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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGAGCTGGTGGATGGAGCCTTGCTCTAACAGCATCAGAGTTTAATGATTTCTGCTATCTTATACAGgtactactgttgcattagattgaacaccttcgaattgatctttgtttgaaattggactcgaacatctactactagccgtgtgcgtatcaaattacttactgatggacgatgagcacttgcag

Basic information

species Physcomitrella patens
transcript PP1S462_4V6.1
intron # 3
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|162242267|gb|FC416075.1|FC416075
EST:     GCCTTGCTCTAACAGCATCAGAGTTTAATGATTTCTGCTATCTTATACAG                         ACCTTGAGAAAGGGCATCGCAACTATGGACGAGGATGGGTTTATAGGAAAG
genomic: GCCTTGCTCTAACAGCATCAGAGTTTAATGATTTCTGCTATCTTATACAGgtactactgt ... gcacttgcagACCTTGAGAAAGGGCATCGCAACTATGGACGAGGATGGGTTTATAGGAAAG
EST: gi|208370018|gb|DC948113.1|DC948113
EST:     GCCTTGCTCTAACAGCATCAGAGTTTAATGATTTCTGCTATCTTATACAG                         ACCTTGAGAAAGGGCATCGCAACTATGGACGAGGATGGGTTTATAGGAAAG
genomic: GCCTTGCTCTAACAGCATCAGAGTTTAATGATTTCTGCTATCTTATACAGgtactactgt ... gcacttgcagACCTTGAGAAAGGGCATCGCAACTATGGACGAGGATGGGTTTATAGGAAAG
EST: gi|18338649|gb|BJ170673.1|BJ170673
EST:     GCCTTGCTCTAACAGCATCAGAGTTTAATGATTTCTGCTATCTTATACAG                         ACCTTGAGAAAGGGCATCGCAACTATGGACGAGGATGGGTTTATAGGAAAG
genomic: GCCTTGCTCTAACAGCATCAGAGTTTAATGATTTCTGCTATCTTATACAGgtactactgt ... gcacttgcagACCTTGAGAAAGGGCATCGCAACTATGGACGAGGATGGGTTTATAGGAAAG
EST: gi|162242266|gb|FC416074.1|FC416074
EST:     GCCTTGCTCTAACAGCATCAGAGTTTAATGATTTCTGCTATCTTATACAG                         ACCTTGAGAAAGGGCATCGCAACTATGGACGAGGATGGGTTTATAGGAAAG
genomic: GCCTTGCTCTAACAGCATCAGAGTTTAATGATTTCTGCTATCTTATACAGgtactactgt ... gcacttgcagACCTTGAGAAAGGGCATCGCAACTATGGACGAGGATGGGTTTATAGGAAAG
EST: gi|162223822|gb|FC400076.1|FC400076
EST:     GCCTTGCTCTAACAGCATCAGAGTTTAATGATTTCTGCTATCTTATACAG                         ACCTTGAGAAAGGGCATCGCAACTATGGACGAGGATGGGTTTATAGGAAAG
genomic: GCCTTGCTCTAACAGCATCAGAGTTTAATGATTTCTGCTATCTTATACAGgtactactgt ... gcacttgcagACCTTGAGAAAGGGCATCGCAACTATGGACGAGGATGGGTTTATAGGAAAG
EST: gi|208373292|gb|DC944949.1|DC944949
EST:     GCCTTGCTCTAACAGCATCAGAGTTTAATGATTTCTGCTATCTTATACAG                         ACCTTGAGAAAGGGCATCGCAACTATGGACGAGGATGGGTTTATAGGAAAG
genomic: GCCTTGCTCTAACAGCATCAGAGTTTAATGATTTCTGCTATCTTATACAGgtactactgt ... gcacttgcagACCTTGAGAAAGGGCATCGCAACTATGGACGAGGATGGGTTTATAGGAAAG
EST: gi|19780797|gb|BQ039613.1|BQ039613
EST:     GCCTTGCTCTAACAGCATCAGAGTTTAATGATTTCTGCTATCTTATACAG                         ACCTTGAGAAAGGGCATCGCAACTATGGACGAGGATGGGTTTATAGGAAAG
genomic: GCCTTGCTCTAACAGCATCAGAGTTTAATGATTTCTGCTATCTTATACAGgtactactgt ... gcacttgcagACCTTGAGAAAGGGCATCGCAACTATGGACGAGGATGGGTTTATAGGAAAG
EST: gi|19782197|gb|BQ039822.1|BQ039822
EST:     GCCTTGCTCTAACAGCATCAGAGTTTAATGATTTCTGCTATCTTATACAG                         ACCTTGAGAAAGGGCATCGCAACTATGGACGAGGATGGGTTTATAGGAAAG
genomic: GCCTTGCTCTAACAGCATCAGAGTTTAATGATTTCTGCTATCTTATACAGgtactactgt ... gcacttgcagACCTTGAGAAAGGGCATCGCAACTATGGACGAGGATGGGTTTATAGGAAAG

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: 21 (upstream exon), 15 (downstream exon)
Score: 2

GTTGGAGCTGGTGGATGGAGCCTTGCTCTAACAGCATCAGAGTTTAATGATTTCTGCTATCTTATACAGgtactactgt ... gcacttgcagACCTTGAGAAAGGGCATCGCAACTATGGACGAGGATGGGTTTATAGGAAAGGAAGAAGTTGTTATGCAG




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