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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctcgagttcaacaacttgagctggtagtggccgtgatcactaccttcaattcaatttgattctgaaatgagaatattggggcattgtgtcaatgaatagGTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATTCTATAAGCAGGGCTGCGGCCTCAGGGGAAGCTTATCTGCATACTTCTCTTTCCAAGG

Basic information

species Physcomitrella patens
transcript PP1S4_80V6.2
intron # 3
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|100432131|gb|BY960350.1|BY960350
EST:     ATCGAAAGTTTGACGTTGACGCAGCTGTGGAGAAAATCACCACAGCCTTG                         GTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATTTCTATA-G
genomic: ATCGAAAGTTTGACGTTGACGCAGCTGTGGAGAAAATCACCACAGCCTTGgtaactgcct ... caatgaatagGTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATT-CTATAAG
EST: gi|162279530|gb|FC455321.1|FC455321
EST:     ATCGAAAGTTTGACGTTGACGCAGCTGTGGAGAAAATCACCACAGCCTTG                         GTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATTCTATAAGC
genomic: ATCGAAAGTTTGACGTTGACGCAGCTGTGGAGAAAATCACCACAGCCTTGgtaactgcct ... caatgaatagGTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATTCTATAAGC
EST: gi|208379109|gb|DC911634.1|DC911634
EST:     ATCGAAAGTTTGACGTTGACGCAGCTGTGGAGAAAATCACCACAGCCTTG                         GTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATTCTATAAGC
genomic: ATCGAAAGTTTGACGTTGACGCAGCTGTGGAGAAAATCACCACAGCCTTGgtaactgcct ... caatgaatagGTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATTCTATAAGC
EST: gi|208344682|gb|DC905131.1|DC905131
EST:     ATCGAAAGTTTGACGTTGACGCAGCTGTGGAGAAAATCACCACAGCCTTG                         GTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATTCTATAAGC
genomic: ATCGAAAGTTTGACGTTGACGCAGCTGTGGAGAAAATCACCACAGCCTTGgtaactgcct ... caatgaatagGTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATTCTATAAGC
EST: gi|208376190|gb|DC911014.1|DC911014
EST:     ATCGAAAGTTTGACGTTGACGCAGCTGTGGAGAAAATCACCACAGCCTTG                         GTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATTCTATAAGC
genomic: ATCGAAAGTTTGACGTTGACGCAGCTGTGGAGAAAATCACCACAGCCTTGgtaactgcct ... caatgaatagGTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATTCTATAAGC
EST: gi|162258991|gb|FC435934.1|FC435934
EST:     ATCGAAAGTTTGACGTTGACGCAGCTGTGGAGAAAATCACCACAGCCTTG                         GTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATTCTATAAGC
genomic: ATCGAAAGTTTGACGTTGACGCAGCTGTGGAGAAAATCACCACAGCCTTGgtaactgcct ... caatgaatagGTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATTCTATAAGC

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), 27 (downstream exon)
Score: 13

TGGGAAGAACGGCCGGGACGACGAAGATCTCCTTCTGTGGTTTCTTCGTGATCGAAAGTTTGACGTTGACGCAGCTGTGGAGAAAATCACCACAGCCTTGgtaactgcct ... caatgaatagGTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATTCTATAAGCAGGGCTGCGGCCTCAGGGGAAGCTTATCTGCATACTTCTCTTTCCAAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaattcaatttgattctgaaatgagaatattggggcattgtgtcaatgaatagGTGTGGCGAAAGGAGTTTGGTGTAGATGAGATTACAAAGGATTCTATAAGCAGGGCTGCGGCCTCAGGGGAAGCTTATCTGCATACTTCTCTTTCCAAGG
         atttgat  putative branch site (score: 13)
        aatttgatt  TA-rich tract