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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggcttgtttaccgcatgtatgtcttcagagagtcccaattcgccggagcgtatgttttcagagtttgggtgttgactgtgatttgtgggttctgtgacagCCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTTGCGGGGGTGCATTGGCACGCTTGAAGCCCGATATATCATCACCGGGTTC

Basic information

species Physcomitrella patens
transcript PP1S47_221V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S47_221V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv13s0101g00100.t01 (Vitis vinifera), 3'ss of exon 1
ggcttgtttaccgcatgtatgtcttcagagagtcccaattcgccggagcgtatgttttcagagtttgggtgttgactgtgatttgtg-----ggttctgtga---cagCCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTTGCGGGGGTGCATTGGCACGCTTGAAGCCCGATATATCATCACCGGGTTC
  |   ||||    ||    || || |   |   | |||   | |     |||| | ||    || |  ||||  |  |  ||           || | ||    ||||||| | ||||| || |||||||||||| |||||||||||||||| || ||||| || || ||||| || |||||||| || |   | ||||  || || 
--cccattta----ataccagtttttaacaacatcaaatgaacagc--tttatgctctccacattggcatgttatcattatttgacacaaataattttctggtttcagCCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTTGCGTGGATGTATTGGAACTCTTGAAGCTCGTTGCTTGATCAATGGCTTT
















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|162162945|gb|FC338142.1|FC338142
EST:     CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTT                         CCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
genomic: CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTTgtaagcttcg ... tctgtgacagCCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
EST: gi|208358222|gb|DC939390.1|DC939390
EST:     CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTT                         CCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
genomic: CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTTgtaagcttcg ... tctgtgacagCCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
EST: gi|162227780|gb|FC402396.1|FC402396
EST:     CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTT                         CCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
genomic: CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTTgtaagcttcg ... tctgtgacagCCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
EST: gi|162197234|gb|FC372534.1|FC372534
EST:     CGAAGAAGGGCAGTT                         CCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
genomic: CGAAGAAGGGCAGTTgtaagcttcg ... tctgtgacagCCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
EST: gi|100401256|gb|BY990911.1|BY990911
EST:     CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTT                         CCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
genomic: CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTTgtaagcttcg ... tctgtgacagCCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
EST: gi|67696785|gb|BJ957018.1|BJ957018
EST:     GAAGAAGGGCANTT                         C
genomic: GAAGAAGGGCAGTTgtaagcttcg ... tctgtgacag-
EST: gi|67696785|gb|BJ957018.1|BJ957018
EST:     GAAGAAGGGCANTT                         C
genomic: GAAGAAGGGCAGTTgtaagcttcg ... tctgtgacag-
EST: gi|100376173|gb|BY968329.1|BY968329
EST:     CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTT                         CCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
genomic: CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTTgtaagcttcg ... tctgtgacagCCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
EST: gi|162195536|gb|FC371837.1|FC371837
EST:     CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTT                         CCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
genomic: CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTTgtaagcttcg ... tctgtgacagCCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
EST: gi|162251201|gb|FC428480.1|FC428480
EST:     CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTT                         CCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
genomic: CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTTgtaagcttcg ... tctgtgacagCCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
EST: gi|162189471|gb|FC365485.1|FC365485
EST:     CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTT                         CCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
genomic: CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTTgtaagcttcg ... tctgtgacagCCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
EST: gi|37828312|gb|BJ586324.1|BJ586324
EST:     GAAGGGCAGTT                         CCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGANCCACGCTT
genomic: GAAGGGCAGTTgtaagcttcg ... tctgtgacagCCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
EST: gi|162229811|gb|FC404264.1|FC404264
EST:     CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTT                         CCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
genomic: CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTTgtaagcttcg ... tctgtgacagCCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
EST: gi|100421718|gb|BY976278.1|BY976278
EST:     CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTT                         CCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
genomic: CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTTgtaagcttcg ... tctgtgacagCCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
EST: gi|162252999|gb|FC429060.1|FC429060
EST:     CGGGCGATGCTGTACCCCCACTTGCGTTCGAAGAAGGGCAGTC                         CCCTTTATTTGTTACATGAAAGAAAGTATTGAATGGTGGGGAACCACGCTT
genomic: CGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTTgtaagcttcg ... tctgtgacagCCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
EST: gi|100435185|gb|BY979115.1|BY979115
EST:     CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTT                         CCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
genomic: CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTTgtaagcttcg ... tctgtgacagCCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
EST: gi|162156121|gb|FC332288.1|FC332288
EST:     CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTT                         CCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
genomic: CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTTgtaagcttcg ... tctgtgacagCCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
EST: gi|18354817|gb|BJ186876.1|BJ186876
EST:     CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTT                         CCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
genomic: CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTTgtaagcttcg ... tctgtgacagCCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
EST: gi|37844642|gb|BJ602650.1|BJ602650
EST:     CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTT                         CCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
genomic: CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTTgtaagcttcg ... tctgtgacagCCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
EST: gi|67578357|gb|BJ950524.1|BJ950524
EST:     CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTT                         CCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
genomic: CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTTgtaagcttcg ... tctgtgacagCCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
EST: gi|208360641|gb|DC957866.1|DC957866
EST:     TACACGGGNGATGCTGTANCCCCCACCTGCGTTCGAAGAAGGGCAGTT                         CCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
genomic: TACACGGGCGATGCTGTA-CCCCCACCTGCGTTCGAAGAAGGGCAGTTgtaagcttcg ... tctgtgacagCCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
EST: gi|162253000|gb|FC429061.1|FC429061
EST:     CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTT                         CCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
genomic: CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTTgtaagcttcg ... tctgtgacagCCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
EST: gi|7147954|gb|AW509876.1|AW509876
EST:     CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTT                         CCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
genomic: CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTTgtaagcttcg ... tctgtgacagCCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
EST: gi|18351844|gb|BJ183896.1|BJ183896
EST:     CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTT                         CCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT
genomic: CATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTTgtaagcttcg ... tctgtgacagCCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTT

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), 33 (downstream exon)
Score: 36

TGTCTGCCAGCATGGAGATGGCGGCCTATTGCTTTGACACGCTAGTCGCCCATTACACGGGCGATGCTGTACCCCCACCTGCGTTCGAAGAAGGGCAGTTgtaagcttcg ... tctgtgacagCCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTTGCGGGGGTGCATTGGCACGCTTGAAGCCCGATATATCATCACCGGGTTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagcgtatgttttcagagtttgggtgttgactgtgatttgtgggttctgtgacagCCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTTGCGGGGGTGCATTGGCACGCTTGAAGCCCGATATATCATCACCGGGTTC
                        tgttgac  putative branch site (score: 36)
     tatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggcttgtttaccgcatgtatgtcttcagagagtcccaattcgccggagcgtatgttttcagagtttgggtgttgactgtgatttgtgggttctgtgacagCCCTTTATTTGTTACATGGAAGAAAGTATTGAATGGTGGGGAACCACGCTTGCGGGGGTGCATTGGCACGCTTGAAGCCCGATATATCATCACCGGGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC