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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggtttgtgaagttgttgattttgcattatattcaaatttttcagatttcctattaggaggagtaattgttcacttcgattggtgggtaagagtttaaagtatagtctcttcctattttcagATTGCTGCCATGCCTAGAGAGCTTGCAATGAAGAGAGGAATTCCCATCCCTTTTTCACCATCATTTTCGAAGGATTACCTGGACCAATTGGCGTGCGACC

Basic information

species Physcomitrella patens
transcript PP1S79_105V6.1
intron # 9
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|67573788|gb|BJ946612.1|BJ946612
EST:     CAATTCGTGAGTATCCGCGTGTCGTACATATTCCTATGCCCCTTTGTCAG                         ATTGCTGCCATGCCTAGAGAGCTTGCAATGAAGAGAGGAATTCCCATCCCT
genomic: CAATTCGTGAGTATCCGCGTGTCGTACATATTCCTATGCCCCTTTGTCAGgtatggtttg ... ctattttcagATTGCTGCCATGCCTAGAGAGCTTGCAATGAAGAGAGGAATTCCCATCCCT
EST: gi|37842479|gb|BJ600487.1|BJ600487
EST:     CAATTCGTGAGTATCCGCGTGTCGTACATATTCCTATGCCCCTTTGTCAG                         ATTGCTGCCATGCCTAGAGAGCTTGCAATGAAGAGAGGAATTCCCATCCCT
genomic: CAATTCGTGAGTATCCGCGTGTCGTACATATTCCTATGCCCCTTTGTCAGgtatggtttg ... ctattttcagATTGCTGCCATGCCTAGAGAGCTTGCAATGAAGAGAGGAATTCCCATCCCT
EST: gi|208367986|gb|DC955393.1|DC955393
EST:     CAATTCGTGAGTATCCGCGTGTCGTACATATTCCTATGCCCCTTTGTCAG                         ATTGCTGCCATGCCTAGAGAGCTTGCAATGAAGAGAGGAATTCCCATCCCT
genomic: CAATTCGTGAGTATCCGCGTGTCGTACATATTCCTATGCCCCTTTGTCAGgtatggtttg ... ctattttcagATTGCTGCCATGCCTAGAGAGCTTGCAATGAAGAGAGGAATTCCCATCCCT
EST: gi|67700799|gb|BJ961032.1|BJ961032
EST:     CAATTCGTGAGTATCCGCGTGTCGTACATATTCCTATGCCCCTTTGTCAG                         ATTGCTGCCATGCCTAGAGAGCTTGCAATGAAGAGAGGAATTCCCATCCCT
genomic: CAATTCGTGAGTATCCGCGTGTCGTACATATTCCTATGCCCCTTTGTCAGgtatggtttg ... ctattttcagATTGCTGCCATGCCTAGAGAGCTTGCAATGAAGAGAGGAATTCCCATCCCT
EST: gi|208352691|gb|DC921425.1|DC921425
EST:     CAATTCGTGAGTATCCGCGTGTCGTACATATTCCTATGCCCCTTTGTCAG                         ATTGCTGCCATGCCTAGAGAGCTTGCAATGAAGAGAGGAATTCCCATCCCT
genomic: CAATTCGTGAGTATCCGCGTGTCGTACATATTCCTATGCCCCTTTGTCAGgtatggtttg ... ctattttcagATTGCTGCCATGCCTAGAGAGCTTGCAATGAAGAGAGGAATTCCCATCCCT
EST: gi|162256291|gb|FC432197.1|FC432197
EST:     CAATTCGTGAGTATCCGCGTGTCGTACATATTCCTATGCCCCTTTGTCAG                         ATTGCTGCCATGCCTAGAGAGCTTGCAATGAAGAGAGGAATTCCCATCCCT
genomic: CAATTCGTGAGTATCCGCGTGTCGTACATATTCCTATGCCCCTTTGTCAGgtatggtttg ... ctattttcagATTGCTGCCATGCCTAGAGAGCTTGCAATGAAGAGAGGAATTCCCATCCCT
EST: gi|208377554|gb|DC922657.1|DC922657
EST:     CAATTCGTGAGTATCCGCGTGTCGTACATATTCCTATGCCCCTTTGTCAG                         ATTGCTGCCATGCCTAGAGAGCTTGCAATGAAGAGAGGAATTCCCATCCCT
genomic: CAATTCGTGAGTATCCGCGTGTCGTACATATTCCTATGCCCCTTTGTCAGgtatggtttg ... ctattttcagATTGCTGCCATGCCTAGAGAGCTTGCAATGAAGAGAGGAATTCCCATCCCT
EST: gi|162259818|gb|FC435953.1|FC435953
EST:     CAATTCGTGAGTATCCGCGTGTCGTACATATTCCTATGCCCCTTTGTCAG                         ATTGCTGCCATGCCTAGAGAGCTTGCAATGAAGAGAGGAATTCCCATCCCT
genomic: CAATTCGTGAGTATCCGCGTGTCGTACATATTCCTATGCCCCTTTGTCAGgtatggtttg ... ctattttcagATTGCTGCCATGCCTAGAGAGCTTGCAATGAAGAGAGGAATTCCCATCCCT
EST: gi|208367694|gb|DC955025.1|DC955025
EST:     CAATTCGTGAGTATCCGCGTGTCGTACATATTCCTATGCCCCTTTGTCAG                         ATTGCTGCCATGCCTAGAGAGCTTGCAATGAAGAGAGGAATTCCCATCCCT
genomic: CAATTCGTGAGTATCCGCGTGTCGTACATATTCCTATGCCCCTTTGTCAGgtatggtttg ... ctattttcagATTGCTGCCATGCCTAGAGAGCTTGCAATGAAGAGAGGAATTCCCATCCCT
EST: gi|162220174|gb|FC396569.1|FC396569
EST:     CAATTCGTGAGTATCCGCGTGTCGTACATATTCCTATGCCCCTTTGTCAG                         ATTGCTGCCATGCCTAGAGAGCTTGCAATGAAGAGAGGAATTCCCATCCCT
genomic: CAATTCGTGAGTATCCGCGTGTCGTACATATTCCTATGCCCCTTTGTCAGgtatggtttg ... ctattttcagATTGCTGCCATGCCTAGAGAGCTTGCAATGAAGAGAGGAATTCCCATCCCT
EST: gi|67700542|gb|BJ960775.1|BJ960775
EST:     CAATTCGTGAGTATCCGCGTGTCGTACATATTCCTATGCCCCTTTGTCAG                         ATTGCTGCCATGCCTAGAGAGCTTGCAATGAAGAGAGGAATTCCCATCCCT
genomic: CAATTCGTGAGTATCCGCGTGTCGTACATATTCCTATGCCCCTTTGTCAGgtatggtttg ... ctattttcagATTGCTGCCATGCCTAGAGAGCTTGCAATGAAGAGAGGAATTCCCATCCCT
EST: gi|67697174|gb|BJ957407.1|BJ957407
EST:     CAATTCGTGAGTATCCGCGTGTCGTACATATTCCTATGCCCCTTTGTCAG                         ATTGCTGCCATGCCTAGAGAGCTTGCAATGAAGAGAGGAATTCCCATCCCT
genomic: CAATTCGTGAGTATCCGCGTGTCGTACATATTCCTATGCCCCTTTGTCAGgtatggtttg ... ctattttcagATTGCTGCCATGCCTAGAGAGCTTGCAATGAAGAGAGGAATTCCCATCCCT
EST: gi|37846724|gb|BJ604732.1|BJ604732
EST:     CAATTCGTGAGTATCCGCGTGTCGTACATATTCCTATGCCCCTTTGTCAG                         ATTGCTGCCATGCCTAGAGAGCTTGCAATGAAGAGAGGAATTCCCATCCCT
genomic: CAATTCGTGAGTATCCGCGTGTCGTACATATTCCTATGCCCCTTTGTCAGgtatggtttg ... ctattttcagATTGCTGCCATGCCTAGAGAGCTTGCAATGAAGAGAGGAATTCCCATCCCT
EST: gi|67578914|gb|BJ951081.1|BJ951081
EST:     CAATTCGTGAGTATCCGCGTGTCGTACATATTCCTATGCCCCTTTGTCAG                         ATTGCTGCCATGCCTAGAGAGCTTGCAATGAAGAGAGGAATTCCCATCCCT
genomic: CAATTCGTGAGTATCCGCGTGTCGTACATATTCCTATGCCCCTTTGTCAGgtatggtttg ... ctattttcagATTGCTGCCATGCCTAGAGAGCTTGCAATGAAGAGAGGAATTCCCATCCCT
EST: gi|162276086|gb|FC452362.1|FC452362
EST:     CAATTCGTGAGTATCCGCGTGTCGTACATATTCCTATGCCCCTTTGTCAG                         ATTGCTGCCATGCCTAGAGAGCTTGCAATGAAGAGAGGAATTCCCATCCCT
genomic: CAATTCGTGAGTATCCGCGTGTCGTACATATTCCTATGCCCCTTTGTCAGgtatggtttg ... ctattttcagATTGCTGCCATGCCTAGAGAGCTTGCAATGAAGAGAGGAATTCCCATCCCT
EST: gi|67577666|gb|BJ949833.1|BJ949833
EST:     CAATTCGTGAGTATCCGCGTGTCGTACATATTCCTATGCCCCTTTGTCAG                         ATTGCTGCCATGCCTAGAGAGCTTGCAATGAAGAGAGGAATTCCCATCCCT
genomic: CAATTCGTGAGTATCCGCGTGTCGTACATATTCCTATGCCCCTTTGTCAGgtatggtttg ... ctattttcagATTGCTGCCATGCCTAGAGAGCTTGCAATGAAGAGAGGAATTCCCATCCCT

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), 35 (downstream exon)
Score: 6

GTTGCGCTGATGTTTGAGGCAATTCGTGAGTATCCGCGTGTCGTACATATTCCTATGCCCCTTTGTCAGgtatggtttg ... ctattttcagATTGCTGCCATGCCTAGAGAGCTTGCAATGAAGAGAGGAATTCCCATCCCTTTTTCACCATCATTTTCGAAGGATTACCTGGACCAATTGGCGTGCGACC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttcacttcgattggtgggtaagagtttaaagtatagtctcttcctattttcagATTGCTGCCATGCCTAGAGAGCTTGCAATGAAGAGAGGAATTCCCATCCCTTTTTCACCATCATTTTCGAAGGATTACCTGGACCAATTGGCGTGCGACC
                                      tctcttcctattttc  CT-rich tract
                          tttaaagtata  TA-rich tract