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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatgccttgaagattatttgtttatttgctgttagatgttattagttgccactttagtggagaaatgtgtaagtttattaccttaatcacgctgatcagATCGATTGCAAGTGGGGGAGGTCGTCTCAACCATCCCAA

Basic information

species Physcomitrella patens
transcript PP1S271_49V6.1
intron # 1
splice site 3'
intron type U12 (go to U12 genes for details)

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|208386675|gb|DC929121.1|DC929121
EST:     GCGTATTCTTGTCCTTGGTTTGGACAATGCCGGGAAAACAACCATCCTTT                         ATCGATTGCAAGTGGGGGAGGTCGTCTCAACCATCCCAA
genomic: GCGTATTCTTGTCCTTGGTTTGGACAATGCCGGGAAAACAACCATCCTTTgtatccatta ... cgctgatcagATCGATTGCAAGTGGGGGAGGTCGTCTCAACCATCCCAA
EST: gi|208374444|gb|DC940717.1|DC940717
EST:     GCGTATTCTTGTCCTTGGTTTGGACAATGCCGGGAAAACAACCATCCTTT                         ATCGATTGCAAGTGGGGGAGGTCGTCTCAACCATCCCAA
genomic: GCGTATTCTTGTCCTTGGTTTGGACAATGCCGGGAAAACAACCATCCTTTgtatccatta ... cgctgatcagATCGATTGCAAGTGGGGGAGGTCGTCTCAACCATCCCAA
EST: gi|162240378|gb|FC419311.1|FC419311
EST:     GCGTATTCTTGTCCTTGGTTTGGACAATGCCGGGAAAACAACCATCCTTT                         ATCGATTGCAAGTGGGGGAGGTCGTCTCAACCATCCCAA
genomic: GCGTATTCTTGTCCTTGGTTTGGACAATGCCGGGAAAACAACCATCCTTTgtatccatta ... cgctgatcagATCGATTGCAAGTGGGGGAGGTCGTCTCAACCATCCCAA
EST: gi|208392443|gb|DC907920.1|DC907920
EST:     GCGTATTCTTGTCCTTGGTTTGGACAATGCCGGGAAAACAACCATCCTTT                         ATCGATTGCAAGTGGGGGAGGTCGTCTCAACCATCCCAA
genomic: GCGTATTCTTGTCCTTGGTTTGGACAATGCCGGGAAAACAACCATCCTTTgtatccatta ... cgctgatcagATCGATTGCAAGTGGGGGAGGTCGTCTCAACCATCCCAA
EST: gi|67569908|gb|BJ942732.1|BJ942732
EST:     GCGTATTCTTGTCCTTGGTTTGGACAATGCCGGGAAAACAACCATCCTTT                         ATCGATTGCAAGTGGGGGAGGTCGTCTCAACCATCCCAA
genomic: GCGTATTCTTGTCCTTGGTTTGGACAATGCCGGGAAAACAACCATCCTTTgtatccatta ... cgctgatcagATCGATTGCAAGTGGGGGAGGTCGTCTCAACCATCCCAA

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: 32 (upstream exon), 24 (downstream exon)
Score: 4

GGCATATTTGTGTCCAGGCTGCTGGCGACGTTGTTCGGGGATAAGGAAGCGCGTATTCTTGTCCTTGGTTTGGACAATGCCGGGAAAACAACCATCCTTTgtatccatta ... cgctgatcagATCGATTGCAAGTGGGGGAGGTCGTCTCAACCATCCCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgccactttagtggagaaatgtgtaagtttattaccttaatcacgctgatcagATCGATTGCAAGTGGGGGAGGTCGTCTCAACCATCCCAA
                                  taccttaat  putative branch site 
                             tttattaccttaat  TA-rich tract