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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgattaaatgttcacttcgagctattttcttgtaataatacttgttaagatgttttgctgaggtaaagaaatatctgatgacattgtttctggtatgcagTGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAAATCTTTCATTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTG

Basic information

species Physcomitrella patens
transcript PP1S3_553V6.1
intron # 22
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|162280078|gb|FC456472.1|FC456472
EST:     GGACTGTTGACTCTCAACCCTTACCATTCAGACCGATTTTTGCTATCAAA                         TGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAA
genomic: GGACTGTTGACTCTCAACCCTTACCATTCAGACCGATTTTTGCTATCAAAgtaagctacc ... tggtatgcagTGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAA
EST: gi|37835828|gb|BJ593840.1|BJ593840
EST:     GGACTGTTGACTCTCAACCCTTACCATTCAGACCGATTTTTGCTATCAAA                         TGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAA
genomic: GGACTGTTGACTCTCAACCCTTACCATTCAGACCGATTTTTGCTATCAAAgtaagctacc ... tggtatgcagTGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAA
EST: gi|37848700|gb|BJ606708.1|BJ606708
EST:     GGACTGTTGACTCTCAACCCTTACCATTCAGACCGATTTTTGCTATCAAA                         TGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAA
genomic: GGACTGTTGACTCTCAACCCTTACCATTCAGACCGATTTTTGCTATCAAAgtaagctacc ... tggtatgcagTGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAA
EST: gi|162176023|gb|FC351024.1|FC351024
EST:     GGACTGTTGACTCTCAACCCTTACCATTCAGACCGATTTTTGCTATCAAA                         TGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAA
genomic: GGACTGTTGACTCTCAACCCTTACCATTCAGACCGATTTTTGCTATCAAAgtaagctacc ... tggtatgcagTGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAA
EST: gi|18336901|gb|BJ168924.1|BJ168924
EST:     GGACTGTTGACTCTCAACCCTTACCATTCAGACCGATTTTTGCTATCAAA                         TGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAA
genomic: GGACTGTTGACTCTCAACCCTTACCATTCAGACCGATTTTTGCTATCAAAgtaagctacc ... tggtatgcagTGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAA
EST: gi|162176009|gb|FC351023.1|FC351023
EST:     GGACTGTTGACTCTCAACCCTTACCATTCAGACCGATTTTTGCTATCAAA                         TGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAA
genomic: GGACTGTTGACTCTCAACCCTTACCATTCAGACCGATTTTTGCTATCAAAgtaagctacc ... tggtatgcagTGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAA
EST: gi|37830143|gb|BJ588155.1|BJ588155
EST:     GGACTGTTGACTCTCAACCCTTACCATTCAGACCGATTTTTGCTATCAAA                         TGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAA
genomic: GGACTGTTGACTCTCAACCCTTACCATTCAGACCGATTTTTGCTATCAAAgtaagctacc ... tggtatgcagTGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAA
EST: gi|37846451|gb|BJ604459.1|BJ604459
EST:     GGACTGTTGACTCTCAACCCTTACCATTCAGACCGATTTTTGCTATCAAA                         TGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAA
genomic: GGACTGTTGACTCTCAACCCTTACCATTCAGACCGATTTTTGCTATCAAAgtaagctacc ... tggtatgcagTGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAA
EST: gi|67578805|gb|BJ950972.1|BJ950972
EST:     GGACTGTTGACTCTCAACCCTTACCATTCAGACCGATTTTTGCTATCAAA                         TGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAA
genomic: GGACTGTTGACTCTCAACCCTTACCATTCAGACCGATTTTTGCTATCAAAgtaagctacc ... tggtatgcagTGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAA
EST: gi|37827765|gb|BJ585777.1|BJ585777
EST:     GGACTGTTGACTCTCAACCCTTACCATTCAGACCGATTTTTGCTATCAAA                         TGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAA
genomic: GGACTGTTGACTCTCAACCCTTACCATTCAGACCGATTTTTGCTATCAAAgtaagctacc ... tggtatgcagTGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAA
EST: gi|162163326|gb|FC339652.1|FC339652
EST:     GGACTGTTGACTCTCAACCCTTACCATTCAGACCGATTTTTGCTATCAAA                         TGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAA
genomic: GGACTGTTGACTCTCAACCCTTACCATTCAGACCGATTTTTGCTATCAAAgtaagctacc ... tggtatgcagTGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAA
EST: gi|18337499|gb|BJ169523.1|BJ169523
EST:     GGACTGTTGACTCTCAACCCTTACCATTCAGACCGATTTTTGCTATCAAA                         TGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAA
genomic: GGACTGTTGACTCTCAACCCTTACCATTCAGACCGATTTTTGCTATCAAAgtaagctacc ... tggtatgcagTGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAA
EST: gi|37839139|gb|BJ597147.1|BJ597147
EST:     GGACTGTTGACTCTCAACCCTTACCATTCAGACCGATTTTTGCTATCAAA                         TGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAA
genomic: GGACTGTTGACTCTCAACCCTTACCATTCAGACCGATTTTTGCTATCAAAgtaagctacc ... tggtatgcagTGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAA
EST: gi|37824468|gb|BJ582534.1|BJ582534
EST:     GGACTGTTGACTCTCAACCCTTACCATTCAGACCGATTTTTGCTATCAAA                         TGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAA
genomic: GGACTGTTGACTCTCAACCCTTACCATTCAGACCGATTTTTGCTATCAAAgtaagctacc ... tggtatgcagTGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAA
EST: gi|37826418|gb|BJ584430.1|BJ584430
EST:     GGACTGTTGACTCTCAACCCTTACCATTCAGACCGATTTTTGCTATCAAA                         TGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAA
genomic: GGACTGTTGACTCTCAACCCTTACCATTCAGACCGATTTTTGCTATCAAAgtaagctacc ... tggtatgcagTGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAA
EST: gi|67507537|gb|BJ940419.1|BJ940419
EST:     GACTGTTGACTCTCAACCCTTACCANTTCAGACCGATTTTTGCTATCAAA                         TGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAA
genomic: GACTGTTGACTCTCAACCCTTACCA-TTCAGACCGATTTTTGCTATCAAAgtaagctacc ... tggtatgcagTGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAA
EST: gi|162186176|gb|FC362108.1|FC362108
EST:     GGACTGTTGACTCTCAACCCTTACCATTCAGACCGATTTTTGCTATCAAA                         TGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAA
genomic: GGACTGTTGACTCTCAACCCTTACCATTCAGACCGATTTTTGCTATCAAAgtaagctacc ... tggtatgcagTGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAA

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: 19 (upstream exon), 34 (downstream exon)
Score: 2

GTTAGGATTGCACAAGGCCTTGTTCACATGGGGAAAGGACTGTTGACTCTCAACCCTTACCATTCAGACCGATTTTTGCTATCAAAgtaagctacc ... tggtatgcagTGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAAATCTTTCATTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagatgttttgctgaggtaaagaaatatctgatgacattgtttctggtatgcagTGTGGCGTTGGCAGGCCTGATCACATTTTTGCATGCTAGCTTTGATATGAAATCTTTCATTCTTGGGAAATACCATTATGTTCTGTATTTTCTTGTGCTG
                           atctgat  putative branch site (score: 2)
                                      ttgtttct  putative PPT
                  taaagaaatat  TA-rich tract