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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCAGgtccgtgacatcttcctgtttattcattttctattgtttagatgtttttgatgccgttgcataccagtggaagccaaagttatatccctttaaaatcatgcttaaatttttctttgaattttgcag

Basic information

species Physcomitrella patens
transcript PP1S7_406V6.1
intron # 5
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|208400722|gb|DC904900.1|DC904900
EST:     AGGCTTGAGCCTGAGCTACTTGGAAACAACAGACTCATCCATCAG
genomic: AGGCTTGAGCCTGAGCTACTTGGAAACAACAGACTCATCCATCAG
EST: gi|67570161|gb|BJ942985.1|BJ942985
EST:     AGGCTTGAGCCTGAGCTACTTGGAAACAACAGACTCATCCATCAG
genomic: AGGCTTGAGCCTGAGCTACTTGGAAACAACAGACTCATCCATCAG
EST: gi|162171829|gb|FC348979.1|FC348979
EST:     CTCATTTCGGACCGAATCCAGTTTGCAGTTTCTGAGATCAGAGATCAGAGCAGATCGGCACGGAGGGGAGAGACCAACCATGGCGTATGAGAGGATGGGGAAGCTGGATTCGAGCTTGCTGT
genomic: CTCATTTCGGACCGAATCCAGTTTGCAGTTTCTGAGATCAGAGATCAGAGCAGATCGGCACGGAGGGGAGAGACCAACCATGGCGTATGAGAGGATGGGGAAGCTGGATTTGAGCTTGCTGT
EST: gi|208377375|gb|DC906644.1|DC906644
EST:     AGTTTCTGAGATCAGAGATCAGAGCAGATCGGCACGGAGGGGAGAGACCAACCATGGCGTATGAGAGGATGGGGAAGCTGGATTTGAGCTTGCTGT
genomic: AGTTTCTGAGATCAGAGATCAGAGCAGATCGGCACGGAGGGGAGAGACCAACCATGGCGTATGAGAGGATGGGGAAGCTGGATTTGAGCTTGCTGT
EST: gi|162195749|gb|FC371140.1|FC371140
EST:     TTGGTGACATTCTAGATCAG
genomic: TTGGTGACATTCTAGATCAG
EST: gi|100425949|gb|BY977201.1|BY977201
EST:     ATACCTCATTTCGGACCGAATCCAGTTTGCAGTTTCTGAGATCAGAGATCAGAGCAGATCGGCACGGAGGGGAGAGACCAACCATGGCGTATGAGAGGATGGGGAAGCTGGATTTGAGCTTGCTGT
genomic: ATACCTCATTTCGGACCGAATCCAGTTTGCAGTTTCTGAGATCAGAGATCAGAGCAGATCGGCACGGAGGGGAGAGACCAACCATGGCGTATGAGAGGATGGGGAAGCTGGATTTGAGCTTGCTGT
EST: gi|100371973|gb|BY967643.1|BY967643
EST:     AGTTTCTGAGATCAGAGATCAGAGCAGATCGGCACGGAGGGGAGAGACCAACCATGGCGTATGAGAGGATGGGGAAGCTGGATTTGAGCTTGCTGT
genomic: AGTTTCTGAGATCAGAGATCAGAGCAGATCGGCACGGAGGGGAGAGACCAACCATGGCGTATGAGAGGATGGGGAAGCTGGATTTGAGCTTGCTGT
EST: gi|162162644|gb|FC338946.1|FC338946
EST:     ATACCTCATTTCGGACCGAATCCAGTTTGCAGTTTCTGAGATCAGAGATCAGAGCAGATCGGCACGGAGGGGAGAGACCAACCATGGCGTATGAGAGGATGGGGAAGCTGGATTCGAGCTTGCTGT
genomic: ATACCTCATTTCGGACCGAATCCAGTTTGCAGTTTCTGAGATCAGAGATCAGAGCAGATCGGCACGGAGGGGAGAGACCAACCATGGCGTATGAGAGGATGGGGAAGCTGGATTTGAGCTTGCTGT
EST: gi|208397325|gb|DC908229.1|DC908229
EST:     AGTTTGCAGTTTCTGAGATCAGAGATCAGAGCAGATCGGCACGGAGGGGAGAGACCAACCATGGCGTATGAGAGGATGGGGAAGCTGGATTTGAGCTTGCTGT
genomic: AGTTTGCAGTTTCTGAGATCAGAGATCAGAGCAGATCGGCACGGAGGGGAGAGACCAACCATGGCGTATGAGAGGATGGGGAAGCTGGATTTGAGCTTGCTGT
EST: gi|18373041|gb|BJ204643.1|BJ204643
EST:     GCAGTTTCTGAGATCAGAGATCAGAGCAGATCGGCACGGAGGGGAGAGACCAACCATGGCGTATGAGAGGATGGGGAAGCTGGATTTGAGCTTGCTGT
genomic: GCAGTTTCTGAGATCAGAGATCAGAGCAGATCGGCACGGAGGGGAGAGACCAACCATGGCGTATGAGAGGATGGGGAAGCTGGATTTGAGCTTGCTGT

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: 30 (upstream exon), 35 (downstream exon)
Score: 6

ATCAGgtccgtgaca ... aattttgcagGGTCACTGCGGATCATGCTGGGCTTTTGGGGCTGTTGAGTCACTGACTGATCGTTTCTGCATTCACTTGAATGAA




<











<


<