279665|gb|FC455898.1|FC455898
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
EST: gi|18340116|gb|BJ172144.1|BJ172144
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
EST: gi|208394580|gb|DC953619.1|DC953619
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
EST: gi|162220470|gb|FC396007.1|FC396007
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
EST: gi|162236276|gb|FC411200.1|FC411200
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
EST: gi|37831873|gb|BJ589885.1|BJ589885
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
EST: gi|162245101|gb|FC422927.1|FC422927
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
EST: gi|67575041|gb|BJ947865.1|BJ947865
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
EST: gi|37844063|gb|BJ602071.1|BJ602071
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
EST: gi|208359876|gb|DC934877.1|DC934877
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
EST: gi|208396632|gb|DC924300.1|DC924300
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
EST: gi|208377690|gb|DC932226.1|DC932226
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
EST: gi|162239498|gb|FC417963.1|FC417963
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCANAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
EST: gi|162220469|gb|FC396006.1|FC396006
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
EST: gi|15728503|gb|BI740820.1|BI740820
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
EST: gi|162271070|gb|FC446097.1|FC446097
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
EST: gi|37844985|gb|BJ602993.1|BJ602993
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
EST: gi|162271071|gb|FC446098.1|FC446098
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
EST: gi|18355513|gb|BJ187572.1|BJ187572
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCAAAGCTCCCAAA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAA
EST: gi|15730197|gb|BI741728.1|BI741728
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
EST: gi|162235066|gb|FC411201.1|FC411201
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
EST: gi|7207711|gb|AW561708.1|AW561708
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
EST: gi|37832457|gb|BJ590469.1|BJ590469
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
EST: gi|162206668|gb|FC382426.1|FC382426
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
EST: gi|67694668|gb|BJ954901.1|BJ954901
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
EST: gi|208386094|gb|DC949005.1|DC949005
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
EST: gi|67698381|gb|BJ958614.1|BJ958614
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
EST: gi|37821180|gb|BJ579246.1|BJ579246
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
EST: gi|37843893|gb|BJ601901.1|BJ601901
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
EST: gi|162279666|gb|FC455899.1|FC455899
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
EST: gi|67574954|gb|BJ947778.1|BJ947778
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
EST: gi|162239497|gb|FC417962.1|FC417962
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
EST: gi|162245074|gb|FC422926.1|FC422926
EST:     CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCG                         GAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA
genomic: CGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTA

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), 26 (downstream exon)
Score: 14

AAGAGGGCTACCAAGATTCGGAAGCTCTTTAACCTCACCAAGGAGGATGACGTGCGGAAATATGTGAACACTTACCGCCGCTCATTTGTGTCAGCGACCGgtatttgatt ... ggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTACGTTGCAGAGGAAGCGCCGCAGAATCGCTATCAAGAAAGAACGAGTTGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttcgtggatctttttagactgacatctgttgtctgtttcgttggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTACGTTGCAGAGGAAGCGCCGCAGAATCGCTATCAAGAAAGAACGAGTTGC
                   gactgac  putative branch site (score: 14)
                                               tttttc  putative PPT
          atcttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttgattaataccctttccttcgcctgttgtcattttggtgaaatagcattagggttttcgtggatctttttagactgacatctgttgtctgtttcgttggtttttcagGAAAGAAACGCAGCAAAGCTCCCAAAATTCAGAGACTAGTGACACCTCTTACGTTGCAGAGGAAGCGCCGCAGAATCGCTATCAAGAAAGAACGAGTTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC