Skip to another splice site:
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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgggactcggtcgcgatctgcgatgcggtctgcatatgatgggagtgtgttagggcgagctgacggtttggagtcgcgttgtttgtgtcgggtgtgcagATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCATGCCACCTTCGTGCCCCACACCGCCGGGCGGTACTCCGTGAAGCGTTTCA

Basic information

species Physcomitrella patens
transcript PP1S114_143V6.1
intron # 1
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|100352574|gb|BY945340.1|BY945340
EST:     CGCAACCTGAAGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAG                         ATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT
genomic: CGCAACCTGAAGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAGgttcgttttt ... gggtgtgcagATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT
EST: gi|162230619|gb|FC406042.1|FC406042
EST:     CGCAACCTGAAGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAG                         ATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT
genomic: CGCAACCTGAAGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAGgttcgttttt ... gggtgtgcagATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT
EST: gi|162226150|gb|FC401610.1|FC401610
EST:     CGCAACCTGAAGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAG                         ATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT
genomic: CGCAACCTGAAGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAGgttcgttttt ... gggtgtgcagATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT
EST: gi|67718339|gb|BJ968598.1|BJ968598
EST:     CGCAACCTGAAGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAG                         ATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT
genomic: CGCAACCTGAAGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAGgttcgttttt ... gggtgtgcagATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT
EST: gi|37826229|gb|BJ584241.1|BJ584241
EST:     CGCAACCTGAAGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAG                         ATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT
genomic: CGCAACCTGAAGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAGgttcgttttt ... gggtgtgcagATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT
EST: gi|162273366|gb|FC449815.1|FC449815
EST:     CGCAACCTGAAGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAG                         ATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT
genomic: CGCAACCTGAAGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAGgttcgttttt ... gggtgtgcagATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT
EST: gi|162273367|gb|FC449816.1|FC449816
EST:     CGCAACCTGAAGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAG                         ATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT
genomic: CGCAACCTGAAGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAGgttcgttttt ... gggtgtgcagATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT
EST: gi|162238753|gb|FC418245.1|FC418245
EST:     CGCAACCTGAAGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAG                         ATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT
genomic: CGCAACCTGAAGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAGgttcgttttt ... gggtgtgcagATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT
EST: gi|67718322|gb|BJ968581.1|BJ968581
EST:     CGCAACCTGAAGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAG                         ATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT
genomic: CGCAACCTGAAGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAGgttcgttttt ... gggtgtgcagATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT
EST: gi|37842087|gb|BJ600095.1|BJ600095
EST:     CGCAACCTGAAGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAG                         ATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT
genomic: CGCAACCTGAAGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAGgttcgttttt ... gggtgtgcagATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT
EST: gi|162226151|gb|FC401611.1|FC401611
EST:     CGCAACCTGAAGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAG                         ATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT
genomic: CGCAACCTGAAGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAGgttcgttttt ... gggtgtgcagATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT
EST: gi|162238063|gb|FC414253.1|FC414253
EST:     CGCAACCTGAAGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAG                         ATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT
genomic: CGCAACCTGAAGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAGgttcgttttt ... gggtgtgcagATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT
EST: gi|162230618|gb|FC406041.1|FC406041
EST:     CGCAACCTGAAGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAG                         ATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT
genomic: CGCAACCTGAAGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAGgttcgttttt ... gggtgtgcagATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT
EST: gi|162229438|gb|FC405824.1|FC405824
EST:     CGCAACCTGAAGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAG                         ATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT
genomic: CGCAACCTGAAGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAGgttcgttttt ... gggtgtgcagATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT
EST: gi|208367427|gb|DC951317.1|DC951317
EST:     CGCAACCCGAAGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAG                         ATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT
genomic: CGCAACCTGAAGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAGgttcgttttt ... gggtgtgcagATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT
EST: gi|37838796|gb|BJ596804.1|BJ596804
EST:     CGCAACCTGAAGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAG                         ATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT
genomic: CGCAACCTGAAGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAGgttcgttttt ... gggtgtgcagATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT
EST: gi|67720579|gb|BJ970838.1|BJ970838
EST:     ACCTGAAGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAG                         ATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT
genomic: ACCTGAAGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAGgttcgttttt ... gggtgtgcagATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT
EST: gi|67720369|gb|BJ970628.1|BJ970628
EST:     AGTCCAGCTTTTCGGGCGCTGGCCGTTCGACGACATCGAG                         ATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT
genomic: AGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAGgttcgttttt ... gggtgtgcagATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCAT

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: 299

CTCGCCTAGACCACTCCCACGCTCCTCTGCCGCGCCAACCATGGCTGTCGCGCAACCTGAAGTCAAGCTTTTCGGGCGCTGGTCGTTCGACGACATCGAGgttcgttttt ... gggtgtgcagATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCATGCCACCTTCGTGCCCCACACCGCCGGGCGGTACTCCGTGAAGCGTTTCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtgttagggcgagctgacggtttggagtcgcgttgtttgtgtcgggtgtgcagATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCATGCCACCTTCGTGCCCCACACCGCCGGGCGGTACTCCGTGAAGCGTTTCA
             agctgac  putative branch site (score: 299)
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgggactcggtcgcgatctgcgatgcggtctgcatatgatgggagtgtgttagggcgagctgacggtttggagtcgcgttgtttgtgtcgggtgtgcagATTAACGATATCTCTCTGGCGGATTACATTGCCGTGTCGGTGGACAAGCATGCCACCTTCGTGCCCCACACCGCCGGGCGGTACTCCGTGAAGCGTTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC