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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttgtcctgaactaatgagcatgtgccttcattttcgtagagacatgaactcgatgcttttgcctctcattgttcttccttcttaacttggacgatttgcattctggtgctcatgtattgtttaatgtcaatctcagTTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGCCTACTTGCGGCTTGAAGTTCCTTCTGGAGGATGAAGCAGCGAAGGTGGTGG

Basic information

species Physcomitrella patens
transcript PP1S259_126V6.1
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|208384851|gb|DC907464.1|DC907464
EST:     TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAA                         TTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGG
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGG
EST: gi|67718671|gb|BJ968930.1|BJ968930
EST:     TCCCCACCGACTATCGCCATATGGACGGATACNCCGTACACACATTCAAA                         TTGATCAANAAGGAG
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAG
EST: gi|208377750|gb|DC940862.1|DC940862
EST:     TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAA-                         TTGATCA-CAAGNAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGC-T
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGCCT
EST: gi|208374471|gb|DC941200.1|DC941200
EST:     TCCCCACCGACTATCGCCATATGGACGGGTACACCGTACACACATTCAAA                         TNGATCAACAAGGAGGGCAAGG
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAGGGCAAGG
EST: gi|208358178|gb|DC939374.1|DC939374
EST:     TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAA                         TTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGCCT
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGCCT
EST: gi|208364305|gb|DC935576.1|DC935576
EST:     TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAA-                         TTGATCANCAAGGAGGGCAAGNAGACGCTCATCA-GTGGCACTGGAG-CCT
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGCCT
EST: gi|208364257|gb|DC935528.1|DC935528
EST:     TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAN                         TTGATCAACAAGNAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGCCT
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGCCT
EST: gi|208390335|gb|DC929283.1|DC929283
EST:     TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAA                         TTGATCAACAAGGAG
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAG
EST: gi|208372156|gb|DC936934.1|DC936934
EST:     TCCCCACCGACTATCGCCATATGGGCGGATACACCGTACACACATTCAAA                         TTGATCAACAAGGAGGGCANG-AGACGCTCAT
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAGGGCAAGGAGACGCTCAT
EST: gi|208390550|gb|DC937482.1|DC937482
EST:     TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAA                         TTGATCAACAAGGAGGGCA
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAGGGCA
EST: gi|208363794|gb|DC943251.1|DC943251
EST:     TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAA                         TTGATCAACAAGGAGGGCAGGGAGACGCTCATCAAGTGGCACTGGAGGCCT
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGCCT
EST: gi|208357002|gb|DC930032.1|DC930032
EST:     TCCCCACCGACTATCGCCATATGGACGGATACNCCGTACACACATTCAAA                         TTGATCAACAAGGAGGGCAAGGANACNCTCATCAAGTGGCACTGGANGCCT
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGCCT
EST: gi|208353748|gb|DC938773.1|DC938773
EST:     TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAA                         TTGATCAACAAGGAGGGCAAGNAGACGCTCATCAAGTGGCACTGGAGGCCT
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGCCT
EST: gi|208353668|gb|DC929711.1|DC929711
EST:     TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAN                         TNGATCAACAAGGAGGGCAAGGAGACGCTCATCANGTGGCACTGGANGCCT
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGCCT
EST: gi|208371487|gb|DC931838.1|DC931838
EST:     TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAN                         TTGATCAACAAGGAGGGCAAGGAAACGCTCATCAAGTGG
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGG
EST: gi|208374632|gb|DC931971.1|DC931971
EST:     TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAA                         TTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGCCT
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGCCT
EST: gi|208366660|gb|DC931317.1|DC931317
EST:     TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAA                         TTGATCAACAAGGAGGGCAAGNAGACGCTCATCAAGTGGCACTGGAGGCCT
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGCCT
EST: gi|67719593|gb|BJ969852.1|BJ969852
EST:     TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAA                         TTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGCCT
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGCCT
EST: gi|208379536|gb|DC911147.1|DC911147
EST:     TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAA-                         TTGATCAACAAGGAGGGCAAGGAGACGCTCATCANGTGGCACTGGAG-CCT
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGCCT
EST: gi|208369236|gb|DC936051.1|DC936051
EST:     TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAA                         TNGATCAACAAGGAGGGCAAGGA
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAGGGCAAGGA
EST: gi|208377086|gb|DC936818.1|DC936818
EST:     TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAN                         TTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGCCT
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGCCT
EST: gi|208346392|gb|DC905297.1|DC905297
EST:     TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAA                         TTGATCAACAAGGAG
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAG
EST: gi|67720025|gb|BJ970284.1|BJ970284
EST:     TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAA-                         TTGATCAACAA
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAA
EST: gi|67718893|gb|BJ969152.1|BJ969152
EST:     TCCCCACCGACTATCGCCATATGGACGGATACNCCGTACACACATTCNAA                         TTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGNACTGGAGGCCT
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGCCT
EST: gi|208346674|gb|DC913320.1|DC913320
EST:     TCCCCACCGACTATCGCCATATGGACGGATACANCGTACACACATTCNAA                         TTGATCANCAAGGAGGGCAAGNAGACGCTCATCAN-TGGCACTGGA
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGCACTGGA
EST: gi|208353664|gb|DC929707.1|DC929707
EST:     TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAA                         TTGATCAACAAGGAG
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAG
EST: gi|208393315|gb|DC942455.1|DC942455
EST:     TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAA                         TNGATCA-CAAGGAGGGCAAGGAGACG
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAGGGCAAGGAGACG
EST: gi|208387871|gb|DC929215.1|DC929215
EST:     TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAA-                         TTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGCCT
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGCCT
EST: gi|208376966|gb|DC936772.1|DC936772
EST:     TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAA                         TTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGCCT
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGCCT
EST: gi|67719757|gb|BJ970016.1|BJ970016
EST:     TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAA                         TTGATCAACAAGGGAGGGCAAGGAGACGCTCATCAAGTGG
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGG-AGGGCAAGGAGACGCTCATCAAGTGG
EST: gi|208362187|gb|DC935629.1|DC935629
EST:     TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAA                         TTGATCAACAAGGAGGGCAAGGAGACGCTCATCA-GTGGCACTGGAGGCCT
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGCCT
EST: gi|208383981|gb|DC907372.1|DC907372
EST:     TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAA                         TTGATCAACAAGGAGGGC
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAGGGC
EST: gi|208357017|gb|DC942707.1|DC942707
EST:     TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAA                         TTGATCANCAAGNAGGGCAAGGAG
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAGGGCAAGGAG
EST: gi|208375476|gb|DC940502.1|DC940502
EST:     TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAA                         TTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGCCT
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGCCT
EST: gi|208372368|gb|DC936484.1|DC936484
EST:     TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAA                         TTGATCAACAAGGAGGGCAAGGAGACGCTCATCANGTGGCACTGGAGGCCT
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGCCT
EST: gi|208389271|gb|DC933299.1|DC933299
EST:     TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAA                         TTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGCCT
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGCCT
EST: gi|208389909|gb|DC937740.1|DC937740
EST:     TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAA                         TTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGCNT
genomic: TCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGCCT

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: 28 (upstream exon), 34 (downstream exon)
Score: 19

CATCCCCGAGAGCACCCACATGTTCTTCTGGTGGTTGGATGACTGGGGTGTCCCCACCGACTATCGCCATATGGACGGATACACCGTACACACATTCAAAgtacttgtcc ... tcaatctcagTTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGCCTACTTGCGGCTTGAAGTTCCTTCTGGAGGATGAAGCAGCGAAGGTGGTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaacttggacgatttgcattctggtgctcatgtattgtttaatgtcaatctcagTTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGCCTACTTGCGGCTTGAAGTTCCTTCTGGAGGATGAAGCAGCGAAGGTGGTGG
                              atgtattgtttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttgtcctgaactaatgagcatgtgccttcattttcgtagagacatgaactcgatgcttttgcctctcattgttcttccttcttaacttggacgatttgcattctggtgctcatgtattgtttaatgtcaatctcagTTGATCAACAAGGAGGGCAAGGAGACGCTCATCAAGTGGCACTGGAGGCCTACTTGCGGCTTGAAGTTCCTTCTGGAGGATGAAGCAGCGAAGGTGGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG