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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaacatgagtctgttgcttataaccccagaaaatgcagttgtttgtgcaatcgctctcggaaagtctgattaaacccgtctggtttttgtgcctggcagGTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCGATTACTGCCTTCATCATTGTGAGTGTCCCGTTATTGTTGTGAGGTTTCC

Basic information

species Physcomitrella patens
transcript PP1S98_214V6.1
intron # 3
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|162252229|gb|FC425907.1|FC425907
EST:     CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAG                         GTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
genomic: CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAGgtaggggttt ... tgcctggcagGTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
EST: gi|37839245|gb|BJ597253.1|BJ597253
EST:     CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAG                         GTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
genomic: CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAGgtaggggttt ... tgcctggcagGTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
EST: gi|208373949|gb|DC944682.1|DC944682
EST:     CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAG                         GTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
genomic: CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAGgtaggggttt ... tgcctggcagGTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
EST: gi|208367582|gb|DC943957.1|DC943957
EST:     CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAG                         GTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
genomic: CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAGgtaggggttt ... tgcctggcagGTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
EST: gi|208387788|gb|DC941357.1|DC941357
EST:     CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAG                         GTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
genomic: CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAGgtaggggttt ... tgcctggcagGTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
EST: gi|37844423|gb|BJ602431.1|BJ602431
EST:     CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAG                         GTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
genomic: CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAGgtaggggttt ... tgcctggcagGTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
EST: gi|162271782|gb|FC448915.1|FC448915
EST:     CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAG                         GTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
genomic: CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAGgtaggggttt ... tgcctggcagGTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
EST: gi|37840221|gb|BJ598229.1|BJ598229
EST:     CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAG                         GTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
genomic: CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAGgtaggggttt ... tgcctggcagGTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
EST: gi|15261883|gb|BI437193.1|BI437193
EST:     CTTGGAGGGTGAGCGGCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAG                         GTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
genomic: CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAGgtaggggttt ... tgcctggcagGTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
EST: gi|162216213|gb|FC392630.1|FC392630
EST:     CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAG                         GTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
genomic: CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAGgtaggggttt ... tgcctggcagGTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
EST: gi|37840816|gb|BJ598824.1|BJ598824
EST:     TGGAGTCAGTGCAATGATCATGGGAAGCCGAG                         GTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
genomic: TGGAGTCAGTGCAATGATCATGGGAAGCCGAGgtaggggttt ... tgcctggcagGTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
EST: gi|162180414|gb|FC355835.1|FC355835
EST:     CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAG                         GTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
genomic: CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAGgtaggggttt ... tgcctggcagGTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
EST: gi|208360624|gb|DC946404.1|DC946404
EST:     CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAG                         GTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
genomic: CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAGgtaggggttt ... tgcctggcagGTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
EST: gi|22492564|gb|BU052487.1|BU052487
EST:     CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAG                         GTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
genomic: CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAGgtaggggttt ... tgcctggcagGTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
EST: gi|162263563|gb|FC440099.1|FC440099
EST:     CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAG                         GTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
genomic: CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAGgtaggggttt ... tgcctggcagGTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
EST: gi|22132388|gb|BQ827128.1|BQ827128
EST:     CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAG                         GTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
genomic: CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAGgtaggggttt ... tgcctggcagGTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
EST: gi|18339851|gb|BJ171878.1|BJ171878
EST:     TTGGAGTCAGTGCAATGATCATGGGAAGCCGAG                         GTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
genomic: TTGGAGTCAGTGCAATGATCATGGGAAGCCGAGgtaggggttt ... tgcctggcagGTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
EST: gi|162252228|gb|FC425906.1|FC425906
EST:     CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAG                         GTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
genomic: CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAGgtaggggttt ... tgcctggcagGTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
EST: gi|162207218|gb|FC382540.1|FC382540
EST:     CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAG                         GTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
genomic: CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAGgtaggggttt ... tgcctggcagGTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
EST: gi|162216212|gb|FC392629.1|FC392629
EST:     CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAG                         GTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
genomic: CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAGgtaggggttt ... tgcctggcagGTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
EST: gi|162266202|gb|FC441731.1|FC441731
EST:     CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAG                         GTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
genomic: CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAGgtaggggttt ... tgcctggcagGTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
EST: gi|208368926|gb|DC947484.1|DC947484
EST:     C-TGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAG                         GTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
genomic: CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAGgtaggggttt ... tgcctggcagGTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
EST: gi|208395153|gb|DC923952.1|DC923952
EST:     CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAG                         GTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
genomic: CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAGgtaggggttt ... tgcctggcagGTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
EST: gi|162245831|gb|FC420472.1|FC420472
EST:     TGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAG                         GTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
genomic: TGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAGgtaggggttt ... tgcctggcagGTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
EST: gi|208363175|gb|DC954361.1|DC954361
EST:     CNTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAG                         GTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
genomic: CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAGgtaggggttt ... tgcctggcagGTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
EST: gi|162239277|gb|FC416520.1|FC416520
EST:     CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAG                         GTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
genomic: CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAGgtaggggttt ... tgcctggcagGTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
EST: gi|162207217|gb|FC382539.1|FC382539
EST:     CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAG                         GTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
genomic: CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAGgtaggggttt ... tgcctggcagGTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
EST: gi|162245832|gb|FC420473.1|FC420473
EST:     CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAG                         GTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
genomic: CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAGgtaggggttt ... tgcctggcagGTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
EST: gi|208396071|gb|DC924537.1|DC924537
EST:     TTGGAGTCAGTGCAATGATCATGGGAAGCCGAG                         GTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
genomic: TTGGAGTCAGTGCAATGATCATGGGAAGCCGAGgtaggggttt ... tgcctggcagGTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
EST: gi|162239278|gb|FC416521.1|FC416521
EST:     CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAG                         GTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
genomic: CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAGgtaggggttt ... tgcctggcagGTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG
EST: gi|100403797|gb|BY955106.1|BY955106
EST:     CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAG                         GTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAACGTCAGCG
genomic: CTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAGgtaggggttt ... tgcctggcagGTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCG

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

CCGTACAAGATTCATATTGTGAAAGACCATGATATGAAAGAGCGAATCTGCTTGGAGGTTGAGCGTCTTGGAGTCAGTGCAATGATCATGGGAAGCCGAGgtaggggttt ... tgcctggcagGTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCGATTACTGCCTTCATCATTGTGAGTGTCCCGTTATTGTTGTGAGGTTTCC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcaatcgctctcggaaagtctgattaaacccgtctggtttttgtgcctggcagGTGTAGGTGCTACAAGACGATCTCGTAAAGCTCGTCTTGGAAGCGTCAGCGATTACTGCCTTCATCATTGTGAGTGTCCCGTTATTGTTGTGAGGTTTCC
                   gtctgat  putative branch site (score: 35)
                                       tttttgt  putative PPT
                      tgattaaa  TA-rich tract