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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtactttctcacccatgcacacttgtgaatcagttgtgatttcatttcattatactctgaagtggcaaatttcgtaatcttttttggggcgggaactgatatttaatctgaatgacttactatgcagGAGCAAAGTTACCGCTCTACGCTTTTGGTGTAAGGCAATCTTCGGGTTCGAACAAGAGGGCGCACACTGGCAGTGACGACCACTGTGTACCCGATAGTGT

Basic information

species Physcomitrella patens
transcript PP1S114_207V6.1
intron # 1
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|100407005|gb|BY973962.1|BY973962
EST:     GCAAGTTCCTGGATGTGGCCGAGACTGTCTTGGGACCTGTTGCATTCCTG                         GAGCAAAGTTACCGCTCTACGCTTTTGGTGTAAGGGAATCTTCGGGGTCGA
genomic: GCAAGTTCCTGGATGTGGCCGAGACTGTCTTGGGACCTGTTGCATTCCTGgtcagtactt ... tactatgcagGAGCAAAGTTACCGCTCTACGCTTTTGGTGTAAGGCAATCTTCGGGTTCGA
EST: gi|162173126|gb|FC348699.1|FC348699
EST:     GCAAGTTCCTGGATGTGGCCGAGACTGTCTTGGGACCTGTTGCATTCCTG                         GAGCAAAGTTACCGCTCTACGCTTTTGGTGTAAGGCAATCTTCGGGTTCGA
genomic: GCAAGTTCCTGGATGTGGCCGAGACTGTCTTGGGACCTGTTGCATTCCTGgtcagtactt ... tactatgcagGAGCAAAGTTACCGCTCTACGCTTTTGGTGTAAGGCAATCTTCGGGTTCGA
EST: gi|67572690|gb|BJ945514.1|BJ945514
EST:     GCAAGTTCCTGGATGTGGCCGAGACTGTCTTGGGACCTGTTGCATTCCTG                         GAGCAAAGTTACCGCTCTACGCTTTTGGTGTAAGGCAATCTTCGGGTTCGA
genomic: GCAAGTTCCTGGATGTGGCCGAGACTGTCTTGGGACCTGTTGCATTCCTGgtcagtactt ... tactatgcagGAGCAAAGTTACCGCTCTACGCTTTTGGTGTAAGGCAATCTTCGGGTTCGA
EST: gi|100406079|gb|BY991529.1|BY991529
EST:     CAAGTTCCTGGATGTGGCCGAGACTGTCTTGGGACCTGTTGCATTCCCTG                         GAGCAA-GTTACCGCTCTACGCTTTTGGTGTAAGGCAATCTTCGGGTTCG
genomic: CAAGTTCCTGGATGTGGCCGAGACTGTCTTGGGACCTGTTGCATTCC-TGgtcagtactt ... tactatgcagGAGCAAAGTTACCGCTCTACGCTTTTGGTGTAAGGCAATCTTCGGGTTCG
EST: gi|100367529|gb|BY984731.1|BY984731
EST:     GCAAGTTCCTGGATGTGGCCGAGACTGTCTTGGGACCTGTTGCATTCCTG                         GAGCAAAGTTACCGCTCTACGCTTTTGGTGTAAGGCAATCTTCGGGTTCGA
genomic: GCAAGTTCCTGGATGTGGCCGAGACTGTCTTGGGACCTGTTGCATTCCTGgtcagtactt ... tactatgcagGAGCAAAGTTACCGCTCTACGCTTTTGGTGTAAGGCAATCTTCGGGTTCGA
EST: gi|162159953|gb|FC336206.1|FC336206
EST:     GCAAGTTCCTGGATGTGGCCGAGACTGTCTTGGGACCTGTTGCATTCCTG                         GAGCAAAGTTACCGCTCTACGCTTTTGGTGTAAGGCAATCTTCGGGTTCGA
genomic: GCAAGTTCCTGGATGTGGCCGAGACTGTCTTGGGACCTGTTGCATTCCTGgtcagtactt ... tactatgcagGAGCAAAGTTACCGCTCTACGCTTTTGGTGTAAGGCAATCTTCGGGTTCGA
EST: gi|100377960|gb|BY949609.1|BY949609
EST:     GCAAGTTCCTGGATGTGGCCGAGACTGTCTTGGGACCTGTTGCATTCCTG                         GAGCAAAGTTACCGCTCTACGCTTTTGGTGTAAGGCAATCTTTCGG-TTCG
genomic: GCAAGTTCCTGGATGTGGCCGAGACTGTCTTGGGACCTGTTGCATTCCTGgtcagtactt ... tactatgcagGAGCAAAGTTACCGCTCTACGCTTTTGGTGTAAGGCAATCTT-CGGGTTCG
EST: gi|208393602|gb|DC904318.1|DC904318
EST:     GCAAGTTCCTGGATGTGGCCGAGACTGTCTTGGGACCTGTTGCATTCCTG                         GAGCAAAGTTACCGCTCTACGCTTTTGGTGTAAGGCAATCTTCGGGTTCGA
genomic: GCAAGTTCCTGGATGTGGCCGAGACTGTCTTGGGACCTGTTGCATTCCTGgtcagtactt ... tactatgcagGAGCAAAGTTACCGCTCTACGCTTTTGGTGTAAGGCAATCTTCGGGTTCGA
EST: gi|162159109|gb|FC334280.1|FC334280
EST:     GCAAGTTCCTGGATGTGGCCGAGACTGTCTTGGGACCTGTTGCATTCCTG                         GAGCAAAGTTACCGCTCTACGCTTTTGGTGTAAGGCAATCTTCGGGTTCGA
genomic: GCAAGTTCCTGGATGTGGCCGAGACTGTCTTGGGACCTGTTGCATTCCTGgtcagtactt ... tactatgcagGAGCAAAGTTACCGCTCTACGCTTTTGGTGTAAGGCAATCTTCGGGTTCGA
EST: gi|162170578|gb|FC347074.1|FC347074
EST:     GCAAGTTCCTGGATGTGGCCGAGACTGTCTTGGGACCTGTTGCATTCCTG                         GAGCAAAGTTACCGCTCTACGCTTTTGGTGTAAGGCAATCTTCGGGTTCGA
genomic: GCAAGTTCCTGGATGTGGCCGAGACTGTCTTGGGACCTGTTGCATTCCTGgtcagtactt ... tactatgcagGAGCAAAGTTACCGCTCTACGCTTTTGGTGTAAGGCAATCTTCGGGTTCGA
EST: gi|162197171|gb|FC374161.1|FC374161
EST:     GCAAGTTCCTGGATGTGGCCGAGACTGTCTTGGGACCTGTTGCATTCCTG                         GAGCAAAGTTACCGCTCTACGCTTTTGGTGTAAGGCAATCTTCGGGTTCGA
genomic: GCAAGTTCCTGGATGTGGCCGAGACTGTCTTGGGACCTGTTGCATTCCTGgtcagtactt ... tactatgcagGAGCAAAGTTACCGCTCTACGCTTTTGGTGTAAGGCAATCTTCGGGTTCGA

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), 35 (downstream exon)
Score: 59

TTGACCATCAAGAGAGTGGAGACTGTGGTTTCAATGCACCAGCAGCTGGAGCAAGTTCCTGGATGTGGCCGAGACTGTCTTGGGACCTGTTGCATTCCTGgtcagtactt ... tactatgcagGAGCAAAGTTACCGCTCTACGCTTTTGGTGTAAGGCAATCTTCGGGTTCGAACAAGAGGGCGCACACTGGCAGTGACGACCACTGTGTACCCGATAGTGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtaatcttttttggggcgggaactgatatttaatctgaatgacttactatgcagGAGCAAAGTTACCGCTCTACGCTTTTGGTGTAAGGCAATCTTCGGGTTCGAACAAGAGGGCGCACACTGGCAGTGACGACCACTGTGTACCCGATAGTGT
                                         gacttac  putative branch site (score: 59)
                          atatttaatctgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtactttctcacccatgcacacttgtgaatcagttgtgatttcatttcattatactctgaagtggcaaatttcgtaatcttttttggggcgggaactgatatttaatctgaatgacttactatgcagGAGCAAAGTTACCGCTCTACGCTTTTGGTGTAAGGCAATCTTCGGGTTCGAACAAGAGGGCGCACACTGGCAGTGACGACCACTGTGTACCCGATAGTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG