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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttctgtttcatgtctcgtgtattttctatattcgtatcttctggttggtaggtagttaagactagttgcattttatgaggcgtatctggtgaattcagGTACCGAGAGCTGGCTAATCGGGTGGACGAAGCACTAGGATTCATGACTGCCTGTGGATTGCCTCTGGATTCTCCAGTGATGACCACCACTGAATTCTGG

Basic information

species Physcomitrella patens
transcript PP1S36_31V6.1
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|162167806|gb|FC344536.1|FC344536
EST:     ATTAAGGACTGGAACCTTGACTTCGCATCTCACAGCGAGCAAGGCGACAG                         GTACCGAGAGCTGGCTAATC
genomic: ATTAAGGACTGGAACCTTGACTTCGCATCTCACAGCGAGCAAGGCGACAGgtaaactttt ... gtgaattcagGTACCGAGAGCTGGCTAATC
EST: gi|162156274|gb|FC332298.1|FC332298
EST:     ATTAAGGACTGGAACCTTGACTTCGCATCTCACAGCGAGCAAGGCGACAG                         GTACCGAGAGCTGGCTAATCGGGTGGACGAAGCACTAGGATTCATGACTGC
genomic: ATTAAGGACTGGAACCTTGACTTCGCATCTCACAGCGAGCAAGGCGACAGgtaaactttt ... gtgaattcagGTACCGAGAGCTGGCTAATCGGGTGGACGAAGCACTAGGATTCATGACTGC
EST: gi|162219668|gb|FC395664.1|FC395664
EST:     ATTAAGGACTGGAACCTTGACTTCGCATCTCACAGCGAGCAAGGCGACAG                         GTACCGAGAGCTGGCTAATCGGGTGGACGAAGCACTAGGATTCATGACTGC
genomic: ATTAAGGACTGGAACCTTGACTTCGCATCTCACAGCGAGCAAGGCGACAGgtaaactttt ... gtgaattcagGTACCGAGAGCTGGCTAATCGGGTGGACGAAGCACTAGGATTCATGACTGC
EST: gi|162185170|gb|FC362304.1|FC362304
EST:     GGACTGGAACCTTGACTTCGCATCTCACAGCGAGCAAGGCGACAG                         GTACCGAGAGCTGGCTAATCGGGTGGACGAAGCACTAGGATTCATGACTGC
genomic: GGACTGGAACCTTGACTTCGCATCTCACAGCGAGCAAGGCGACAGgtaaactttt ... gtgaattcagGTACCGAGAGCTGGCTAATCGGGTGGACGAAGCACTAGGATTCATGACTGC
EST: gi|162248092|gb|FC420097.1|FC420097
EST:     ATTAAGGACTGGAACCTTGACTTCGCATCTCACAGCGAGCAAGGCGACAG                         GTACCGAGAGCTGGCTAATCGGGTGGACGAAGCACTAGGATTCATGACTGC
genomic: ATTAAGGACTGGAACCTTGACTTCGCATCTCACAGCGAGCAAGGCGACAGgtaaactttt ... gtgaattcagGTACCGAGAGCTGGCTAATCGGGTGGACGAAGCACTAGGATTCATGACTGC
EST: gi|162187914|gb|FC364488.1|FC364488
EST:     ATTAAGGACTGGAACCTTGACTTCGCATCTCACAGCGAGCAAGGCGACAG                         GTACCGAGAGCTGGCTAATCGGGTGGACGAAGCACTAGGATTCATGACTGC
genomic: ATTAAGGACTGGAACCTTGACTTCGCATCTCACAGCGAGCAAGGCGACAGgtaaactttt ... gtgaattcagGTACCGAGAGCTGGCTAATCGGGTGGACGAAGCACTAGGATTCATGACTGC
EST: gi|162270228|gb|FC447240.1|FC447240
EST:     ATTAAGGACTGGAACCTTGACTTCGCATCTCACAGCGAGCAAGGCGACAG                         GTACCGAGAGCTGGCTAATCGGGTGGACGAAGCACTAGGATTCATGACTGC
genomic: ATTAAGGACTGGAACCTTGACTTCGCATCTCACAGCGAGCAAGGCGACAGgtaaactttt ... gtgaattcagGTACCGAGAGCTGGCTAATCGGGTGGACGAAGCACTAGGATTCATGACTGC
EST: gi|162163356|gb|FC339682.1|FC339682
EST:     ATTAAGGACTGGAACCTTGACTTCGCATCTCACAGCGAGCAAGGCGACAG                         GTACCGAGAGCTGGCTAATCGGGTGGACGAAGCACTAGGATTCATGACTGC
genomic: ATTAAGGACTGGAACCTTGACTTCGCATCTCACAGCGAGCAAGGCGACAGgtaaactttt ... gtgaattcagGTACCGAGAGCTGGCTAATCGGGTGGACGAAGCACTAGGATTCATGACTGC
EST: gi|162176951|gb|FC353628.1|FC353628
EST:     ATTAAGGACTGGAACCTTGACTTCGCATCTCACAGCGAGCAAGGCGACAG                         GTACCGAGAGCTGGCTAATCGGGTGGACGAAGCACTAGGATTCATGACTGC
genomic: ATTAAGGACTGGAACCTTGACTTCGCATCTCACAGCGAGCAAGGCGACAGgtaaactttt ... gtgaattcagGTACCGAGAGCTGGCTAATCGGGTGGACGAAGCACTAGGATTCATGACTGC
EST: gi|162160220|gb|FC337117.1|FC337117
EST:     ATTAAGGACTGGAACCTTGACTTCGCATCTCACAGCGAGCAAGGCGACAG                         GTACCGAGAGCTGGCTAATCGGGTGGACGAAGCACTAGGATTCATGACTGC
genomic: ATTAAGGACTGGAACCTTGACTTCGCATCTCACAGCGAGCAAGGCGACAGgtaaactttt ... gtgaattcagGTACCGAGAGCTGGCTAATCGGGTGGACGAAGCACTAGGATTCATGACTGC

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: 34 (upstream exon), 28 (downstream exon)
Score: 51

TGAACCTTCTTCGTGCTTTCGCCACTGGAGGGTATGCTGCCATGCAGAGGATTAAGGACTGGAACCTTGACTTCGCATCTCACAGCGAGCAAGGCGACAGgtaaactttt ... gtgaattcagGTACCGAGAGCTGGCTAATCGGGTGGACGAAGCACTAGGATTCATGACTGCCTGTGGATTGCCTCTGGATTCTCCAGTGATGACCACCACTGAATTCTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttggtaggtagttaagactagttgcattttatgaggcgtatctggtgaattcagGTACCGAGAGCTGGCTAATCGGGTGGACGAAGCACTAGGATTCATGACTGCCTGTGGATTGCCTCTGGATTCTCCAGTGATGACCACCACTGAATTCTGG
                          attttatga  TA-rich tract