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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cccttacatgcaggcgtgaatggtggttgaaatatgtgtgcactgcactgagaggaggctgtgaccttcctggctcatttttgtccacgattgttgacagGGCCAGATGAGAGGACGGAGTTCAGAATTCTGTGCAGACGAGTTGAATCCACCATACGTGCTTGGTACAACCTTCAGTTTGAGGACTTGAAT

Basic information

species Physcomitrella patens
transcript PP1S60_139V6.2
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|100390135|gb|BY989215.1|BY989215
EST:     GATTGTCATCTCCAAGACGAAGCTCACAGATGGCTTACTCCATCTGCTAG                         GGCCAGATGAGAGGACGGAGTTCAGAATTCTGTGCAGACGAGTTGAATCCA
genomic: GATTGTCATCTCCAAGACGAAGCTCACAGATGGCTTACTCCATCTGCTAGgtgcgtactt ... ttgttgacagGGCCAGATGAGAGGACGGAGTTCAGAATTCTGTGCAGACGAGTTGAATCCA
EST: gi|18373830|gb|BJ205408.1|BJ205408
EST:     GATTGTCATCTCCAAGACGAAGCTCACAGATGGCTTACTCCATCTGCTAG                         GGCCAGATGAGAGGACGGAGTTCAGAATTCTGTGCAGACGAGTTGAATCCA
genomic: GATTGTCATCTCCAAGACGAAGCTCACAGATGGCTTACTCCATCTGCTAGgtgcgtactt ... ttgttgacagGGCCAGATGAGAGGACGGAGTTCAGAATTCTGTGCAGACGAGTTGAATCCA
EST: gi|100404207|gb|BY955309.1|BY955309
EST:     GATTGTCATCTCCAAGACGAAGCTCACAGATGGCTTACTCCATCTGCTAG                         GGCCAGATGAGAGGACGGAGTTCAGAATTCTGTGCAGACGAGTTGAATCCA
genomic: GATTGTCATCTCCAAGACGAAGCTCACAGATGGCTTACTCCATCTGCTAGgtgcgtactt ... ttgttgacagGGCCAGATGAGAGGACGGAGTTCAGAATTCTGTGCAGACGAGTTGAATCCA
EST: gi|18374527|gb|BJ206105.1|BJ206105
EST:     GATTGTCATCTCCAAGACGAAGCTCACAGATGGCTTACTCCATCTGCTAG                         GGCCAGATGAGAGGACGGAGTTCAGAATTCTGTGCAGACGAGTTGAATCCA
genomic: GATTGTCATCTCCAAGACGAAGCTCACAGATGGCTTACTCCATCTGCTAGgtgcgtactt ... ttgttgacagGGCCAGATGAGAGGACGGAGTTCAGAATTCTGTGCAGACGAGTTGAATCCA
EST: gi|18365192|gb|BJ197266.1|BJ197266
EST:     GATTGTCATCTCCAAGACGAAGCTCACAGATGGCTTACTCCATCTGCTAG                         GGCCAGATGAGAGGACGGAGTTCAGAATTCTGTGCAGACGAGTTGAATCCA
genomic: GATTGTCATCTCCAAGACGAAGCTCACAGATGGCTTACTCCATCTGCTAGgtgcgtactt ... ttgttgacagGGCCAGATGAGAGGACGGAGTTCAGAATTCTGTGCAGACGAGTTGAATCCA
EST: gi|18374502|gb|BJ206080.1|BJ206080
EST:     GATTGTCATCTCCAAGACGAAGCTCACAGATGGCTTACTCCATCTGCTAG                         GGCCAGATGAGAGGACGGAGTTCAGAATTCTGTGCAGACGAGTTGAATCCA
genomic: GATTGTCATCTCCAAGACGAAGCTCACAGATGGCTTACTCCATCTGCTAGgtgcgtactt ... ttgttgacagGGCCAGATGAGAGGACGGAGTTCAGAATTCTGTGCAGACGAGTTGAATCCA
EST: gi|100387548|gb|BY988419.1|BY988419
EST:     GATTGTCATCTCCAAGACGAAGCTCACAGATGGCTTACTCCATCTGCTAG                         GGCCAGATGAGAGGACGGAGTTCAGAATTCTGTGCAGACGAGTTGAATCCA
genomic: GATTGTCATCTCCAAGACGAAGCTCACAGATGGCTTACTCCATCTGCTAGgtgcgtactt ... ttgttgacagGGCCAGATGAGAGGACGGAGTTCAGAATTCTGTGCAGACGAGTTGAATCCA
EST: gi|100401308|gb|BY990937.1|BY990937
EST:     GATTGTCATCTCCAAGACGAAGCTCACAGATGGCTTACCCCATCTGCTAG                         GGCCAGATGAGAGGACGGAGTTCAGAATTCTGTGCAGACGAGTTGAATCCA
genomic: GATTGTCATCTCCAAGACGAAGCTCACAGATGGCTTACTCCATCTGCTAGgtgcgtactt ... ttgttgacagGGCCAGATGAGAGGACGGAGTTCAGAATTCTGTGCAGACGAGTTGAATCCA

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), 33 (downstream exon)
Score: 16

AAGATGATGCAAACGCGGAAGGACATTTTGGAAATCGACAGGGAGAGTGTGATTGTCATCTCCAAGACGAAGCTCACAGATGGCTTACTCCATCTGCTAGgtgcgtactt ... ttgttgacagGGCCAGATGAGAGGACGGAGTTCAGAATTCTGTGCAGACGAGTTGAATCCACCATACGTGCTTGGTACAACCTTCAGTTTGAGGACTTGAAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactgagaggaggctgtgaccttcctggctcatttttgtccacgattgttgacagGGCCAGATGAGAGGACGGAGTTCAGAATTCTGTGCAGACGAGTTGAATCCACCATACGTGCTTGGTACAACCTTCAGTTTGAGGACTTGAAT
                             tcattttt  TA-rich tract