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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCCAATACGGGTCCCAGCGGAGTTACGGTGCTTCTGGTGTCCTCTGCTATCATCGGTTGGGGAATGTACCAAGTCGGCCAAGGCAACATTTACCGTAGgtacgcattttttaggtcttctatgtcgtgatcagggttgctcgtgtgcatgcgattgtgcgctccttgagcataaagatagttttacaacgaatctaat...

Basic information

species Physcomitrella patens
transcript PP1S41_263V6.1
intron # 1
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|18341968|gb|BJ174003.1|BJ174003
EST:     ATCATCGGTTGGGGAATGTACCAAGTCGGCCAAGGCAACATTTACCGTAG                         GGGCTTGAAAGCTGAGAAGATTGCTGCAAGACAAGCTATATTACCTCTCAT
genomic: ATCATCGGTTGGGGAATGTACCAAGTCGGCCAAGGCAACATTTACCGTAGgtacgcattt ... catattgtagGGGCTTGAAAGCTGAGAAGATTGCTGCAAGACAAGCTATATTACCTCTCAT
EST: gi|37821040|gb|BJ579106.1|BJ579106
EST:     ATCATCGGTTGGGGAATGTACCAAGTCGGCCAAGGCAACATTTACCGTAG                         GGGCTTGAAAGCTGAGAAGATTGCTGCAAGACAAGCTATATTACCTCTCAT
genomic: ATCATCGGTTGGGGAATGTACCAAGTCGGCCAAGGCAACATTTACCGTAGgtacgcattt ... catattgtagGGGCTTGAAAGCTGAGAAGATTGCTGCAAGACAAGCTATATTACCTCTCAT
EST: gi|162201625|gb|FC377455.1|FC377455
EST:     ATCATCGGTTGGGGAATGTACCAAGTCGGCCAAGGCAACATTTACCGTAG                         GGGCTTGAAAGCTGAGAAGATTGCTGCAAGACAAGCTATATTACCTCTCAT
genomic: ATCATCGGTTGGGGAATGTACCAAGTCGGCCAAGGCAACATTTACCGTAGgtacgcattt ... catattgtagGGGCTTGAAAGCTGAGAAGATTGCTGCAAGACAAGCTATATTACCTCTCAT
EST: gi|162247022|gb|FC422196.1|FC422196
EST:     ATCATCGGTTGGGGAATGTACCAAGTCGGCCAAGGCAACATTTACCGTAG                         GGGCTTGAAAGCTGAGAAGATTGCTGCAAGACAAGCTATATTACCTCTCAT
genomic: ATCATCGGTTGGGGAATGTACCAAGTCGGCCAAGGCAACATTTACCGTAGgtacgcattt ... catattgtagGGGCTTGAAAGCTGAGAAGATTGCTGCAAGACAAGCTATATTACCTCTCAT
EST: gi|67699224|gb|BJ959457.1|BJ959457
EST:     ATCATCGGTTGGGGAATGTACCAAGTCGGCCAAGGCAACATTTACCGTAG                         GGGCTTGAAAGCTGAGAAGATTGCTGCAAGACAAGCTATATTACCTCTCAT
genomic: ATCATCGGTTGGGGAATGTACCAAGTCGGCCAAGGCAACATTTACCGTAGgtacgcattt ... catattgtagGGGCTTGAAAGCTGAGAAGATTGCTGCAAGACAAGCTATATTACCTCTCAT
EST: gi|67692079|gb|BJ952312.1|BJ952312
EST:     ATCATCGGTTGGGGAATGTACCAAGTCGGCCAAGGCAACATTTACCGTAG                         GGGCTTGAAAGCTGAGAAGATTGCTGCAAGACAAGCTATATTACCTCTCAT
genomic: ATCATCGGTTGGGGAATGTACCAAGTCGGCCAAGGCAACATTTACCGTAGgtacgcattt ... catattgtagGGGCTTGAAAGCTGAGAAGATTGCTGCAAGACAAGCTATATTACCTCTCAT
EST: gi|18371220|gb|BJ202822.1|BJ202822
EST:     ATCATCGGTTGGGGAATGTACCAAGTCGGCCAAGGCAACATTTACCGTAG                         GGGCTTGAAAGCTGAGAAGATTGCTGCAAGACAAGCTATATTACCTCTCAT
genomic: ATCATCGGTTGGGGAATGTACCAAGTCGGCCAAGGCAACATTTACCGTAGgtacgcattt ... catattgtagGGGCTTGAAAGCTGAGAAGATTGCTGCAAGACAAGCTATATTACCTCTCAT
EST: gi|37851383|gb|BJ609391.1|BJ609391
EST:     ATCATCGGTTGGGGAATGTACCAAGTCGGCCAAGGCAACATTTACCGTAG                         GGGCTTGAAAGCTGAGAAGATTGCTGCAAGACAAGCTATATTACCTCTCAT
genomic: ATCATCGGTTGGGGAATGTACCAAGTCGGCCAAGGCAACATTTACCGTAGgtacgcattt ... catattgtagGGGCTTGAAAGCTGAGAAGATTGCTGCAAGACAAGCTATATTACCTCTCAT
EST: gi|67709799|gb|BJ965615.1|BJ965615
EST:     ATCATCGGTTGGGGAATGTACCAAGTCGGCCAAGGCAACATTTACCGTAG                         GGGCTTGAAAGCTGAGAAGATTGCTGCAAGACAAGCTATATTACCTCTCAT
genomic: ATCATCGGTTGGGGAATGTACCAAGTCGGCCAAGGCAACATTTACCGTAGgtacgcattt ... catattgtagGGGCTTGAAAGCTGAGAAGATTGCTGCAAGACAAGCTATATTACCTCTCAT
EST: gi|162243734|gb|FC419567.1|FC419567
EST:     ATCATCGGTTGGGGAATGTACCAAGTCGGCCAAGGCAACATTTACCGTAG                         GGGCTTGAAAGCTGAGAAGATTGCTGCAAGACAAGCTATATTACCTCTCAT
genomic: ATCATCGGTTGGGGAATGTACCAAGTCGGCCAAGGCAACATTTACCGTAGgtacgcattt ... catattgtagGGGCTTGAAAGCTGAGAAGATTGCTGCAAGACAAGCTATATTACCTCTCAT
EST: gi|6227421|gb|AW156020.1|AW156020
EST:     ATCATCGGTTGGGGAATGTACCAAGTCGGCCAAGGCAACATTTACCGTAG                         GGGCTTGAAAGCTGAGAAGATTGCTGCAAGACAAGCTATATTACCTCTCAT
genomic: ATCATCGGTTGGGGAATGTACCAAGTCGGCCAAGGCAACATTTACCGTAGgtacgcattt ... catattgtagGGGCTTGAAAGCTGAGAAGATTGCTGCAAGACAAGCTATATTACCTCTCAT
EST: gi|15327561|gb|BI488315.1|BI488315
EST:     ATCATCGGTTGGGGAATGTACCAAGTCGGCCAAGGCAACATTTACCGTAG                         GGGCTTGAAAGCTGAGAAGATTGCTGCAAGACAAGCTATATTACCTCTCAT
genomic: ATCATCGGTTGGGGAATGTACCAAGTCGGCCAAGGCAACATTTACCGTAGgtacgcattt ... catattgtagGGGCTTGAAAGCTGAGAAGATTGCTGCAAGACAAGCTATATTACCTCTCAT
EST: gi|67568872|gb|BJ941696.1|BJ941696
EST:     ATCATCGGTTGGGGAATGTACCAAGTCGGCCAAGGCAACATTTACCGTAG                         GGGCTTGAAAGCTGAGAAGATTGCTGCAAGACAAGCTATATTACCTCTCAT
genomic: ATCATCGGTTGGGGAATGTACCAAGTCGGCCAAGGCAACATTTACCGTAGgtacgcattt ... catattgtagGGGCTTGAAAGCTGAGAAGATTGCTGCAAGACAAGCTATATTACCTCTCAT
EST: gi|162247023|gb|FC422197.1|FC422197
EST:     ATCATCGGTTGGGGAATGTACCAAGTCGGCCAAGGCAACATTTACCGTAG                         GGGCTTGAAAGCTGAGAAGATTGCTGCAAGACAAGCTATATTACCTCTCAT
genomic: ATCATCGGTTGGGGAATGTACCAAGTCGGCCAAGGCAACATTTACCGTAGgtacgcattt ... catattgtagGGGCTTGAAAGCTGAGAAGATTGCTGCAAGACAAGCTATATTACCTCTCAT

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), 28 (downstream exon)
Score: 12

TTGCCAATACGGGTCCCAGCGGAGTTACGGTGCTTCTGGTGTCCTCTGCTATCATCGGTTGGGGAATGTACCAAGTCGGCCAAGGCAACATTTACCGTAGgtacgcattt ... catattgtagGGGCTTGAAAGCTGAGAAGATTGCTGCAAGACAAGCTATATTACCTCTCATCCAGGCTGAGGAAGATGCAAG




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