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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtttaggtcttgttgccgtaactaggcaatgtacggcactatttcagcattttcaacctgtaggttccctgtgttgactttctctgtcgatgataacagAGGCTCGGTGCTGGGGAATGGTTCACCGCACGAGTGTCAGCCTGCGGGCTTTTCCACGTCGCTTACCCTAGTTCTCCAGATCTTCTTCGGGCTGAGTTGC

Basic information

species Physcomitrella patens
transcript PP1S197_114V6.1
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|18360814|gb|BJ192877.1|BJ192877
EST:     CGCAGATGAAGGAGCGAGATGTCGTGGAGTGGTTCATTCCGCTTGTTAAG                         AGGCTCGGTGCTGGGGAATGGTTCACCGCACGAGTGTCAGCCTGCGGGCTT
genomic: CGCAGATGAAGGAGCGAGATGTCGTGGAGTGGTTCATTCCGCTTGTTAAGgttagcaggg ... atgataacagAGGCTCGGTGCTGGGGAATGGTTCACCGCACGAGTGTCAGCCTGCGGGCTT
EST: gi|67718294|gb|BJ968553.1|BJ968553
EST:     CGCAGATGAAGGAGCGAGATGTCGTGGAGTGGTTCATTCCGCTTGTTAAG                         AGGCTCGGTGCTGGGGAATGGTTCACCGCACGAGTGTCAGCCTGCGGGCTT
genomic: CGCAGATGAAGGAGCGAGATGTCGTGGAGTGGTTCATTCCGCTTGTTAAGgttagcaggg ... atgataacagAGGCTCGGTGCTGGGGAATGGTTCACCGCACGAGTGTCAGCCTGCGGGCTT
EST: gi|162173325|gb|FC349496.1|FC349496
EST:     CGCAGATGAAGGAGCGAGATGTCGTGGAGTGGTTCATTCCGCTTGTTAAG                         AGGCTCGGTGCTGGGGAATGGTTCACCGCACGAGTGTCAGCCTGCGGGCTT
genomic: CGCAGATGAAGGAGCGAGATGTCGTGGAGTGGTTCATTCCGCTTGTTAAGgttagcaggg ... atgataacagAGGCTCGGTGCTGGGGAATGGTTCACCGCACGAGTGTCAGCCTGCGGGCTT
EST: gi|18325512|gb|BJ157509.1|BJ157509
EST:     CGCAGATGAAGGAGCGAGATGTCGTGGAGTGGTTCATTCCGCTTGTTAAG                         AGGCTCGGTGCTGGGGAATGGTTCACCGCACGAGTGTCAGCCTGCGGGCTT
genomic: CGCAGATGAAGGAGCGAGATGTCGTGGAGTGGTTCATTCCGCTTGTTAAGgttagcaggg ... atgataacagAGGCTCGGTGCTGGGGAATGGTTCACCGCACGAGTGTCAGCCTGCGGGCTT
EST: gi|18365472|gb|BJ197549.1|BJ197549
EST:     CGCAGATGAAGGAGCGAGATGTCGTGGAGTGGTTCATTCCGCTTGTTAAG                         AGGCTCGGTGCTGGGGAATGGTTCACCGCACGAGTGTCAGCCTGCGGGCTT
genomic: CGCAGATGAAGGAGCGAGATGTCGTGGAGTGGTTCATTCCGCTTGTTAAGgttagcaggg ... atgataacagAGGCTCGGTGCTGGGGAATGGTTCACCGCACGAGTGTCAGCCTGCGGGCTT
EST: gi|162169852|gb|FC346208.1|FC346208
EST:     CGCAGATGAAGGAGCGAGATGTCGTGGAGTGGTTCATTCCGCTTGTTAAG                         AGGCTCGGTGCTGGGGAATGGTTCACCGCACGAGTGTCAGCCTGCGGGCTT
genomic: CGCAGATGAAGGAGCGAGATGTCGTGGAGTGGTTCATTCCGCTTGTTAAGgttagcaggg ... atgataacagAGGCTCGGTGCTGGGGAATGGTTCACCGCACGAGTGTCAGCCTGCGGGCTT
EST: gi|18354276|gb|BJ186332.1|BJ186332
EST:     CGCAGATGAAGGAGCGAGATGTCGTGGAGTGGTTCATTCCGCTTGTTAAG                         AGGCTCGGTGCTGGGGAATGGTTCACCGCACGAGTGTCAGCCTGCGGGCTT
genomic: CGCAGATGAAGGAGCGAGATGTCGTGGAGTGGTTCATTCCGCTTGTTAAGgttagcaggg ... atgataacagAGGCTCGGTGCTGGGGAATGGTTCACCGCACGAGTGTCAGCCTGCGGGCTT
EST: gi|100448230|gb|CJ972529.1|CJ972529
EST:     CGCAGATGAAGGAGCGAGATGTCGTGGAGTGGTTCATTCCGCTTGTTAAG                         AGGCTCGGTGCTGGGGAATGGTTCACCGCACGAGTGTCAGCCTGCGGGCTT
genomic: CGCAGATGAAGGAGCGAGATGTCGTGGAGTGGTTCATTCCGCTTGTTAAGgttagcaggg ... atgataacagAGGCTCGGTGCTGGGGAATGGTTCACCGCACGAGTGTCAGCCTGCGGGCTT

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), 17 (downstream exon)
Score: 3

GGAAACCGTGGTGCGGGACAAGTCTGTGGAGTCGCTTTGCAAGATTGGCTCGCAGATGAAGGAGCGAGATGTCGTGGAGTGGTTCATTCCGCTTGTTAAGgttagcaggg ... atgataacagAGGCTCGGTGCTGGGGAATGGTTCACCGCACGAGTGTCAGCCTGCGGGCTTTTCCACGTCGCTTACCCTAGTTCTCCAGATCTTCTTCGGGCTGAGTTGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagcattttcaacctgtaggttccctgtgttgactttctctgtcgatgataacagAGGCTCGGTGCTGGGGAATGGTTCACCGCACGAGTGTCAGCCTGCGGGCTTTTCCACGTCGCTTACCCTAGTTCTCCAGATCTTCTTCGGGCTGAGTTGC
                           tgttgac  putative branch site (score: 3)
     ttttcaa  TA-rich tract