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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtctgctatcttctaagtattcccgtttcaattgatggattcacactaactctaaccctggtaccgatttccctttttctttcttgtggtgtgggtagATAATAAGAAGGATCCGCTTCATGAAAAAGCCCCCAGTGAGCAGGTGTTTGTTCCGATTCGTGAGCCAAAATCATCAGACGAGATACTTCAGGGAGGGAA

Basic information

species Physcomitrella patens
transcript PP1S207_2V6.1
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|162154037|gb|FC330272.1|FC330272
EST:     GTCTAAGGCAGGTGGTACTCCTGCGGCAACTAGCAGTGTTCACCACTCAG                         ATAATAAGAAGGATCCGCTTCATGAAAAAGCCCCCAGTGAGCAGGTGTTTG
genomic: GTCTAAGGCAGGTGGTACTCCTGCGGCAACTAGCAGTGTTCACCACTCAGgtttgaaaac ... gtgtgggtagATAATAAGAAGGATCCGCTTCATGAAAAAGCCCCCAGTGAGCAGGTGTTTG
EST: gi|100424210|gb|BY958370.1|BY958370
EST:     GTCTAAGGCAGGTGGTACTCCTGCGGCAACTAGCAGTGTTCACCACTCAG                         ATAATAAGAAGGATCCGCTTCATGAAAAAGCCCCCAGTGAGCAGGTGTTTG
genomic: GTCTAAGGCAGGTGGTACTCCTGCGGCAACTAGCAGTGTTCACCACTCAGgtttgaaaac ... gtgtgggtagATAATAAGAAGGATCCGCTTCATGAAAAAGCCCCCAGTGAGCAGGTGTTTG
EST: gi|18359366|gb|BJ191427.1|BJ191427
EST:     GTCTAAGGCAGGTGGTACTCCTGCGGCAACTAGCAGTGTTCACCACTCAG                         ATAATAAGAAGGATCCGCTTCATGAAAAAGCCCCCAGTGAGCAGGTGTTTG
genomic: GTCTAAGGCAGGTGGTACTCCTGCGGCAACTAGCAGTGTTCACCACTCAGgtttgaaaac ... gtgtgggtagATAATAAGAAGGATCCGCTTCATGAAAAAGCCCCCAGTGAGCAGGTGTTTG
EST: gi|100444240|gb|BY982269.1|BY982269
EST:     GTCTAAGGCAGGTGGTACTCCTGCGGCAACTAGCAGTGTTCACCACTCAG                         ATAATAAGAAGGATCCGCTTCATGAAAAAGCCCCCAGTGAGCAGGTGTTTG
genomic: GTCTAAGGCAGGTGGTACTCCTGCGGCAACTAGCAGTGTTCACCACTCAGgtttgaaaac ... gtgtgggtagATAATAAGAAGGATCCGCTTCATGAAAAAGCCCCCAGTGAGCAGGTGTTTG
EST: gi|162196860|gb|FC374734.1|FC374734
EST:     GTCTAAGGCAGGTGGTACTCCTGCGGCAACTAGCAGTGTTCACCACTCAG                         ATAATAAGAAGGATCCGCTTCATGAAAAAGCCCCCAGTGAGCAGGTGTTTG
genomic: GTCTAAGGCAGGTGGTACTCCTGCGGCAACTAGCAGTGTTCACCACTCAGgtttgaaaac ... gtgtgggtagATAATAAGAAGGATCCGCTTCATGAAAAAGCCCCCAGTGAGCAGGTGTTTG
EST: gi|67575843|gb|BJ948667.1|BJ948667
EST:     GTCTAAGGCAGGTGGTACTCCTGCGGCAACTAGCAGTGTTCACCACTCAG                         ATAATAAGAAGGATCCGCTTCATGAAAAAGCCCCCAGTGAGCAGGTGTTTG
genomic: GTCTAAGGCAGGTGGTACTCCTGCGGCAACTAGCAGTGTTCACCACTCAGgtttgaaaac ... gtgtgggtagATAATAAGAAGGATCCGCTTCATGAAAAAGCCCCCAGTGAGCAGGTGTTTG
EST: gi|67570462|gb|BJ943286.1|BJ943286
EST:     GTCTAAGGCAGGTGGTACTCCTGCGGCAACTANCAGTGTTCACCACTCAG                         ATAATAAGAAGGATCCGCTTCATGAAAAAGCCCCCAGTGAGCAGGTGTTTG
genomic: GTCTAAGGCAGGTGGTACTCCTGCGGCAACTAGCAGTGTTCACCACTCAGgtttgaaaac ... gtgtgggtagATAATAAGAAGGATCCGCTTCATGAAAAAGCCCCCAGTGAGCAGGTGTTTG
EST: gi|18363961|gb|BJ196034.1|BJ196034
EST:     GTCTAAGGCAGGTGGTACTCCTGCGGCAACTAGCAGTGTTCACCACTCAG                         ATAATAAGAAGGATCCGCTTCATGAAAAAGCCCCCAGTGAGCAGGTGTTTG
genomic: GTCTAAGGCAGGTGGTACTCCTGCGGCAACTAGCAGTGTTCACCACTCAGgtttgaaaac ... gtgtgggtagATAATAAGAAGGATCCGCTTCATGAAAAAGCCCCCAGTGAGCAGGTGTTTG

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), 35 (downstream exon)
Score: 27

TGCACTTGCTGGAACGCCCTCGATGGGGCGTGGCTCGGTAACTGTTGGTGGTCTAAGGCAGGTGGTACTCCTGCGGCAACTAGCAGTGTTCACCACTCAGgtttgaaaac ... gtgtgggtagATAATAAGAAGGATCCGCTTCATGAAAAAGCCCCCAGTGAGCAGGTGTTTGTTCCGATTCGTGAGCCAAAATCATCAGACGAGATACTTCAGGGAGGGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactaactctaaccctggtaccgatttccctttttctttcttgtggtgtgggtagATAATAAGAAGGATCCGCTTCATGAAAAAGCCCCCAGTGAGCAGGTGTTTGTTCCGATTCGTGAGCCAAAATCATCAGACGAGATACTTCAGGGAGGGAA
                        tttccctttttctttc  CT-rich tract
                              tttttcttt  TA-rich tract