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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatcaaagagctggaagcgattgcttgactttccgcacgagatagtgtgcaattcaatggcccgattttgtgatttacccaagttattttttattcgcagTTTCTCGACTTTCCTGGGGCTAAGGTTGGGTTTATCAACAAAATCAAGTTCACAGCGGAGCGACCGCAGGAACCGGTGCCCTGTTTTCGTGTCCTGGACG

Basic information

species Physcomitrella patens
transcript PP1S207_68V6.1
intron # 1
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|100449092|gb|CJ973391.1|CJ973391
EST:     TCTGCTCGAGTTCCTCTAGCGGCGACGAGAGCGAGGATCATCTTGATGAG                         TTTCTCGACTTTCCTGGGGCTAAGGTTGGGTTTATCAACAAAATCAAGTTC
genomic: TCTGCTCGAGTTCCTCTAGCGGCGACGAGAGCGAGGATCATCTTGATGAGgtttgcgttg ... ttattcgcagTTTCTCGACTTTCCTGGGGCTAAGGTTGGGTTTATCAACAAAATCAAGTTC
EST: gi|162152382|gb|FC328569.1|FC328569
EST:     TCTGCTCGAGTTCCTCTAGCGGCGACGAGAGCGAGGATCATCTTGATGAG                         TTTCTCGACTTTCCTGGGGCTAAGGTTGGGTTTATCAACAAAATCAAGTTC
genomic: TCTGCTCGAGTTCCTCTAGCGGCGACGAGAGCGAGGATCATCTTGATGAGgtttgcgttg ... ttattcgcagTTTCTCGACTTTCCTGGGGCTAAGGTTGGGTTTATCAACAAAATCAAGTTC
EST: gi|208388056|gb|DC933162.1|DC933162
EST:     TCTGCTCGAGTTCCTCTAGCGGCGACGAGAGCGAGGATCATCTTGATGAG                         TTTCTCGACTTTCCTGGGGCTAAGGTTGGGTTTATCAACAAAATCAAGTTC
genomic: TCTGCTCGAGTTCCTCTAGCGGCGACGAGAGCGAGGATCATCTTGATGAGgtttgcgttg ... ttattcgcagTTTCTCGACTTTCCTGGGGCTAAGGTTGGGTTTATCAACAAAATCAAGTTC
EST: gi|100386870|gb|BY988139.1|BY988139
EST:     TCTGCTCGAGTTCCTCTAGCGGCGACGAGAGCGAGGATCATCTTGATGAG                         TTTCTCGACTTTCCTGGGGCTAAGGTTGGGTTTATCAACAAAATCAAGTTC
genomic: TCTGCTCGAGTTCCTCTAGCGGCGACGAGAGCGAGGATCATCTTGATGAGgtttgcgttg ... ttattcgcagTTTCTCGACTTTCCTGGGGCTAAGGTTGGGTTTATCAACAAAATCAAGTTC
EST: gi|100447364|gb|CJ971663.1|CJ971663
EST:     TCTGCTCGAGTTCCTCTAGCGGCGACGAGAGCGAGGATCATCTTGATGAG                         TTTCTCGACTTTCCTGGGGCTAAGGTTGGGTTTATCAACAAAATCAAGTTC
genomic: TCTGCTCGAGTTCCTCTAGCGGCGACGAGAGCGAGGATCATCTTGATGAGgtttgcgttg ... ttattcgcagTTTCTCGACTTTCCTGGGGCTAAGGTTGGGTTTATCAACAAAATCAAGTTC
EST: gi|100385474|gb|BY969811.1|BY969811
EST:     TCTGCTCGAGTTCCTCTAGCGGCGACGAGAGCGAGGATCATCTTGATGAG                         TTTCTCGACTTTCCTGGGGCTAAGGTTGGGTTTATCAACAAAATCAAGTTC
genomic: TCTGCTCGAGTTCCTCTAGCGGCGACGAGAGCGAGGATCATCTTGATGAGgtttgcgttg ... ttattcgcagTTTCTCGACTTTCCTGGGGCTAAGGTTGGGTTTATCAACAAAATCAAGTTC
EST: gi|162255613|gb|FC431611.1|FC431611
EST:     TCTGCTCGAGTTCCTCTAGCGGCGACGAGAGCGAGGATCATCTTGATGAG                         TTTCTCGACTTTCCTGGGGCTAAGGTTGGGTTTATCAACAAAATCAAGTTC
genomic: TCTGCTCGAGTTCCTCTAGCGGCGACGAGAGCGAGGATCATCTTGATGAGgtttgcgttg ... ttattcgcagTTTCTCGACTTTCCTGGGGCTAAGGTTGGGTTTATCAACAAAATCAAGTTC
EST: gi|100352194|gb|BY983086.1|BY983086
EST:     TCTGCTCGAGTTCCTCTAGCGGCGACTAGAGCGAGGATCATCTTGATGAG                         TTTCTCGACTTTCCTGGGGCTAAGGTTGGGTTTATCAACAAAATCAAGTTC
genomic: TCTGCTCGAGTTCCTCTAGCGGCGACGAGAGCGAGGATCATCTTGATGAGgtttgcgttg ... ttattcgcagTTTCTCGACTTTCCTGGGGCTAAGGTTGGGTTTATCAACAAAATCAAGTTC
EST: gi|18346832|gb|BJ178877.1|BJ178877
EST:     TCTGCTCGAGTTCCTCTAGCGGCGACGAGAGCGAGGATCATCTTGATGAG                         TTTCTCGACTTTCCTGGGGCTAAGGTTGGGTTTATCAACAAAATCAAGTTC
genomic: TCTGCTCGAGTTCCTCTAGCGGCGACGAGAGCGAGGATCATCTTGATGAGgtttgcgttg ... ttattcgcagTTTCTCGACTTTCCTGGGGCTAAGGTTGGGTTTATCAACAAAATCAAGTTC
EST: gi|18352293|gb|BJ184347.1|BJ184347
EST:     TCTGCTCGAGTTCCTCTAGCGGCGACGAGAGCGAGGATCATCTTGATGAG                         TTTCTCGACTTTCCTGGGGCTAAGGTTGGGTTTATCAACAAAATCAAGTTC
genomic: TCTGCTCGAGTTCCTCTAGCGGCGACGAGAGCGAGGATCATCTTGATGAGgtttgcgttg ... ttattcgcagTTTCTCGACTTTCCTGGGGCTAAGGTTGGGTTTATCAACAAAATCAAGTTC

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: 31 (upstream exon), 16 (downstream exon)
Score: 5

TTCTTCGCCGTCGTGTGGTCCTTTCGCTTCCGTCTTGCGCGAACGCCAATTCTGCTCGAGTTCCTCTAGCGGCGACGAGAGCGAGGATCATCTTGATGAGgtttgcgttg ... ttattcgcagTTTCTCGACTTTCCTGGGGCTAAGGTTGGGTTTATCAACAAAATCAAGTTCACAGCGGAGCGACCGCAGGAACCGGTGCCCTGTTTTCGTGTCCTGGACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgcaattcaatggcccgattttgtgatttacccaagttattttttattcgcagTTTCTCGACTTTCCTGGGGCTAAGGTTGGGTTTATCAACAAAATCAAGTTCACAGCGGAGCGACCGCAGGAACCGGTGCCCTGTTTTCGTGTCCTGGACG
                                         ttttttattc  CT-rich tract
                                   aagttattttttatt  TA-rich tract