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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCATCAGAAAAGTTGTTTCTGTCTTCACGCTTCTGCCATCGAATGGGAGGTCTCACGCTTGACCTCCGGCCCGGGGCGGGTCTGGGTGCTTTCAATCTCGgtaacaaatttatttattttgcttttctagagcttctcggtgacgaatttcagttgggtgtggtgggtttttttgatgaggagttgtggcgatttaagtc...

Basic information

species Physcomitrella patens
transcript PP1S58_197V6.1
intron # 1
splice site 5'
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|18342243|gb|BJ174278.1|BJ174278
EST:     TCTCACGCTTGACCTCCGGCCCGGGGCGGGTCTGGGTGCTTTCAATCTCG                         GAATGCCGGTGTGTGAGGCCTTGGCGTACGTTCAGCAGCACAGGTCGTCGT
genomic: TCTCACGCTTGACCTCCGGCCCGGGGCGGGTCTGGGTGCTTTCAATCTCGgtaacaaatt ... aatgattcagGAATGCCGGTGTGTGAGGCCTTGGCGTACGTTCAGCAGCACAGGTCGTCGT
EST: gi|208380031|gb|DC914581.1|DC914581
EST:     TCTCACGCTTGACCTCCGGCCCGGGGCGGGTCTGGGTGCTTTCAATCTCG                         GAATGCCGGTGTGTGAGGCCTTGGCGTACGTTCAGCAGCACAGGTCGTCGT
genomic: TCTCACGCTTGACCTCCGGCCCGGGGCGGGTCTGGGTGCTTTCAATCTCGgtaacaaatt ... aatgattcagGAATGCCGGTGTGTGAGGCCTTGGCGTACGTTCAGCAGCACAGGTCGTCGT
EST: gi|100407853|gb|BY955811.1|BY955811
EST:     TCTCACGCTTGACCTCCGGCCCGGGGCGGGTCTGGGTGCTTTCAATCTCG                         GAATGCCGGTGTGTGAGGCCTTGGCGTACGTTCAGCAGCACAGGTCGTCGT
genomic: TCTCACGCTTGACCTCCGGCCCGGGGCGGGTCTGGGTGCTTTCAATCTCGgtaacaaatt ... aatgattcagGAATGCCGGTGTGTGAGGCCTTGGCGTACGTTCAGCAGCACAGGTCGTCGT
EST: gi|208355357|gb|DC929804.1|DC929804
EST:     TCTCACGCTTGACCTCCGGCCCGGGGCGGGTCTGGGTGCTTTCAATCTCG                         GAATGCCGGTGTGTGAGGCCTTGGCGTACGTTCAGCAGCACAGGTCGTCGT
genomic: TCTCACGCTTGACCTCCGGCCCGGGGCGGGTCTGGGTGCTTTCAATCTCGgtaacaaatt ... aatgattcagGAATGCCGGTGTGTGAGGCCTTGGCGTACGTTCAGCAGCACAGGTCGTCGT
EST: gi|162155579|gb|FC331530.1|FC331530
EST:     TCTCACGCTTGACCTCCGGCCCGGGGCGGGTCTGGGTGCTTTCAATCTCG                         GAATGCCGGTGTGTGAGGCCTTGGCGTACGTTCAGCAGCACAGGTCGTCGT
genomic: TCTCACGCTTGACCTCCGGCCCGGGGCGGGTCTGGGTGCTTTCAATCTCGgtaacaaatt ... aatgattcagGAATGCCGGTGTGTGAGGCCTTGGCGTACGTTCAGCAGCACAGGTCGTCGT
EST: gi|67718012|gb|BJ968271.1|BJ968271
EST:     TCTCACGCTTGACCTCCGGCCCGGGGCGGGTCTGGGTGCTTTCAATCTCG                         GAATGCCGGTGTGTGAGGCCTTGGCGTACGTTCAGCAGCACAGGTCGTCGT
genomic: TCTCACGCTTGACCTCCGGCCCGGGGCGGGTCTGGGTGCTTTCAATCTCGgtaacaaatt ... aatgattcagGAATGCCGGTGTGTGAGGCCTTGGCGTACGTTCAGCAGCACAGGTCGTCGT
EST: gi|18357519|gb|BJ189578.1|BJ189578
EST:     TCTCACGCTTGACCTCCGGCCCGGGGCGGGTCTGGGTGCTTTCAATCTCG                         GAATGCCGGTGTGTGAGGCCTTGGCGTACGTTCAGCAGCACAGGTCGTCGT
genomic: TCTCACGCTTGACCTCCGGCCCGGGGCGGGTCTGGGTGCTTTCAATCTCGgtaacaaatt ... aatgattcagGAATGCCGGTGTGTGAGGCCTTGGCGTACGTTCAGCAGCACAGGTCGTCGT
EST: gi|67578657|gb|BJ950824.1|BJ950824
EST:     TCTCACGCTTGACCTCCGGCCCGGGGCGGGTCTGGGTGCTTTCAATCTCG                         GAATGCCGGTGTGTGAGGCCTTGGCGTACGTTCAGCAGCACAGGTCGTCGT
genomic: TCTCACGCTTGACCTCCGGCCCGGGGCGGGTCTGGGTGCTTTCAATCTCGgtaacaaatt ... aatgattcagGAATGCCGGTGTGTGAGGCCTTGGCGTACGTTCAGCAGCACAGGTCGTCGT
EST: gi|18371944|gb|BJ203546.1|BJ203546
EST:     TCTCACGCTTGACCTCCGGCCCGGGGCGGGTCTGGGTGCTTTCAATCTCG                         GAATGCCGGTGTGTGAGGCCTTGGCGTACGTTCAGCAGCACAGGTCGTCGT
genomic: TCTCACGCTTGACCTCCGGCCCGGGGCGGGTCTGGGTGCTTTCAATCTCGgtaacaaatt ... aatgattcagGAATGCCGGTGTGTGAGGCCTTGGCGTACGTTCAGCAGCACAGGTCGTCGT
EST: gi|18344030|gb|BJ176069.1|BJ176069
EST:     TCTCACGCTTGACCTCCGGCCCGGGGCGGGTCTGGGTGCTTTCAATCTCG                         GAATGCCGGTGTGTGAGGCCTTGGCGTACGTTCAGCAGCACAGGTCGTCGT
genomic: TCTCACGCTTGACCTCCGGCCCGGGGCGGGTCTGGGTGCTTTCAATCTCGgtaacaaatt ... aatgattcagGAATGCCGGTGTGTGAGGCCTTGGCGTACGTTCAGCAGCACAGGTCGTCGT
EST: gi|18348917|gb|BJ180966.1|BJ180966
EST:     TCTCACGCTTGACCTCCGGCCCGGGGCGGGTCTGGGTGCTTTCAATCTCG                         GAATGCCGGTGTGTGAGGCCTTGGCGTACGTTCAGCAGCACAGGTCGTCGT
genomic: TCTCACGCTTGACCTCCGGCCCGGGGCGGGTCTGGGTGCTTTCAATCTCGgtaacaaatt ... aatgattcagGAATGCCGGTGTGTGAGGCCTTGGCGTACGTTCAGCAGCACAGGTCGTCGT
EST: gi|100409673|gb|BY956049.1|BY956049
EST:     TCTCACGCTTGACCTCCGGCCCGGGGCGGGTCTGGGTGCTTTCAATCTCG                         GAATGCCGGTGTGTGAGGCCTTGGCGTACGTTCAGCAGCACAGGTCGTCGT
genomic: TCTCACGCTTGACCTCCGGCCCGGGGCGGGTCTGGGTGCTTTCAATCTCGgtaacaaatt ... aatgattcagGAATGCCGGTGTGTGAGGCCTTGGCGTACGTTCAGCAGCACAGGTCGTCGT
EST: gi|100435291|gb|BY979169.1|BY979169
EST:     TCTCACGCTTGACCTCCGGCCCGGGGCGGGTCTGGGTGCTTTCAATCTCG                         GAATGCCGGTGTGTGAGGCCTTGGCGTACGTTCAGCAGCACAGGTCGTCGT
genomic: TCTCACGCTTGACCTCCGGCCCGGGGCGGGTCTGGGTGCTTTCAATCTCGgtaacaaatt ... aatgattcagGAATGCCGGTGTGTGAGGCCTTGGCGTACGTTCAGCAGCACAGGTCGTCGT
EST: gi|100423150|gb|BY958171.1|BY958171
EST:     CTCACGCTTGACCTCCGGCCCGGGGGCGG-TCTGGGTGCTTTCAATCTCG                         GAATGCCGGTGTGTGAGGCCTTGGCGTACGTTCAGCAGCACAGGTCGTCGT
genomic: CTCACGCTTGACCTCCGGCCCGGGG-CGGGTCTGGGTGCTTTCAATCTCGgtaacaaatt ... aatgattcagGAATGCCGGTGTGTGAGGCCTTGGCGTACGTTCAGCAGCACAGGTCGTCGT

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), 35 (downstream exon)
Score: 10

CCATCAGAAAAGTTGTTTCTGTCTTCACGCTTCTGCCATCGAATGGGAGGTCTCACGCTTGACCTCCGGCCCGGGGCGGGTCTGGGTGCTTTCAATCTCGgtaacaaatt ... aatgattcagGAATGCCGGTGTGTGAGGCCTTGGCGTACGTTCAGCAGCACAGGTCGTCGTTCGATGTTGTACAAGTGAAATATAACGATGAG




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