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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgcagttgtgatttgcacgctcattgtcagttttggaatcctcgagaattttccgacaggtcgtgattgttaacttgtgtgatgtttttgaaaatttcagGACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAACTTCATGAACTTGGTGCTTGTCACCAACGTCGGAGGCATGGGGGACGTG

Basic information

species Physcomitrella patens
transcript PP1S9_119V6.2
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|208355515|gb|DC942635.1|DC942635
EST:     GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAG                         GACTNCTTGTGTAAGGACTGGTGGCATTCACT
genomic: GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAGgtgtgcagtt ... aaaatttcagGACTTCTTGTGTAAGGACTGGTGGCATTCACT
EST: gi|208385909|gb|DC956747.1|DC956747
EST:     GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAG                         GACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAA
genomic: GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAGgtgtgcagtt ... aaaatttcagGACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAA
EST: gi|208398571|gb|DC916092.1|DC916092
EST:     GAGCAAATCGCAACTTACAAGGCCCGCATTGTGCCTGTGATGTACCGAAG                         GACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAA
genomic: GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAGgtgtgcagtt ... aaaatttcagGACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAA
EST: gi|100388610|gb|BY970758.1|BY970758
EST:     GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAG                         GACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGGTCACA
genomic: GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAGgtgtgcagtt ... aaaatttcagGACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGG-TCACA
EST: gi|100378909|gb|BY986478.1|BY986478
EST:     GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAG                         GACTTCTTGTGTAAG
genomic: GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAGgtgtgcagtt ... aaaatttcagGACTTCTTGTGTAAG
EST: gi|100423154|gb|BY958173.1|BY958173
EST:     AGCAAATCGCAACTTTACA-GGCCGGCATTGTGCCTGTGATGTACCGAAG                         GACTTCTTGTGGTA-GGACTGGTGGCATTCACTTCACCATGAG
genomic: AGCAAATCGCAACTT-ACAAGGCCGGCATTGTGCCTGTGATGTACCGAAGgtgtgcagtt ... aaaatttcagGACTTCTTGTG-TAAGGACTGGTGGCATTCACTTCACCATGAG
EST: gi|208393097|gb|DC929592.1|DC929592
EST:     GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAG                         GACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAA
genomic: GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAGgtgtgcagtt ... aaaatttcagGACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAA
EST: gi|100445620|gb|CJ969919.1|CJ969919
EST:     NANCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAN                         GACTNCTTGTGTAAGGACTGGTGGCATTCACTTCACNATGANCGGTCACA
genomic: GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAGgtgtgcagtt ... aaaatttcagGACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACA
EST: gi|208370503|gb|DC952206.1|DC952206
EST:     GAGCAAATCGCAACNTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAG                         GACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAA
genomic: GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAGgtgtgcagtt ... aaaatttcagGACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAA
EST: gi|208356238|gb|DC902232.1|DC902232
EST:     GAGCAAATCGCAACTTACAAGGCCCGCATTGTGCCTGTGATGTACCGAAG                         GACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAA
genomic: GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAGgtgtgcagtt ... aaaatttcagGACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAA
EST: gi|208366580|gb|DC955628.1|DC955628
EST:     GAGCNAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGNAG                         GACTTCTTGTGTNAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAA
genomic: GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAGgtgtgcagtt ... aaaatttcagGACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAA
EST: gi|100397014|gb|BY953941.1|BY953941
EST:     GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAN                         GACTTCTTGTTGTAAG-ACTGGTGGCATTCACTTCACCATGAGCGGTCACA
genomic: GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAGgtgtgcagtt ... aaaatttcagGACTTCTTGT-GTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACA
EST: gi|208373726|gb|DC952703.1|DC952703
EST:     GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAG                         GACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAA
genomic: GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAGgtgtgcagtt ... aaaatttcagGACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAA
EST: gi|208396785|gb|DC920409.1|DC920409
EST:     GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAG                         GACTTCTTGTGTANGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAA
genomic: GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAGgtgtgcagtt ... aaaatttcagGACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAA
EST: gi|208356203|gb|DC946251.1|DC946251
EST:     GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAG                         GACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAA
genomic: GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAGgtgtgcagtt ... aaaatttcagGACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAA
EST: gi|100390511|gb|BY952919.1|BY952919
EST:     GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAG                         GACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAA
genomic: GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAGgtgtgcagtt ... aaaatttcagGACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAA
EST: gi|208395795|gb|DC920301.1|DC920301
EST:     GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAG                         GACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAA
genomic: GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAGgtgtgcagtt ... aaaatttcagGACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAA
EST: gi|208352533|gb|DC918242.1|DC918242
EST:     GAGCAATTCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAG                         GACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAA
genomic: GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAGgtgtgcagtt ... aaaatttcagGACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAA
EST: gi|208349736|gb|DC917914.1|DC917914
EST:     GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAG                         GACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAA
genomic: GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAGgtgtgcagtt ... aaaatttcagGACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAA
EST: gi|100386566|gb|BY951362.1|BY951362
EST:     GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAA                         GACTTCTTGTGT
genomic: GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAGgtgtgcagtt ... aaaatttcagGACTTCTTGTGT
EST: gi|208393357|gb|DC904017.1|DC904017
EST:     NAGCAAATCGCAACTTACNAGNCCGGCATTGTGCCTGTGATGTACCGAAG                         GACTNCTTGTGTAA
genomic: GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAGgtgtgcagtt ... aaaatttcagGACTTCTTGTGTAA
EST: gi|208375068|gb|DC956436.1|DC956436
EST:     GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAG                         GACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAA
genomic: GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAGgtgtgcagtt ... aaaatttcagGACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAA
EST: gi|208368765|gb|DC940060.1|DC940060
EST:     GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAG                         GACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAA
genomic: GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAGgtgtgcagtt ... aaaatttcagGACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAA
EST: gi|208387945|gb|DC932869.1|DC932869
EST:     GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAG                         GACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAA
genomic: GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAGgtgtgcagtt ... aaaatttcagGACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAA
EST: gi|100421778|gb|BY993639.1|BY993639
EST:     GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAG                         GACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAA
genomic: GAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAGgtgtgcagtt ... aaaatttcagGACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAA

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: 32 (upstream exon), 33 (downstream exon)
Score: 10

GATGGTGCAACCTCCCTCTGCATCATTTCGACATGTCCATGCCTGCCTTCGAGCAAATCGCAACTTACAAGGCCGGCATTGTGCCTGTGATGTACCGAAGgtgtgcagtt ... aaaatttcagGACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAACTTCATGAACTTGGTGCTTGTCACCAACGTCGGAGGCATGGGGGACGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaattttccgacaggtcgtgattgttaacttgtgtgatgtttttgaaaatttcagGACTTCTTGTGTAAGGACTGGTGGCATTCACTTCACCATGAGCGGTCACAACTTCATGAACTTGGTGCTTGTCACCAACGTCGGAGGCATGGGGGACGTG
                      tgttaac  putative branch site (score: 10)
                                    atgtttttgaaaattt  TA-rich tract