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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatcaacctagcggttatttcattcacacaatctcccatttactttcattgaatatttatgaagtttcaagcatttatcacatcgtacggtcaccttacgtgcgtccttttgtgtttccttcagAGGAATTCCAAAGTTGTGGTCATTGACGACTACCAAGACGTGCCTACCCAATCTGAGAGCGCTCTGATGAAGGCACTGACGAAAAACCCTGTCAGTGTTG

Basic information

species Physcomitrella patens
transcript PP1S285_10V6.1
intron # 2
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|162186545|gb|FC363309.1|FC363309
EST:     AGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGA                         AGGAATTCCAAAGTTGTGGTCATTGACGACTACCAAGACGTGCCTACCCAA
genomic: AGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGAgtaagtatca ... tttccttcagAGGAATTCCAAAGTTGTGGTCATTGACGACTACCAAGACGTGCCTACCCAA
EST: gi|162157752|gb|FC335466.1|FC335466
EST:     AGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGA                         AGGAATTCCAAAGTTGTGGTCATTGACGACTACCAAGACGTGCCTACCCAA
genomic: AGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGAgtaagtatca ... tttccttcagAGGAATTCCAAAGTTGTGGTCATTGACGACTACCAAGACGTGCCTACCCAA
EST: gi|162255174|gb|FC431484.1|FC431484
EST:     AGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGA                         AGGAATTCCAAAGTTGTGGTCATTGACGACTACCAAGACGTGCCTACCCAA
genomic: AGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGAgtaagtatca ... tttccttcagAGGAATTCCAAAGTTGTGGTCATTGACGACTACCAAGACGTGCCTACCCAA
EST: gi|162177962|gb|FC354068.1|FC354068
EST:     AGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGA                         AGGAATTCCAAAGTTGTGGTCATTGACGACTACCAAGACGTGCCTACCCAA
genomic: AGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGAgtaagtatca ... tttccttcagAGGAATTCCAAAGTTGTGGTCATTGACGACTACCAAGACGTGCCTACCCAA
EST: gi|100397513|gb|BY990264.1|BY990264
EST:     AGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGA                         GGGAATTCCAA-GTTGTGGTCATTGACGACTACCAAGACGTGCCTACCCAA
genomic: AGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGAgtaagtatca ... tttccttcagAGGAATTCCAAAGTTGTGGTCATTGACGACTACCAAGACGTGCCTACCCAA
EST: gi|100433239|gb|BY978858.1|BY978858
EST:     AGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGA                         AGGAATTCCAAAGTTGTGGTCATTGACGACTACCAAGACGTGCCTACCCAA
genomic: AGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGAgtaagtatca ... tttccttcagAGGAATTCCAAAGTTGTGGTCATTGACGACTACCAAGACGTGCCTACCCAA
EST: gi|162163721|gb|FC340307.1|FC340307
EST:     AGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGA                         AGGAATTCCAAAGTTGTGGTCATTGACGACTACCAAGACGTGCCTACCCAA
genomic: AGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGAgtaagtatca ... tttccttcagAGGAATTCCAAAGTTGTGGTCATTGACGACTACCAAGACGTGCCTACCCAA

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: 66

TATGGACTATGCATTCGAGTTTATTATCAAGAATGGTGGTATTGACACTGAGAAGGATTATCCTTACAAGGCCAGAGATGGTCGGTGCGATGAGGGAAGAgtaagtatca ... tttccttcagAGGAATTCCAAAGTTGTGGTCATTGACGACTACCAAGACGTGCCTACCCAATCTGAGAGCGCTCTGATGAAGGCACTGACGAAAAACCCTGTCAGTGTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcatttatcacatcgtacggtcaccttacgtgcgtccttttgtgtttccttcagAGGAATTCCAAAGTTGTGGTCATTGACGACTACCAAGACGTGCCTACCCAATCTGAGAGCGCTCTGATGAAGGCACTGACGAAAAACCCTGTCAGTGTTG
                       accttac  putative branch site (score: 66)
                                   tccttttgtgtttcct  putative PPT