Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaaaaagtttctgagcctcagaaatttatcgtccgctcttggtttgaaagggaaggttttactgtgttgtctaaaggtctattatgactttggatgcagGCAAGTTCTTGGTAGGCTATATGCCAGTTGGTGGAGAGAAGGAGTACTACTTGGCAAGCGCATGCTCAGAACTGTATGCACCCCCGGGGGCATATATTTC

Basic information

species Physcomitrella patens
transcript PP1S25_21V6.1
intron # 5
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|162257211|gb|FC433087.1|FC433087
EST:     GGGAAAGCTTGATGAAATCCGACGACACATGGAATATTACAAGCAATCCG                         GCAAGTTCTTGGTAGGCTATATGCCAGTTGGTGGAGAGAAGGAGTACTACT
genomic: GGGAAAGCTTGATGAAATCCGACGACACATGGAATATTACAAGCAATCCGgtacgtaacc ... ttggatgcagGCAAGTTCTTGGTAGGCTATATGCCAGTTGGTGGAGAGAAGGAGTACTACT
EST: gi|162197312|gb|FC372274.1|FC372274
EST:     GGGAAAGCTTGATGAAATCCGACGACACATGGAATATTACAAGCAATCCG                         GCAAGTTCTTGGTAGGCTATATGCCAGTTGGTGGAGAGAAGGAGTACTACT
genomic: GGGAAAGCTTGATGAAATCCGACGACACATGGAATATTACAAGCAATCCGgtacgtaacc ... ttggatgcagGCAAGTTCTTGGTAGGCTATATGCCAGTTGGTGGAGAGAAGGAGTACTACT
EST: gi|162168391|gb|FC344705.1|FC344705
EST:     GGGAAAGCTTGATGAAATCCGACGACACATGGAATATTACAAGCAATCCG                         GCAAGTTCTTGGTAGGCTATATGCCAGTTGGTGGAGAGAAGGAGTACTACT
genomic: GGGAAAGCTTGATGAAATCCGACGACACATGGAATATTACAAGCAATCCGgtacgtaacc ... ttggatgcagGCAAGTTCTTGGTAGGCTATATGCCAGTTGGTGGAGAGAAGGAGTACTACT
EST: gi|162158571|gb|FC334574.1|FC334574
EST:     GGGAAAGCTTGATGAAATCCGACGACACATGGAATATTACAAGCAATCCG                         GCAAGTTCTTGGTAGGCTATATGCCAGTTGGTGGAGAGAAGGAGTACTACT
genomic: GGGAAAGCTTGATGAAATCCGACGACACATGGAATATTACAAGCAATCCGgtacgtaacc ... ttggatgcagGCAAGTTCTTGGTAGGCTATATGCCAGTTGGTGGAGAGAAGGAGTACTACT
EST: gi|162181980|gb|FC356851.1|FC356851
EST:     GGGAAAGCTTGATGAAATCCGACGACACATGGAATATTACAAGCAATCCG                         GCAAGTTCTTGGTAGGCTATATGCCAGTTGGTGGAGAGAAGGAGTACTACT
genomic: GGGAAAGCTTGATGAAATCCGACGACACATGGAATATTACAAGCAATCCGgtacgtaacc ... ttggatgcagGCAAGTTCTTGGTAGGCTATATGCCAGTTGGTGGAGAGAAGGAGTACTACT
EST: gi|162153222|gb|FC329004.1|FC329004
EST:     GGGAAAGCTTGATGAAATCCGACGACACATGGAATATTACAAGCAATCCG                         GCAAGTTCTTGGTAGGCTATATGCCAGTTGGTGGAGAGAAGGAGTACTACT
genomic: GGGAAAGCTTGATGAAATCCGACGACACATGGAATATTACAAGCAATCCGgtacgtaacc ... ttggatgcagGCAAGTTCTTGGTAGGCTATATGCCAGTTGGTGGAGAGAAGGAGTACTACT

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: 33 (upstream exon), 33 (downstream exon)
Score: 11

CCACGCATAGAGGGCGTCGTTCTATCAATTGAGCCCTTGGCCTGTGGTTGGGGAAAGCTTGATGAAATCCGACGACACATGGAATATTACAAGCAATCCGgtacgtaacc ... ttggatgcagGCAAGTTCTTGGTAGGCTATATGCCAGTTGGTGGAGAGAAGGAGTACTACTTGGCAAGCGCATGCTCAGAACTGTATGCACCCCCGGGGGCATATATTTC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaagggaaggttttactgtgttgtctaaaggtctattatgactttggatgcagGCAAGTTCTTGGTAGGCTATATGCCAGTTGGTGGAGAGAAGGAGTACTACTTGGCAAGCGCATGCTCAGAACTGTATGCACCCCCGGGGGCATATATTTC
                        gtctaaa  putative branch site (score: 11)
                                 tctattat  TA-rich tract