Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGCCGTTGAGCATTCGGGATTGAGTATTGTGATTGCGAGGAGCTCAATCAATCGGATCATCCATAATGCCTCTCTTCTACCCTTCCATCCTTTTCCAGgttagtgtttggtcgtcgaagaaattcttccgcgcttcgcttcggtgactgaattcggatttgttgttgttcctacgatgatggaatgggggtgggggggtttggttggtgggtcgaattgtggcag

Basic information

species Physcomitrella patens
transcript PP1S42_179V6.1
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|67699611|gb|BJ959844.1|BJ959844
EST:     CAATCGGATCATCCATAATGCCTCTCTTCTACCCTTCCATCCTTTTCCAG                         GAGCGGGTGCTGGGCTTCGTTATGGGAGGATTGGTCGGGGCGGGGGTTTCC
genomic: CAATCGGATCATCCATAATGCCTCTCTTCTACCCTTCCATCCTTTTCCAGgttagtgttt ... attgtggcagGAGCGGGTGCTGGGCTTCGTTATGGGAGGATTGGTCGGGGCGGGGGTTTCC
EST: gi|67700202|gb|BJ960435.1|BJ960435
EST:     CAATCGGATCATCCATAATGCCTCTCTTCTACCCTTCCATCCTTTTCCAG                         GAGCGGGTGCTGGGCTTCGTTATGGGAGGATTGGTCGGGGCGGGGGTTTCC
genomic: CAATCGGATCATCCATAATGCCTCTCTTCTACCCTTCCATCCTTTTCCAGgttagtgttt ... attgtggcagGAGCGGGTGCTGGGCTTCGTTATGGGAGGATTGGTCGGGGCGGGGGTTTCC
EST: gi|67573858|gb|BJ946682.1|BJ946682
EST:     CTCTTCTACCCTTCCATCCTTTTCCAG                         GAGCGGGTGCTGGGCTTCGTTATGGGAGGATTGGTCGGGGCGGGGGTTTCC
genomic: CTCTTCTACCCTTCCATCCTTTTCCAGgttagtgttt ... attgtggcagGAGCGGGTGCTGGGCTTCGTTATGGGAGGATTGGTCGGGGCGGGGGTTTCC
EST: gi|37840142|gb|BJ598150.1|BJ598150
EST:     CAATCGGATCATCCATAATGCCTCTCTTCTACCCTTCCATCCTTTTCCAG                         GAGCGGGTGCTGGGCTTCGTTATGGGAGGATTGGTCGGGGCGGGGGTTTCC
genomic: CAATCGGATCATCCATAATGCCTCTCTTCTACCCTTCCATCCTTTTCCAGgttagtgttt ... attgtggcagGAGCGGGTGCTGGGCTTCGTTATGGGAGGATTGGTCGGGGCGGGGGTTTCC
EST: gi|18362927|gb|BJ194999.1|BJ194999
EST:     CAATCGGATCATCCATAATGCCTCTCTTCTACCCTTCCATCCTTTTCCAG                         GAGCGGGTGCTGGGCTTCGTTATGGGAGGATTGGTCGGGGCGGGGGTTTCC
genomic: CAATCGGATCATCCATAATGCCTCTCTTCTACCCTTCCATCCTTTTCCAGgttagtgttt ... attgtggcagGAGCGGGTGCTGGGCTTCGTTATGGGAGGATTGGTCGGGGCGGGGGTTTCC
EST: gi|67697245|gb|BJ957478.1|BJ957478
EST:     ATCCATAATGCCTCTCTTCTACCCTTCCATCCTTTTCCAG                         GAGCGGGTGCTGGGCTTCGTTATGGGAGGATTGGTCGGGGCGGGGGTTTCC
genomic: ATCCATAATGCCTCTCTTCTACCCTTCCATCCTTTTCCAGgttagtgttt ... attgtggcagGAGCGGGTGCTGGGCTTCGTTATGGGAGGATTGGTCGGGGCGGGGGTTTCC
EST: gi|67576669|gb|BJ949493.1|BJ949493
EST:     CAATCGGATCATCCATAATGCCTCTCTTCTACCCTTCCATCCTTTTCCAG                         GAGCGGGTGCTGGGCTTCGTTATGGGAGGATTGGTCGGGGCGGGGGTTTCC
genomic: CAATCGGATCATCCATAATGCCTCTCTTCTACCCTTCCATCCTTTTCCAGgttagtgttt ... attgtggcagGAGCGGGTGCTGGGCTTCGTTATGGGAGGATTGGTCGGGGCGGGGGTTTCC
EST: gi|67570787|gb|BJ943611.1|BJ943611
EST:     CAATCGGATCATCCATAATGCCTCTCTTCTACCCTTCCATCCTTTTCCAG                         GAGCGGGTGCTGGGCTTCGTTATGGGAGGATTGGTCGGGGCGGGGGTTTCC
genomic: CAATCGGATCATCCATAATGCCTCTCTTCTACCCTTCCATCCTTTTCCAGgttagtgttt ... attgtggcagGAGCGGGTGCTGGGCTTCGTTATGGGAGGATTGGTCGGGGCGGGGGTTTCC
EST: gi|162229865|gb|FC404318.1|FC404318
EST:     CAATCGGATCATCCATAATGCCTCTCTTCTACCCTTCCATCCTTTTCCAG                         GAGCGGGTGCTGGGCTTCGTTATGGGAGGATTGGTCGGGGCGGGGGTTTCC
genomic: CAATCGGATCATCCATAATGCCTCTCTTCTACCCTTCCATCCTTTTCCAGgttagtgttt ... attgtggcagGAGCGGGTGCTGGGCTTCGTTATGGGAGGATTGGTCGGGGCGGGGGTTTCC
EST: gi|67694084|gb|BJ954317.1|BJ954317
EST:     CAATCGGATCATCCATAATGCCTCTCTTCTACCCTTCCATCCTTTTCCAG                         GAGCGGGTGCTGGGCTTCGTTATGGGAGGATTGGTCGGGGCGGGGGTTTCC
genomic: CAATCGGATCATCCATAATGCCTCTCTTCTACCCTTCCATCCTTTTCCAGgttagtgttt ... attgtggcagGAGCGGGTGCTGGGCTTCGTTATGGGAGGATTGGTCGGGGCGGGGGTTTCC
EST: gi|162259072|gb|FC435157.1|FC435157
EST:     CAATCGGATCATCCATAATGCCTCTCTTCTACCCTTCCATCCTTTTCCAG                         GAGCGGGTGCTGGGCTTCGTTATGGGAGGATTGGTCGGGGCGGGGGTTTCC
genomic: CAATCGGATCATCCATAATGCCTCTCTTCTACCCTTCCATCCTTTTCCAGgttagtgttt ... attgtggcagGAGCGGGTGCTGGGCTTCGTTATGGGAGGATTGGTCGGGGCGGGGGTTTCC
EST: gi|13251314|gb|BG362217.1|BG362217
EST:     CAATCGGATCATCCATAATGCCTCTCTTCTACCCTTCCATCCTTTTCCAG                         GAGCGGGTGCTGGGCTTCGTTATGGGAGGATTGGTCGGGGCGGGGGTTTCC
genomic: CAATCGGATCATCCATAATGCCTCTCTTCTACCCTTCCATCCTTTTCCAGgttagtgttt ... attgtggcagGAGCGGGTGCTGGGCTTCGTTATGGGAGGATTGGTCGGGGCGGGGGTTTCC
EST: gi|67576120|gb|BJ948944.1|BJ948944
EST:     CAATCGGATCATCCATAATGCCTCTCTTCTACCCTTCCATCCTTTTCCAG                         GAGCGGGTGCTGGGCTTCGTTATGGGAGGATTGGTCGGGGCGGGGGTTTCC
genomic: CAATCGGATCATCCATAATGCCTCTCTTCTACCCTTCCATCCTTTTCCAGgttagtgttt ... attgtggcagGAGCGGGTGCTGGGCTTCGTTATGGGAGGATTGGTCGGGGCGGGGGTTTCC

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: 22 (upstream exon), 28 (downstream exon)
Score: 4

ATTGCCGTTGAGCATTCGGGATTGAGTATTGTGATTGCGAGGAGCTCAATCAATCGGATCATCCATAATGCCTCTCTTCTACCCTTCCATCCTTTTCCAGgttagtgttt ... attgtggcagGAGCGGGTGCTGGGCTTCGTTATGGGAGGATTGGTCGGGGCGGGGGTTTCCATGTACGACCAACGAGAGATTTGGAAGTCGACTGCAGGTCTTGCCGAGA




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