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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttaatatcctgcgctgcaaattttcagttcaattacactacatgaccacattgtttgacccggtacttcctgtccatccccagGTACTCTCAAAAGAGCGATGTGTACAGCTTCGGCGTTGTGATCGCTCAGCTGGTGACAGCCCGTAACCCAACCGACCACTTCGTCGTGGAAAATGGCGGT

Basic information

species Physcomitrella patens
transcript PP1S48_117V6.1
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|162199015|gb|FC375785.1|FC375785
EST:     CTTGCTGGCACTATCGGCTTCATTGCACCAGAATATCATCAAACATTGAG                         GTACTCTCAAAAGAGCGATGTGTACAGCTTCGGCGTTGTGATCGCTCAGCT
genomic: CTTGCTGGCACTATCGGCTTCATTGCACCAGAATATCATCAAACATTGAGgtgagttaat ... ccatccccagGTACTCTCAAAAGAGCGATGTGTACAGCTTCGGCGTTGTGATCGCTCAGCT
EST: gi|162191222|gb|FC367900.1|FC367900
EST:     CTTGCTGGCACTATCGGCTTCATTGCACCAGAATATCATCAAACATTGAG                         GTACTCTCAAAAGAGCGATGTGTACAGCTTCGGCGTTGTGATCGCTCAGCT
genomic: CTTGCTGGCACTATCGGCTTCATTGCACCAGAATATCATCAAACATTGAGgtgagttaat ... ccatccccagGTACTCTCAAAAGAGCGATGTGTACAGCTTCGGCGTTGTGATCGCTCAGCT
EST: gi|162188226|gb|FC364720.1|FC364720
EST:     CTTGCTGGCACTATCGGCTTCATTGCACCAGAATATCATCAAACATTGAG                         GTACTCTCAAAAGAGCGATGTGTACAGCTTCGGCGTTGTGATCGCTCAGCT
genomic: CTTGCTGGCACTATCGGCTTCATTGCACCAGAATATCATCAAACATTGAGgtgagttaat ... ccatccccagGTACTCTCAAAAGAGCGATGTGTACAGCTTCGGCGTTGTGATCGCTCAGCT
EST: gi|162199016|gb|FC375786.1|FC375786
EST:     CTTGCTGGCACTATCGGCTTCATTGCACCAGAATATCATCAAACATTGAG                         GTACTCTCAAAAGAGCGATGTGTACAGCTTCGGCGTTGTGATCGCTCAGCT
genomic: CTTGCTGGCACTATCGGCTTCATTGCACCAGAATATCATCAAACATTGAGgtgagttaat ... ccatccccagGTACTCTCAAAAGAGCGATGTGTACAGCTTCGGCGTTGTGATCGCTCAGCT

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), 19 (downstream exon)
Score: 4

GCCTGGCTGCCATCGTTCCCCTCAAGGCCACGCATGCTACCACTGAAGTTCTTGCTGGCACTATCGGCTTCATTGCACCAGAATATCATCAAACATTGAGgtgagttaat ... ccatccccagGTACTCTCAAAAGAGCGATGTGTACAGCTTCGGCGTTGTGATCGCTCAGCTGGTGACAGCCCGTAACCCAACCGACCACTTCGTCGTGGAAAATGGCGGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaattacactacatgaccacattgtttgacccggtacttcctgtccatccccagGTACTCTCAAAAGAGCGATGTGTACAGCTTCGGCGTTGTGATCGCTCAGCTGGTGACAGCCCGTAACCCAACCGACCACTTCGTCGTGGAAAATGGCGGT
                        gtttgac  putative branch site (score: 4)
                                     cttcctgtccatcccc  putative PPT
                     attgttt  TA-rich tract