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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcgatgctgtctacgacgtgggtcttatgttttgatttcgcgtgtgcttgtcgtctttgttcttaaagctagtgtctgacaaagctgaaaatcgtgtagGACCGATTTGGGGTGAGAGATATAAGCGGTGACTTCAGCGAGATGACAGCGGCCATCTACCTGCAAGTCAGCATCATCAGTCAGGCCCTTATCTTCGTCA

Basic information

species Physcomitrella patens
transcript PP1S6_11V6.1
intron # 14
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|162193951|gb|FC371764.1|FC371764
EST:     TGATGACGGTCCTGTTCTTCTGGCTCATGCACGAGACCACGTTTTTCCCG                         GACCGATTTGGGGTGAGAGATATAAGCGGTGACTTCAGCGAGATGACAGCG
genomic: TGATGACGGTCCTGTTCTTCTGGCTCATGCACGAGACCACGTTTTTCCCGgtacatgata ... aatcgtgtagGACCGATTTGGGGTGAGAGATATAAGCGGTGACTTCAGCGAGATGACAGCG
EST: gi|162198821|gb|FC374304.1|FC374304
EST:     TGATGACGGTCCTGTTCTTCTGGCTCATGCACGAGACCACGTTTTTCCCG                         GACCGATTTGGGGTGAGAGATATAAGCGGTGACTTCAGCGAGATGACAGCG
genomic: TGATGACGGTCCTGTTCTTCTGGCTCATGCACGAGACCACGTTTTTCCCGgtacatgata ... aatcgtgtagGACCGATTTGGGGTGAGAGATATAAGCGGTGACTTCAGCGAGATGACAGCG
EST: gi|162252827|gb|FC428858.1|FC428858
EST:     TGATGACGGTCCTGTTCTTCTGGCTCATGCACGAGACCACGTTTTTCCCG                         GACCGATTTGGGGTGAGAGATATAAGCGGTGACTTCAGCGAGATGACAGCG
genomic: TGATGACGGTCCTGTTCTTCTGGCTCATGCACGAGACCACGTTTTTCCCGgtacatgata ... aatcgtgtagGACCGATTTGGGGTGAGAGATATAAGCGGTGACTTCAGCGAGATGACAGCG
EST: gi|162267612|gb|FC444675.1|FC444675
EST:     TGATGACGGTCCTGTTCTTCTGGCTCATGCACGAGACCACGTTTTTCCCG                         GACCGATTTGGGGTGAGAGATATAAGCGGTGACTTCAGCGAGATGACAGCG
genomic: TGATGACGGTCCTGTTCTTCTGGCTCATGCACGAGACCACGTTTTTCCCGgtacatgata ... aatcgtgtagGACCGATTTGGGGTGAGAGATATAAGCGGTGACTTCAGCGAGATGACAGCG
EST: gi|162185478|gb|FC362560.1|FC362560
EST:     TGATGACGGTCCTGTTCTTCTGGCTCATGCACGAGACCACGTTTTTCCCG                         GACCGATTTGGGGTGAGAGATATAAGCGGTGACTTCAGCGAGATGACAGCG
genomic: TGATGACGGTCCTGTTCTTCTGGCTCATGCACGAGACCACGTTTTTCCCGgtacatgata ... aatcgtgtagGACCGATTTGGGGTGAGAGATATAAGCGGTGACTTCAGCGAGATGACAGCG
EST: gi|162198374|gb|FC375547.1|FC375547
EST:     TGATGACGGTCCTGTTCTTCTGGCTCATGCACGAGACCACGTTTTTCCCG                         GACCGATTTGGGGTGAGAGATATAAGCGGTGACTTCAGCGAGATGACAGCG
genomic: TGATGACGGTCCTGTTCTTCTGGCTCATGCACGAGACCACGTTTTTCCCGgtacatgata ... aatcgtgtagGACCGATTTGGGGTGAGAGATATAAGCGGTGACTTCAGCGAGATGACAGCG
EST: gi|162183362|gb|FC359277.1|FC359277
EST:     TGATGACGGTCCTGTTCTTCTGGCTCATGCACGAGACCACGTTTTTCCCG                         GACCGATTTGGGGTGAGAGATATAAGCGGTGACTTCAGCGAGATGACAGCG
genomic: TGATGACGGTCCTGTTCTTCTGGCTCATGCACGAGACCACGTTTTTCCCGgtacatgata ... aatcgtgtagGACCGATTTGGGGTGAGAGATATAAGCGGTGACTTCAGCGAGATGACAGCG
EST: gi|162184822|gb|FC361124.1|FC361124
EST:     TGATGACGGTCCTGTTCTTCTGGCTCATGCACGAGACCACGTTTTTCCCG                         GACCGATTTGGGGTGAGAGATATAAGCGGTGACTTCAGCGAGATGACAGCG
genomic: TGATGACGGTCCTGTTCTTCTGGCTCATGCACGAGACCACGTTTTTCCCGgtacatgata ... aatcgtgtagGACCGATTTGGGGTGAGAGATATAAGCGGTGACTTCAGCGAGATGACAGCG
EST: gi|162164471|gb|FC341584.1|FC341584
EST:     TGATGACGGTCCTGTTCTTCTGGCTCATGCACGAGACCACGTTTTTCCCG                         GACCGATTTGGGGTGAGAGATATAAGCGGTGACTTCAGCGAGATGACAGCG
genomic: TGATGACGGTCCTGTTCTTCTGGCTCATGCACGAGACCACGTTTTTCCCGgtacatgata ... aatcgtgtagGACCGATTTGGGGTGAGAGATATAAGCGGTGACTTCAGCGAGATGACAGCG
EST: gi|162179356|gb|FC356305.1|FC356305
EST:     TGATGACGGTCCTGTTCTTCTGGCTCATGCACGAGACCACGTTTTTCCCG                         GACCGATTTGGGGTGAGAGATATAAGCGGTGACTTCAGCGAGATGACAGCG
genomic: TGATGACGGTCCTGTTCTTCTGGCTCATGCACGAGACCACGTTTTTCCCGgtacatgata ... aatcgtgtagGACCGATTTGGGGTGAGAGATATAAGCGGTGACTTCAGCGAGATGACAGCG
EST: gi|162157211|gb|FC332845.1|FC332845
EST:     TGATGACGGTCCTGTTCTTCTGGCTCATGCACGAGACCACGTTTTTCCCG                         GACCGATTTGGGGTGAGAGATATAAGCGGTGACTTCAGCGAGATGACAGCG
genomic: TGATGACGGTCCTGTTCTTCTGGCTCATGCACGAGACCACGTTTTTCCCGgtacatgata ... aatcgtgtagGACCGATTTGGGGTGAGAGATATAAGCGGTGACTTCAGCGAGATGACAGCG
EST: gi|162176072|gb|FC351866.1|FC351866
EST:     TGATGACGGTCCTGTTCTTCTGGCTCATGCACGAGACCACGTTTTTCCCG                         GACCGATTTGGGGTGAGAGATATAAGCGGTGACTTCAGCGAGATGACAGCG
genomic: TGATGACGGTCCTGTTCTTCTGGCTCATGCACGAGACCACGTTTTTCCCGgtacatgata ... aatcgtgtagGACCGATTTGGGGTGAGAGATATAAGCGGTGACTTCAGCGAGATGACAGCG
EST: gi|162198177|gb|FC375480.1|FC375480
EST:     TGATGACGGTCCTGTTCTTCTGGCTCATGCACGAGACCACGTTTTTCCCG                         GACCGATTTGGGGTGAGAGATATAAGCGGTGACTTCAGCGAGATGACAGCG
genomic: TGATGACGGTCCTGTTCTTCTGGCTCATGCACGAGACCACGTTTTTCCCGgtacatgata ... aatcgtgtagGACCGATTTGGGGTGAGAGATATAAGCGGTGACTTCAGCGAGATGACAGCG
EST: gi|162168958|gb|FC345640.1|FC345640
EST:     TGATGACGGTCCTGTTCTTCTGGCTCATGCACGAGACCACGTTTTTCCCG                         GACCGATTTGGGGTGAGAGATATAAGCGGTGACTTCAGCGAGATGACAGCG
genomic: TGATGACGGTCCTGTTCTTCTGGCTCATGCACGAGACCACGTTTTTCCCGgtacatgata ... aatcgtgtagGACCGATTTGGGGTGAGAGATATAAGCGGTGACTTCAGCGAGATGACAGCG
EST: gi|162185798|gb|FC362354.1|FC362354
EST:     TGATGACGGTCCTGTTCTTCTGGCTCATGCACGAGACCACGTTTTTCCCG                         GACCGATTTGGGGTGAGAGATATAAGCGGTGACTTCAGCGAGATGACAGCG
genomic: TGATGACGGTCCTGTTCTTCTGGCTCATGCACGAGACCACGTTTTTCCCGgtacatgata ... aatcgtgtagGACCGATTTGGGGTGAGAGATATAAGCGGTGACTTCAGCGAGATGACAGCG

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: 26

GTTGAGGGAGATTTTTGGTGTCGGTGTTGTGCTCGGCACCTACATGGCATTGATGACGGTCCTGTTCTTCTGGCTCATGCACGAGACCACGTTTTTCCCGgtacatgata ... aatcgtgtagGACCGATTTGGGGTGAGAGATATAAGCGGTGACTTCAGCGAGATGACAGCGGCCATCTACCTGCAAGTCAGCATCATCAGTCAGGCCCTTATCTTCGTCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttgtcgtctttgttcttaaagctagtgtctgacaaagctgaaaatcgtgtagGACCGATTTGGGGTGAGAGATATAAGCGGTGACTTCAGCGAGATGACAGCGGCCATCTACCTGCAAGTCAGCATCATCAGTCAGGCCCTTATCTTCGTCA
                             gtctgac  putative branch site (score: 26)
               ttcttaaa  TA-rich tract