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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagggactctctttctgccgttgtggtgctctttgaacctgtttttttcttttcttttcttttcttttctttttgttagatgcactgacctgggaaatttacttaaagtatttgattgcattttcagGTACCACACAGATCCATCTGGAACATTTTGGCAATGTGATGCTAAGGCAATTGGTTCAGGATCAGAAGGTGCCGATACTTCCCTTCAGGAACATTTCAAC

Basic information

species Physcomitrella patens
transcript PP1S69_9V6.1
intron # 6
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|37852229|gb|BJ610237.1|BJ610237
EST:     TTCGGAGTTTCTCTGCTCATTGCTGGCCATGATGAGAGTGGACCATGCTT                         GTACCACACAGATCCATCTGGAACATTTTGGCAATGTGATGCTAAGGCAAT
genomic: TTCGGAGTTTCTCTGCTCATTGCTGGCCATGATGAGAGTGGACCATGCTTgtaagggact ... gcattttcagGTACCACACAGATCCATCTGGAACATTTTGGCAATGTGATGCTAAGGCAAT
EST: gi|7583756|gb|AW699661.1|AW699661
EST:     TTCGGAGTTTCTCTGCTCATTGCTGGCCATGATGAGAGTGGACCATGCTT                         GTACCACACAGATCCATCTGGAACATTTTGGCAATGTGATGCTAAGGCAAT
genomic: TTCGGAGTTTCTCTGCTCATTGCTGGCCATGATGAGAGTGGACCATGCTTgtaagggact ... gcattttcagGTACCACACAGATCCATCTGGAACATTTTGGCAATGTGATGCTAAGGCAAT
EST: gi|162189533|gb|FC365755.1|FC365755
EST:     TTCGGAGTTTCTCTGCTCATTGCTGGCCATGATGAGAGTGGACCATGCTT                         GTACCACACAGATCCATCTGGAACATTTTGGCAATGTGATGCTAAGGCAAT
genomic: TTCGGAGTTTCTCTGCTCATTGCTGGCCATGATGAGAGTGGACCATGCTTgtaagggact ... gcattttcagGTACCACACAGATCCATCTGGAACATTTTGGCAATGTGATGCTAAGGCAAT
EST: gi|162230158|gb|FC406306.1|FC406306
EST:     TTCGGAGTTTCTCTGCTCATTGCTGGCCATGATGAGAGTGGACCATGCTT                         GTACCACACAGATCCATCTGGAACATTTTGGCAATGTGATGCTAAGGCAAT
genomic: TTCGGAGTTTCTCTGCTCATTGCTGGCCATGATGAGAGTGGACCATGCTTgtaagggact ... gcattttcagGTACCACACAGATCCATCTGGAACATTTTGGCAATGTGATGCTAAGGCAAT
EST: gi|162189532|gb|FC365754.1|FC365754
EST:     TTCGGAGTTTCTCTGCTCATTGCTGGCCATGATGAGAGTGGACCATGCTT                         GTACCACACAGATCCATCTGGAACATTTTGGCAATGTGATGCTAAGGCAAT
genomic: TTCGGAGTTTCTCTGCTCATTGCTGGCCATGATGAGAGTGGACCATGCTTgtaagggact ... gcattttcagGTACCACACAGATCCATCTGGAACATTTTGGCAATGTGATGCTAAGGCAAT
EST: gi|37846603|gb|BJ604611.1|BJ604611
EST:     TTCGGAGTTTCTCTGCTCATTGCTGGCCATGATGAGAGTGGACCATGCTT                         GTACCACACAGATCCATCTGGAACATTTTGGCAATGTGATGCTAAGGCAAT
genomic: TTCGGAGTTTCTCTGCTCATTGCTGGCCATGATGAGAGTGGACCATGCTTgtaagggact ... gcattttcagGTACCACACAGATCCATCTGGAACATTTTGGCAATGTGATGCTAAGGCAAT
EST: gi|37841581|gb|BJ599589.1|BJ599589
EST:     TTCGGAGTTTCTCTGCTCATTGCTGGCCATGATGAGAGTGGACCATGCTT                         GTACCACACAGATCCATCTGGAACATTTTGGCAATGTGATGCTAAGGCAAT
genomic: TTCGGAGTTTCTCTGCTCATTGCTGGCCATGATGAGAGTGGACCATGCTTgtaagggact ... gcattttcagGTACCACACAGATCCATCTGGAACATTTTGGCAATGTGATGCTAAGGCAAT

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: 28 (upstream exon), 32 (downstream exon)
Score: 7

TCACGTCCTTTCGGAGTTTCTCTGCTCATTGCTGGCCATGATGAGAGTGGACCATGCTTgtaagggact ... gcattttcagGTACCACACAGATCCATCTGGAACATTTTGGCAATGTGATGCTAAGGCAATTGGTTCAGGATCAGAAGGTGCCGATACTTCCCTTCAGGAACATTTCAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttagatgcactgacctgggaaatttacttaaagtatttgattgcattttcagGTACCACACAGATCCATCTGGAACATTTTGGCAATGTGATGCTAAGGCAATTGGTTCAGGATCAGAAGGTGCCGATACTTCCCTTCAGGAACATTTCAAC
                                              cattttc  CT-rich tract
                      aaatttacttaaagta  TA-rich tract