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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctcattctgctatatcacattgttttctgttgcatatgggacaccgctgttacacaaagtgaaaaaacaactcataaaaagacaccttatgaattattaggaacactctggtctcatgtattcctctaattgtagtgttaacttggtgtgttttgtaatattttcctaacaatttcaaacacttgccaccacagGATGATCTCGACCGAATGGCAGCAGAACGCCCAGACCAGTTCAAAGTCTACTATGTTCTGAACGAG

Basic information

species Physcomitrella patens
transcript PP1S165_105V6.1
intron # 6
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|162157574|gb|FC333832.1|FC333832
EST:     AGATATCTTTGATATATGCAAATGTCACATATGAGGACATTTTACTCAAG                         GATGATCTCGACCGAATGGCAGCAGAACGCCCAGAC
genomic: AGATATCTTTGATATATGCAAATGTCACATATGAGGACATTTTACTCAAGgtgctcattc ... gccaccacagGATGATCTCGACCGAATGGCAGCAGAACGCCCAGAC
EST: gi|100411604|gb|BY992247.1|BY992247
EST:     GATATCTTTGATATATGCAAATGTCACATATGAGGACATTTTACTNCA-G                         GATGATCTCGACCGAATGGCAGCAGAACGCCCAGACCAGTTCAAAGTCTA
genomic: GATATCTTTGATATATGCAAATGTCACATATGAGGACATTTTACT-CAAGgtgctcattc ... gccaccacagGATGATCTCGACCGAATGGCAGCAGAACGCCCAGACCAGTTCAAAGTCTA
EST: gi|208352513|gb|DC910213.1|DC910213
EST:     AGATATCTTTGATATATGCAAATGTCACATATGAGGACATTTTACTCAAG                         GATGATCTCGACCGAATGGCAGCAGAACGCCNAGACCAGTTCAA-GTCTAC
genomic: AGATATCTTTGATATATGCAAATGTCACATATGAGGACATTTTACTCAAGgtgctcattc ... gccaccacagGATGATCTCGACCGAATGGCAGCAGAACGCCCAGACCAGTTCAAAGTCTAC
EST: gi|162232093|gb|FC407695.1|FC407695
EST:     AGATATCTTTGATATATGCAAATGTCACATATGAGGACATTTTACTCAAG                         GATGATCTCGACCGAATGGCAGCAGAACGCCCAGACCAGTTCAAAGTCTAC
genomic: AGATATCTTTGATATATGCAAATGTCACATATGAGGACATTTTACTCAAGgtgctcattc ... gccaccacagGATGATCTCGACCGAATGGCAGCAGAACGCCCAGACCAGTTCAAAGTCTAC
EST: gi|100409366|gb|BY991976.1|BY991976
EST:     AGATATCTTTGATATATGCAAATGTCACATATGAGGACATTTTACTCAAG                         GATGATCTCGACCGAATGGCAGCAGAACGCCCAGACCAGTTCAAAGTCTAC
genomic: AGATATCTTTGATATATGCAAATGTCACATATGAGGACATTTTACTCAAGgtgctcattc ... gccaccacagGATGATCTCGACCGAATGGCAGCAGAACGCCCAGACCAGTTCAAAGTCTAC
EST: gi|208358223|gb|DC939391.1|DC939391
EST:     AGATATCTTTGATATATGCAAATGTCACATATGANGACATTTTACTCAAG                         GATGATCTCGACCGAATGGCAGCAGAACGCCCAGACNAGTTCAA-GTCTAC
genomic: AGATATCTTTGATATATGCAAATGTCACATATGAGGACATTTTACTCAAGgtgctcattc ... gccaccacagGATGATCTCGACCGAATGGCAGCAGAACGCCCAGACCAGTTCAAAGTCTAC
EST: gi|162216664|gb|FC392730.1|FC392730
EST:     AGATATCTTTGATATATGCAAATGTCACATATGAGGACATTTTACTCAAG                         GATGATCTCGACCGAATGGCAGCAGAACGCCCAGACCAGTTCAAAGTCTAC
genomic: AGATATCTTTGATATATGCAAATGTCACATATGAGGACATTTTACTCAAGgtgctcattc ... gccaccacagGATGATCTCGACCGAATGGCAGCAGAACGCCCAGACCAGTTCAAAGTCTAC
EST: gi|7583600|gb|AW699509.1|AW699509
EST:     AGATATCTTTGATATATGCAAATGTCACATATGAGGACATTTTACTCAAG                         GATGATCTCGACCGAATGGCAGCAGAACGCCCAGACCAGTTCAAAGTCTAC
genomic: AGATATCTTTGATATATGCAAATGTCACATATGAGGACATTTTACTCAAGgtgctcattc ... gccaccacagGATGATCTCGACCGAATGGCAGCAGAACGCCCAGACCAGTTCAAAGTCTAC
EST: gi|208368598|gb|DC940019.1|DC940019
EST:     AAATATCTTTGATATATGCAAATGTCACATATGANGACATTTTACTCAAG                         AATGATCTCGACNGAATGGCA
genomic: AGATATCTTTGATATATGCAAATGTCACATATGAGGACATTTTACTCAAGgtgctcattc ... gccaccacagGATGATCTCGACCGAATGGCA
EST: gi|208365412|gb|DC950879.1|DC950879
EST:     AGATATCTTTGATATATGCAAATGTCACATATGAGGACATTTTACTCAAG                         GATGATCTCGACCGAATGGCAGCAGAACGCCCAGACCAGTTCAAAGTCTAC
genomic: AGATATCTTTGATATATGCAAATGTCACATATGAGGACATTTTACTCAAGgtgctcattc ... gccaccacagGATGATCTCGACCGAATGGCAGCAGAACGCCCAGACCAGTTCAAAGTCTAC
EST: gi|100384199|gb|BY950585.1|BY950585
EST:     ATATCTTTGNATATATGCAA-TGTCACATATGAGGACATTTTACCTCAAG                         -ATGATCTCGACCGAATGGCAGCAGAACGCCCAGACCAGTTCAAAGTCTA
genomic: ATATCTTTG-ATATATGCAAATGTCACATATGAGGACATTTTAC-TCAAGgtgctcattc ... gccaccacagGATGATCTCGACCGAATGGCAGCAGAACGCCCAGACCAGTTCAAAGTCTA
EST: gi|208391805|gb|DC942339.1|DC942339
EST:     AGATATCTTTGATATATGCAAATGTCACATATGANGACATTTTACTCAAG                         GATGATCTCGACCGAATGGCAGCA
genomic: AGATATCTTTGATATATGCAAATGTCACATATGAGGACATTTTACTCAAGgtgctcattc ... gccaccacagGATGATCTCGACCGAATGGCAGCA
EST: gi|162222464|gb|FC397198.1|FC397198
EST:     AGATATCTTTGATATATGCAAATGTCACATATGAGGACATTTTACTCAAG                         GATGATCTCGACCGAATGGCAGCAGAACGCCCAGACCAGTTCAAAGTCTAC
genomic: AGATATCTTTGATATATGCAAATGTCACATATGAGGACATTTTACTCAAGgtgctcattc ... gccaccacagGATGATCTCGACCGAATGGCAGCAGAACGCCCAGACCAGTTCAAAGTCTAC
EST: gi|208378861|gb|DC927563.1|DC927563
EST:     AGATATCTTTGATATATGCAAATGTCACATATGAGGACATTTTACTCAAG                         GATGATCTCGACCGAATGGCAGCAGAACGCCCAGACCAGTTCAAAGTCTAC
genomic: AGATATCTTTGATATATGCAAATGTCACATATGAGGACATTTTACTCAAGgtgctcattc ... gccaccacagGATGATCTCGACCGAATGGCAGCAGAACGCCCAGACCAGTTCAAAGTCTAC
EST: gi|208374639|gb|DC931978.1|DC931978
EST:     AGATATCTTTGATATATGCAAATGTCACATATGAGGACATTTTACTCAAG                         GATGATCTCGACCGAATG
genomic: AGATATCTTTGATATATGCAAATGTCACATATGAGGACATTTTACTCAAGgtgctcattc ... gccaccacagGATGATCTCGACCGAATG
EST: gi|208357969|gb|DC938840.1|DC938840
EST:     AGATATCTTTGATATATGCAAATGTCACATATGAGGACATTTNACTCAAG                         GATGATCTCGACC
genomic: AGATATCTTTGATATATGCAAATGTCACATATGAGGACATTTTACTCAAGgtgctcattc ... gccaccacagGATGATCTCGACC

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), 34 (downstream exon)
Score: 7

GTTGCAAGAGCGATTCTGGAGAACTCTCATGATAAGACTAAGATATCTTTGATATATGCAAATGTCACATATGAGGACATTTTACTCAAGgtgctcattc ... gccaccacagGATGATCTCGACCGAATGGCAGCAGAACGCCCAGACCAGTTCAAAGTCTACTATGTTCTGAACGAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacttggtgtgttttgtaatattttcctaacaatttcaaacacttgccaccacagGATGATCTCGACCGAATGGCAGCAGAACGCCCAGACCAGTTCAAAGTCTACTATGTTCTGAACGAG
                        tcctaac  putative branch site (score: 7)
         tgttttgtaatatttt  TA-rich tract