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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggacccctaaaaaattggtatatgtaactacttcttggtttcaaatgtttcaagtttttcggccacgctcgcttagtatttggtatggtatttgaacagGCTCCAGCTGCGGCAGCTCAAGAAAATAAAGTCAGCGCTGACATTGCCCCGGGTACACCTGAAATTCTCACCAATTGAAACCTTAGATTGAGTACGATAC

Basic information

species Physcomitrella patens
transcript PP1S142_120V6.1
intron # 7
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|208396648|gb|DC929027.1|DC929027
EST:     TTAAAAAGGACACCAAGAAAGACAGCAAAACAAAGAATCCCCAGGCTAAG                         GCTCCAGCTGCGGCAGCTCAAGAAAATAAAGTCAGCGCTGACATTGCCCCG
genomic: TTAAAAAGGACACCAAGAAAGACAGCAAAACAAAGAATCCCCAGGCTAAGgtacatcact ... atttgaacagGCTCCAGCTGCGGCAGCTCAAGAAAATAAAGTCAGCGCTGACATTGCCCCG
EST: gi|162204299|gb|FC380487.1|FC380487
EST:     TTAAAAAGGACACCAAGAAAGACAGCAAAACAAAGAATCCCCAGGCTAAG                         GCTCCAGCTGCGGCAGCTCAAGAAAATAAAGTCAGCGCTGACATTGCCCCG
genomic: TTAAAAAGGACACCAAGAAAGACAGCAAAACAAAGAATCCCCAGGCTAAGgtacatcact ... atttgaacagGCTCCAGCTGCGGCAGCTCAAGAAAATAAAGTCAGCGCTGACATTGCCCCG
EST: gi|67724461|gb|BJ974720.1|BJ974720
EST:     TTAAAAAGGACACCAAGAAAGACAGCAAAACAAAGAATCCCCAGGCTAAG                         GCTCCAGCTGCGGCAGCTCAAGAAAATAAAGTCAGCGCTGACATTGCCCCG
genomic: TTAAAAAGGACACCAAGAAAGACAGCAAAACAAAGAATCCCCAGGCTAAGgtacatcact ... atttgaacagGCTCCAGCTGCGGCAGCTCAAGAAAATAAAGTCAGCGCTGACATTGCCCCG
EST: gi|37842186|gb|BJ600194.1|BJ600194
EST:     TTAAAAAGGACACCAAGAAAGACAGCAAAACAAAGAATCCCCAGGCTAAG                         GCTCCAGCTGCGGCAGCTCAAGAAAATAAAGTCAGCGCTGACATTGCCCCG
genomic: TTAAAAAGGACACCAAGAAAGACAGCAAAACAAAGAATCCCCAGGCTAAGgtacatcact ... atttgaacagGCTCCAGCTGCGGCAGCTCAAGAAAATAAAGTCAGCGCTGACATTGCCCCG
EST: gi|208353284|gb|DC926167.1|DC926167
EST:     TTAAAAAGGACACCAAGAAAGACAGCAAAACAAAGAATCCCCAGGCTAAG                         GCTCCAGCTGCGGCAGCTCAAGAAAATAAAGTCAGCGCTGACATTGCCCCG
genomic: TTAAAAAGGACACCAAGAAAGACAGCAAAACAAAGAATCCCCAGGCTAAGgtacatcact ... atttgaacagGCTCCAGCTGCGGCAGCTCAAGAAAATAAAGTCAGCGCTGACATTGCCCCG
EST: gi|15728767|gb|BI740962.1|BI740962
EST:     TTAAAAAGGACACCAAGAAAGACAGCAAAACAAAGAATCCCCAGGCTAAG                         GCTCCAGCTGCGGCAGCTCAAGAAAATAAAGTCAGCGCTGACATTGCCCCG
genomic: TTAAAAAGGACACCAAGAAAGACAGCAAAACAAAGAATCCCCAGGCTAAGgtacatcact ... atttgaacagGCTCCAGCTGCGGCAGCTCAAGAAAATAAAGTCAGCGCTGACATTGCCCCG
EST: gi|67697454|gb|BJ957687.1|BJ957687
EST:     TTAAAAAGGACACCAAGAAAGACAGCAAAACAAAGAATCCCCAGGCTAAG                         GCTCCAGCTGCGGCAGCTCAAGAAAATAAAGTCAGCGCTGACATTGCCCCG
genomic: TTAAAAAGGACACCAAGAAAGACAGCAAAACAAAGAATCCCCAGGCTAAGgtacatcact ... atttgaacagGCTCCAGCTGCGGCAGCTCAAGAAAATAAAGTCAGCGCTGACATTGCCCCG
EST: gi|7584284|gb|AW700180.1|AW700180
EST:     TTAAAAAGGACACCAAGAAAGACAGCAAAACAAAGAATCCCCAGGCTAAG                         GCTCCAGCTGCGGCAGCTCAAGAAAATAAAGTCAGCGCTGACATTGCCCCG
genomic: TTAAAAAGGACACCAAGAAAGACAGCAAAACAAAGAATCCCCAGGCTAAGgtacatcact ... atttgaacagGCTCCAGCTGCGGCAGCTCAAGAAAATAAAGTCAGCGCTGACATTGCCCCG
EST: gi|37839193|gb|BJ597201.1|BJ597201
EST:     TTAAAAAGGACACCAAGAAAGACAGCAAAACAAAGAATCCCCAGGCTAAG                         GCTCCAGCTGCGGCAGCTCAAGAAAATAAAGTCAGCGCTGACATTGCCCCG
genomic: TTAAAAAGGACACCAAGAAAGACAGCAAAACAAAGAATCCCCAGGCTAAGgtacatcact ... atttgaacagGCTCCAGCTGCGGCAGCTCAAGAAAATAAAGTCAGCGCTGACATTGCCCCG
EST: gi|15728849|gb|BI741008.1|BI741008
EST:     TTAAAAAGGACACCAAGAAAGACAGCAAAACAAAGAATCCCCAGGCTAAG                         GCTCCAGCTGCGGCAGCTCAAGAAAATAAAGTCAGCGCTGACATTGCCCCG
genomic: TTAAAAAGGACACCAAGAAAGACAGCAAAACAAAGAATCCCCAGGCTAAGgtacatcact ... atttgaacagGCTCCAGCTGCGGCAGCTCAAGAAAATAAAGTCAGCGCTGACATTGCCCCG
EST: gi|162243432|gb|FC425128.1|FC425128
EST:     TTAAAAAGGACACCAAGAAAGACAGCAAAACAAAGAATCCCCAGGCTAAG                         GCTCCAGCTGCGGCAGCTCAAGAAAATAAAGTCAGCGCTGACATTGCCCCG
genomic: TTAAAAAGGACACCAAGAAAGACAGCAAAACAAAGAATCCCCAGGCTAAGgtacatcact ... atttgaacagGCTCCAGCTGCGGCAGCTCAAGAAAATAAAGTCAGCGCTGACATTGCCCCG
EST: gi|208368352|gb|DC955535.1|DC955535
EST:     TTAAAAAGGACACCAAGAAAGACAGCAAAACAAAGAATCCCCAGGCTAAG                         GCTCCAGCTGCGGCAGCTCAAGAAAATAAAGTCAGCGCTGACATTGCCCCG
genomic: TTAAAAAGGACACCAAGAAAGACAGCAAAACAAAGAATCCCCAGGCTAAGgtacatcact ... atttgaacagGCTCCAGCTGCGGCAGCTCAAGAAAATAAAGTCAGCGCTGACATTGCCCCG
EST: gi|37838367|gb|BJ596375.1|BJ596375
EST:     TTAAAAAGGACACCAAGAAAGACAGCAAAACAAAGAATCCCCAGGCTAAG                         GCTCCAGCTGCGGCAGCTCAAGAAAATAAAGTCAGCGCTGACATTGCCCCG
genomic: TTAAAAAGGACACCAAGAAAGACAGCAAAACAAAGAATCCCCAGGCTAAGgtacatcact ... atttgaacagGCTCCAGCTGCGGCAGCTCAAGAAAATAAAGTCAGCGCTGACATTGCCCCG
EST: gi|67725840|gb|BJ976099.1|BJ976099
EST:     TTAAAAAGGACACCAAGAAAGACAGCAAAACAAAGAATCCCCAGGCTAAG                         GCTCCAGCTGCGGCAGCTCAAGAAAATAAAGTCAGCGCTGACATTGCCCCG
genomic: TTAAAAAGGACACCAAGAAAGACAGCAAAACAAAGAATCCCCAGGCTAAGgtacatcact ... atttgaacagGCTCCAGCTGCGGCAGCTCAAGAAAATAAAGTCAGCGCTGACATTGCCCCG

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: 8 (upstream exon), 28 (downstream exon)
Score: 1

GCTCGGCACCGATTTCCTTCCCTTCACCCAGGAAGCTCCTAAGAAAGATGTTAAAAAGGACACCAAGAAAGACAGCAAAACAAAGAATCCCCAGGCTAAGgtacatcact ... atttgaacagGCTCCAGCTGCGGCAGCTCAAGAAAATAAAGTCAGCGCTGACATTGCCCCGGGTACACCTGAAATTCTCACCAATTGAAACCTTAGATTGAGTACGATAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtttcaagtttttcggccacgctcgcttagtatttggtatggtatttgaacagGCTCCAGCTGCGGCAGCTCAAGAAAATAAAGTCAGCGCTGACATTGCCCCGGGTACACCTGAAATTCTCACCAATTGAAACCTTAGATTGAGTACGATAC
                            ttagtattt  TA-rich tract