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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcggatttttgttgttgatctctagtttttctggtaagatggctgtaattctagtgttatgagaggttagactgggagaacgcttgggtgtttaattttgttgtttatatttttgttgcagTATGGAATTCCTTTGGAGGTCGTTTCATACAAGACACTGTATAATTGGACTATGGATGAAATAGTCAAAGAAATTGGGCTGAAGAACAACTGTACATTCT

Basic information

species Physcomitrella patens
transcript PP1S54_267V6.1
intron # 3
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|100385871|gb|BY951065.1|BY951065
EST:     CTGGATACAGGGACGACTCACTTGAGACTGTAAATCGGAACGAAACACAG                         TATGGAATTCCTTTGGAGGTCGTTTCATACAAGACACTGTATAATTGGACT
genomic: CTGGATACAGGGACGACTCCCTTGAGACTGTAAAGCGGAACGAAACACAGgtgcggattt ... tttgttgcagTATGGAATTCCTTTGGAGGTCGTTTCATACAAGACACTGTATAATTGGACT
EST: gi|100385874|gb|BY951068.1|BY951068
EST:     CTGGATACAGGGACGACTCACTTGAGACTGTAAATCGGAACGAAACACAG                         TATGGAATTCCTTTGGAGGTCGTTTCATACAAGACACTGTATAATTGGACT
genomic: CTGGATACAGGGACGACTCCCTTGAGACTGTAAAGCGGAACGAAACACAGgtgcggattt ... tttgttgcagTATGGAATTCCTTTGGAGGTCGTTTCATACAAGACACTGTATAATTGGACT
EST: gi|100425875|gb|BY977164.1|BY977164
EST:     CTGGATACAGGGACGACTCCCTTGAGACTGTAAAGCGGAACGAAACACAG                         TATGGAATTCCTTTGGAGGTCGTTTCATACAAGACACTGTATAATTGGACT
genomic: CTGGATACAGGGACGACTCCCTTGAGACTGTAAAGCGGAACGAAACACAGgtgcggattt ... tttgttgcagTATGGAATTCCTTTGGAGGTCGTTTCATACAAGACACTGTATAATTGGACT
EST: gi|208386768|gb|DC937160.1|DC937160
EST:     CTGGATACAGGGACGACTCCCTTGAGACTGTAAAGCGGAACGAAACACAG                         TATGGAATTCCTTTGGAGGTCGTTTCATACAAGACACTGTATAATTGGACT
genomic: CTGGATACAGGGACGACTCCCTTGAGACTGTAAAGCGGAACGAAACACAGgtgcggattt ... tttgttgcagTATGGAATTCCTTTGGAGGTCGTTTCATACAAGACACTGTATAATTGGACT
EST: gi|100379791|gb|BY949946.1|BY949946
EST:     CTGGATACAGGGACGACTCCCTTGAGACTGTAAAGCGGAACGAAACACAG                         TATGGAATTCCTTTGGAGGTCGTTTCATACAAGACACTGTATAATTGGACT
genomic: CTGGATACAGGGACGACTCCCTTGAGACTGTAAAGCGGAACGAAACACAGgtgcggattt ... tttgttgcagTATGGAATTCCTTTGGAGGTCGTTTCATACAAGACACTGTATAATTGGACT
EST: gi|18342250|gb|BJ174285.1|BJ174285
EST:     CTGGATACAGGGACGACTCCCTTGAGACTGTAAAGCGGAACGAAACACAG                         TATGGAATTCCTTTGGAGGTCGTTTCATACNAGACACTGTATAATTGGACT
genomic: CTGGATACAGGGACGACTCCCTTGAGACTGTAAAGCGGAACGAAACACAGgtgcggattt ... tttgttgcagTATGGAATTCCTTTGGAGGTCGTTTCATACAAGACACTGTATAATTGGACT
EST: gi|162160669|gb|FC337205.1|FC337205
EST:     CTGGATACAGGGACGACTCCCTTGAGACTGTAAAGCGGAACGAAACACAG                         TATGGAATTCCTTTGGAGGTCGTTTCATACAAGACACTGTATAATTGGACT
genomic: CTGGATACAGGGACGACTCCCTTGAGACTGTAAAGCGGAACGAAACACAGgtgcggattt ... tttgttgcagTATGGAATTCCTTTGGAGGTCGTTTCATACAAGACACTGTATAATTGGACT
EST: gi|208354247|gb|DC957439.1|DC957439
EST:     CTGGATACAGGGACGACTCCCTTGAGACTGTAAAGCGGAACGAAACACAG                         TATGGAATTCCTTTGGAGGTCGTTTCATACAAGACACTGTATAATTGGACT
genomic: CTGGATACAGGGACGACTCCCTTGAGACTGTAAAGCGGAACGAAACACAGgtgcggattt ... tttgttgcagTATGGAATTCCTTTGGAGGTCGTTTCATACAAGACACTGTATAATTGGACT
EST: gi|208358391|gb|DC943222.1|DC943222
EST:     CTGGATACAGGGACGACTCCCTTGAGACTGTAAAGCGGAACGAAACACAG                         TATGGAATTCCTTTGGAGGTCGTTTCATACAAGACACTGTATAATTGGACT
genomic: CTGGATACAGGGACGACTCCCTTGAGACTGTAAAGCGGAACGAAACACAGgtgcggattt ... tttgttgcagTATGGAATTCCTTTGGAGGTCGTTTCATACAAGACACTGTATAATTGGACT

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: 29 (upstream exon), 34 (downstream exon)
Score: 6

ACACGACTACGGCCTGGACTTGTTTTTACTATCGATTGATGAAGGTATTGCTGGATACAGGGACGACTCCCTTGAGACTGTAAAGCGGAACGAAACACAGgtgcggattt ... tttgttgcagTATGGAATTCCTTTGGAGGTCGTTTCATACAAGACACTGTATAATTGGACTATGGATGAAATAGTCAAAGAAATTGGGCTGAAGAACAACTGTACATTCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagactgggagaacgcttgggtgtttaattttgttgtttatatttttgttgcagTATGGAATTCCTTTGGAGGTCGTTTCATACAAGACACTGTATAATTGGACTATGGATGAAATAGTCAAAGAAATTGGGCTGAAGAACAACTGTACATTCT
                       gtttaat  putative branch site (score: 6)
                                           tttttgtt  putative PPT
                      tgtttaattttgttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcggatttttgttgttgatctctagtttttctggtaagatggctgtaattctagtgttatgagaggttagactgggagaacgcttgggtgtttaattttgttgtttatatttttgttgcagTATGGAATTCCTTTGGAGGTCGTTTCATACAAGACACTGTATAATTGGACTATGGATGAAATAGTCAAAGAAATTGGGCTGAAGAACAACTGTACATTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC