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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGCGGTCGGGTTGCTGAGGAGATGGTCTTTGGGCCTGATCAAGTTACTAGCGGGGCTCGGAGTGATTTGCAGCAGGCGACTGCCCTTGCTCGTCACATGgtactgttacgcaaaattctgaaactcttgaagaggaatatgattttttgttattgctcgttatgacacgttctgttaagcaagagaagtgccatttacaatttgtaacatgtttgatcactattcgtatttaccttctatgcag

Basic information

species Physcomitrella patens
transcript PP1S9_238V6.1
intron # 14
splice site 5'
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|162202060|gb|FC377266.1|FC377266
EST:     CAGCAGGCGACTGCCCTTGCTCGTCACATG                         GTGACCGAGTGTGGTATGAGTGATGCAGTAGGTCCCGTATTTATTGATTCA
genomic: CAGCAGGCGACTGCCCTTGCTCGTCACATGgtactgttac ... ttctatgcagGTGACCGAGTGTGGTATGAGTGATGCAGTAGGTCCCGTATTTATTGATTCA
EST: gi|162188456|gb|FC365054.1|FC365054
EST:     GCGGGGCTCGGAGTGATTTGCAGCAGGCGACTGCCCTTGCTCGTCACATG                         GTGACCGAGTGTGGTATGAGTGATGCAGTAGGTCCCGTATTTATTGATTCA
genomic: GCGGGGCTCGGAGTGATTTGCAGCAGGCGACTGCCCTTGCTCGTCACATGgtactgttac ... ttctatgcagGTGACCGAGTGTGGTATGAGTGATGCAGTAGGTCCCGTATTTATTGATTCA
EST: gi|162188457|gb|FC365055.1|FC365055
EST:     GCGGGGCTCGGAGTGATTTGCAGCAGGCGACTGCCCTTGCTCGTCACATG                         GTGACCGAGTGTGGTATGAGTGATGCAGTAGGTCCCGTATTTATTGATTCA
genomic: GCGGGGCTCGGAGTGATTTGCAGCAGGCGACTGCCCTTGCTCGTCACATGgtactgttac ... ttctatgcagGTGACCGAGTGTGGTATGAGTGATGCAGTAGGTCCCGTATTTATTGATTCA
EST: gi|162195892|gb|FC375625.1|FC375625
EST:     GCGGGGCTCGGAGTGATTTGCAGCAGGCGACTGCCCTTGCTCGTCACATG                         GTGACCGAGTGTGGTATGAGTGATGCAGTAGGTCCCGTATTTATTGATTCA
genomic: GCGGGGCTCGGAGTGATTTGCAGCAGGCGACTGCCCTTGCTCGTCACATGgtactgttac ... ttctatgcagGTGACCGAGTGTGGTATGAGTGATGCAGTAGGTCCCGTATTTATTGATTCA
EST: gi|162191141|gb|FC367403.1|FC367403
EST:     GCGGGGCTCGGAGTGATTTGCAGCAGGCGACTGCCCTTGCTCGTCACATG                         GTGACCGAGTGTGGTATGAGTGATGCAGTAGGTCCCGTATTTATTGATTCA
genomic: GCGGGGCTCGGAGTGATTTGCAGCAGGCGACTGCCCTTGCTCGTCACATGgtactgttac ... ttctatgcagGTGACCGAGTGTGGTATGAGTGATGCAGTAGGTCCCGTATTTATTGATTCA
EST: gi|162191671|gb|FC367404.1|FC367404
EST:     GCGGGGCTCGGAGTGATTTGCAGCAGGCGACTGCCCTTGCTCGTCACATG                         GTGACCGAGTGTGGTATGAGTGATGCAGTAGGT
genomic: GCGGGGCTCGGAGTGATTTGCAGCAGGCGACTGCCCTTGCTCGTCACATGgtactgttac ... ttctatgcagGTGACCGAGTGTGGTATGAGTGATGCAGTAGGT
EST: gi|162246868|gb|FC424746.1|FC424746
EST:     GCGGGGCTCGGAGTGATTTGCAGCAGGCGACTGCCCTTGCTCGTCACATG                         GTGACCGAGTGTGGTATGAGTGATGCAGTAGGTCCCGTATTTATTGATTCA
genomic: GCGGGGCTCGGAGTGATTTGCAGCAGGCGACTGCCCTTGCTCGTCACATGgtactgttac ... ttctatgcagGTGACCGAGTGTGGTATGAGTGATGCAGTAGGTCCCGTATTTATTGATTCA
EST: gi|162177322|gb|FC353479.1|FC353479
EST:     GCGGGGCTCGGAGTGATTTGCAGCAGGCGACTGCCCTTGCTCGTCACATG                         GTGACCGAGTGTGGTATGAGTGATGCAGTAGGTCCCGTATTTATTGATTCA
genomic: GCGGGGCTCGGAGTGATTTGCAGCAGGCGACTGCCCTTGCTCGTCACATGgtactgttac ... ttctatgcagGTGACCGAGTGTGGTATGAGTGATGCAGTAGGTCCCGTATTTATTGATTCA
EST: gi|162177323|gb|FC353480.1|FC353480
EST:     GCGGGGCTCGGAGTGATTTGCAGCAGGCGACTGCCCTTGCTCGTCACATG                         GTGACCGAGTGTGGTATGAGTGATGCAGTAGGTCCCGTATTTATTGATTCA
genomic: GCGGGGCTCGGAGTGATTTGCAGCAGGCGACTGCCCTTGCTCGTCACATGgtactgttac ... ttctatgcagGTGACCGAGTGTGGTATGAGTGATGCAGTAGGTCCCGTATTTATTGATTCA
EST: gi|162191707|gb|FC367440.1|FC367440
EST:     GCGGGGCTCGGAGTGATTTGCAGCAGGCGACTGCCCTTGCTCGTCACATG                         GTGACCGAGTGTGGTATGAGTGATGCAGTAGGTCCCGTATTTATTGATTCA
genomic: GCGGGGCTCGGAGTGATTTGCAGCAGGCGACTGCCCTTGCTCGTCACATGgtactgttac ... ttctatgcagGTGACCGAGTGTGGTATGAGTGATGCAGTAGGTCCCGTATTTATTGATTCA

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), 34 (downstream exon)
Score: 12

GGGCGGTCGGGTTGCTGAGGAGATGGTCTTTGGGCCTGATCAAGTTACTAGCGGGGCTCGGAGTGATTTGCAGCAGGCGACTGCCCTTGCTCGTCACATGgtactgttac ... ttctatgcagGTGACCGAGTGTGGTATGAGTGATGCAGTAGGTCCCGTATTTATTGATTCAAAACTTAGTGGCGATTTTCAGAAAAGTATCGATGCTGAG




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