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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccactttattacctacttttatcatgtctctcatgcctcgctttttatttgatccacctggtcatgatatcgcagggattggaacttctgtgaagattgatatgtctccgacatgtgtgcactacttacagGGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTCGAACAAGCTTGCAAGAGTGCGGGGATGCCCATCGACATGCGCATACAAC

Basic information

species Physcomitrella patens
transcript PP1S61_17V6.2
intron # 6
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|162270961|gb|FC447367.1|FC447367
EST:     TGCTCGTAACGAAATACAACGGCCCTAAAACAACCATCCTTATTGACCAG                         GGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTC
genomic: TGCTCGTAACGAAATACAACGGCCCTAAAACAACCATCCTTATTGACCAGgtccacttta ... ctacttacagGGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTC
EST: gi|7067447|gb|AW497302.1|AW497302
EST:     TGCTCGTAACGAAATACAACGGCCCTAAAACAACCATCCTTATTGACCAG                         GGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTC
genomic: TGCTCGTAACGAAATACAACGGCCCTAAAACAACCATCCTTATTGACCAGgtccacttta ... ctacttacagGGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTC
EST: gi|208364085|gb|DC943397.1|DC943397
EST:     TGCTCGTAACGAAATACAACGGCCCTAAAACAACCATCCTTATTGACCAG                         GGTGACGCANATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGA
genomic: TGCTCGTAACGAAATACAACGGCCCTAAAACAACCATCCTTATTGACCAGgtccacttta ... ctacttacagGGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGA
EST: gi|208380226|gb|DC919062.1|DC919062
EST:     TGCTCGTAACGAAATACAACGGCCCTAAAACAACCATCCTTATTGACCAG                         GGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTC
genomic: TGCTCGTAACGAAATACAACGGCCCTAAAACAACCATCCTTATTGACCAGgtccacttta ... ctacttacagGGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTC
EST: gi|208381483|gb|DC919485.1|DC919485
EST:     TGCTCGTAACGAAATACAACGGCCCTAAAACAACCATCCTTATTGACCAG                         GGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTC
genomic: TGCTCGTAACGAAATACAACGGCCCTAAAACAACCATCCTTATTGACCAGgtccacttta ... ctacttacagGGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTC
EST: gi|67727505|gb|BJ977764.1|BJ977764
EST:     TGCTCGTAACGAAATACAACGGCCCTAAAACAACCATCCTTATTGACCAG                         GGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTC
genomic: TGCTCGTAACGAAATACAACGGCCCTAAAACAACCATCCTTATTGACCAGgtccacttta ... ctacttacagGGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTC
EST: gi|208348165|gb|DC920956.1|DC920956
EST:     TGCTCGTAACGAAATACAACGGCCCTAAAACAACCATCCTTATTGACCAG                         GGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTC
genomic: TGCTCGTAACGAAATACAACGGCCCTAAAACAACCATCCTTATTGACCAGgtccacttta ... ctacttacagGGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTC
EST: gi|208396633|gb|DC924301.1|DC924301
EST:     TGCTCGTAACGAAATACAACGGCCCTAAAACAACCATCCTTATTGACCAG                         GGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTC
genomic: TGCTCGTAACGAAATACAACGGCCCTAAAACAACCATCCTTATTGACCAGgtccacttta ... ctacttacagGGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTC
EST: gi|37822595|gb|BJ580661.1|BJ580661
EST:     TGCTCGTAACGAAATACAACGGCCCTAAAACAACCATCCTTATTGACCAG                         GGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTC
genomic: TGCTCGTAACGAAATACAACGGCCCTAAAACAACCATCCTTATTGACCAGgtccacttta ... ctacttacagGGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTC
EST: gi|162192828|gb|FC370160.1|FC370160
EST:     TGCTCGTAACGAAATACAACGGCCCTAAAACAACCATCCTTATTGACCAG                         GGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTC
genomic: TGCTCGTAACGAAATACAACGGCCCTAAAACAACCATCCTTATTGACCAGgtccacttta ... ctacttacagGGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTC
EST: gi|162261130|gb|FC437485.1|FC437485
EST:     TGCTCGTAACGAAATACAACGGCCCTAAAACAACCATCCTTATTGACCAG                         GGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTC
genomic: TGCTCGTAACGAAATACAACGGCCCTAAAACAACCATCCTTATTGACCAGgtccacttta ... ctacttacagGGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTC
EST: gi|162267024|gb|FC443073.1|FC443073
EST:     TGCTCGTAACGAAATACAACGGCCCTAAAACAACCATCCTTATTGACCAG                         GGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTC
genomic: TGCTCGTAACGAAATACAACGGCCCTAAAACAACCATCCTTATTGACCAGgtccacttta ... ctacttacagGGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTC
EST: gi|67694518|gb|BJ954751.1|BJ954751
EST:     TGCTCGTAACGAAATACAACGGCCCTAAAACAACCATCCTTATTGACCAG                         GGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTC
genomic: TGCTCGTAACGAAATACAACGGCCCTAAAACAACCATCCTTATTGACCAGgtccacttta ... ctacttacagGGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTC
EST: gi|37846788|gb|BJ604796.1|BJ604796
EST:     TGCTCGTAACGAAATACAACGGCCCTAAAACAACCATCCTTATTGACCAG                         GGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTC
genomic: TGCTCGTAACGAAATACAACGGCCCTAAAACAACCATCCTTATTGACCAGgtccacttta ... ctacttacagGGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTC
EST: gi|37852990|gb|BJ610998.1|BJ610998
EST:     TGCTCGTAACGAAATACAACGGCCCTAAAACAACCATCCTTATTGACCAG                         GGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTC
genomic: TGCTCGTAACGAAATACAACGGCCCTAAAACAACCATCCTTATTGACCAGgtccacttta ... ctacttacagGGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTC
EST: gi|208371948|gb|DC948351.1|DC948351
EST:     TGCTCGTAACGAAGTACAACGGCCCTAAAACAACCATCCTTATTGACCAG                         GGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTC
genomic: TGCTCGTAACGAAATACAACGGCCCTAAAACAACCATCCTTATTGACCAGgtccacttta ... ctacttacagGGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTC
EST: gi|208385518|gb|DC953109.1|DC953109
EST:     TGCTCGTAACGAAATACAACGGCCCTAAAACAACCATCCTTATTGACCAG                         GGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTC
genomic: TGCTCGTAACGAAATACAACGGCCCTAAAACAACCATCCTTATTGACCAGgtccacttta ... ctacttacagGGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTC

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: 33 (upstream exon), 35 (downstream exon)
Score: 21

TGGATACTTGGGAGCGGAGAAGTCAGCATGGGAGGAATATGACGCTACTTTGCTCGTAACGAAATACAACGGCCCTAAAACAACCATCCTTATTGACCAGgtccacttta ... ctacttacagGGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTCGAACAAGCTTGCAAGAGTGCGGGGATGCCCATCGACATGCGCATACAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattggaacttctgtgaagattgatatgtctccgacatgtgtgcactacttacagGGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTCGAACAAGCTTGCAAGAGTGCGGGGATGCCCATCGACATGCGCATACAAC
                  gattgat  putative branch site (score: 21)
                   attgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccactttattacctacttttatcatgtctctcatgcctcgctttttatttgatccacctggtcatgatatcgcagggattggaacttctgtgaagattgatatgtctccgacatgtgtgcactacttacagGGTGACGCAGATAAGTTCTACAAAGAGAATCAGCTCCTGCCAGAGAATTTCGAACAAGCTTGCAAGAGTGCGGGGATGCCCATCGACATGCGCATACAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA