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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcgtgttttaggatggtattgattctacaaacttttgatgtaggttagttgatttgttccggaagtactgacattgtactgcttgtcattcgtttgcagCTTGTACAACAACATTTTGCAACCTAGCAAGCTGATTGCTGGGGCAGATTTTCACTGCTTCAAGAGCGGAATTGAGCCTAAATGGGAGGACCCTAAGTGT

Basic information

species Physcomitrella patens
transcript PP1S39_197V6.3
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|67712745|gb|BJ966194.1|BJ966194
EST:     AGCTCTCTGCGTTCCGTCTACACGTTTCACACTGTTGAGGAATTTTGGTG                         CTTGTACAACAACATTTTGCAACCTAGCAAGCTGATTGCTGGGGCAGATTT
genomic: AGCTCTCTGCGTTCCGTCTACACGTTTCACACTGTTGAGGAATTTTGGTGgtatggatag ... tcgtttgcagCTTGTACAACAACATTTTGCAACCTAGCAAGCTGATTGCTGGGGCAGATTT
EST: gi|67569897|gb|BJ942721.1|BJ942721
EST:     AGCTCTCTGCGTTCCGTCTACACGTTTCACACTGTTGAGGAATTTTGGTG                         CTTGTACAACAACATTTTGCAACCTAGCAAGCTGATTGCTGGGGCAGATTT
genomic: AGCTCTCTGCGTTCCGTCTACACGTTTCACACTGTTGAGGAATTTTGGTGgtatggatag ... tcgtttgcagCTTGTACAACAACATTTTGCAACCTAGCAAGCTGATTGCTGGGGCAGATTT
EST: gi|67578237|gb|BJ950404.1|BJ950404
EST:     AGCTCTCTGCGTTCCGTCTACACGTTTCACACTGTTGAGGAATTTTGGTG                         CTTGTACAACAACATTTTGCAACCTAGCAAGCTGATTGCTGGGGCAGATTT
genomic: AGCTCTCTGCGTTCCGTCTACACGTTTCACACTGTTGAGGAATTTTGGTGgtatggatag ... tcgtttgcagCTTGTACAACAACATTTTGCAACCTAGCAAGCTGATTGCTGGGGCAGATTT
EST: gi|208362463|gb|DC939471.1|DC939471
EST:     AGCTCTCTGCGTTCCGTCTACACGTTTCACACTGTTGAGGAATTTTGGTG                         CTTGTACAACAACATTTTGCAACCTANCAAGCTGATTGCTGGGGCAGATTT
genomic: AGCTCTCTGCGTTCCGTCTACACGTTTCACACTGTTGAGGAATTTTGGTGgtatggatag ... tcgtttgcagCTTGTACAACAACATTTTGCAACCTAGCAAGCTGATTGCTGGGGCAGATTT
EST: gi|67576793|gb|BJ949617.1|BJ949617
EST:     AGCTCTCTGCGTTCCGTCTACACGTTTCACACTGTTGAGGAATTTTGGTG                         CTTGTACAACAACATTTTGCAACCTAGCAAGCTGATTGCTGGGGCAGATTT
genomic: AGCTCTCTGCGTTCCGTCTACACGTTTCACACTGTTGAGGAATTTTGGTGgtatggatag ... tcgtttgcagCTTGTACAACAACATTTTGCAACCTAGCAAGCTGATTGCTGGGGCAGATTT
EST: gi|67575480|gb|BJ948304.1|BJ948304
EST:     AGCTCTCTGCGTTCCGTCTACACGTTTCACACTGTTGAGGAATTTTGGTG                         CTTGTACAACAACATTTTGCAACCTAGCAAGCTGATTGCTGGGGCAGATTT
genomic: AGCTCTCTGCGTTCCGTCTACACGTTTCACACTGTTGAGGAATTTTGGTGgtatggatag ... tcgtttgcagCTTGTACAACAACATTTTGCAACCTAGCAAGCTGATTGCTGGGGCAGATTT
EST: gi|19788032|gb|BQ040702.1|BQ040702
EST:     AGCTCTCTGCGTTCCGTCTACACGTTTCACACTGTTGAGGAATTTTGGTG                         CTTGTACAACAACATTTTGCAACCTAGCAAGCTGATTGCTGGGGCAGATTT
genomic: AGCTCTCTGCGTTCCGTCTACACGTTTCACACTGTTGAGGAATTTTGGTGgtatggatag ... tcgtttgcagCTTGTACAACAACATTTTGCAACCTAGCAAGCTGATTGCTGGGGCAGATTT
EST: gi|67704161|gb|BJ964394.1|BJ964394
EST:     AGCTCTCTGCGTTCCGTCTACACGTTTCACACTGTTGAGGAATTTTGGTG                         CTTGTACAACAACATTTTGCAACCTANCAAGCTGATTGCTGG
genomic: AGCTCTCTGCGTTCCGTCTACACGTTTCACACTGTTGAGGAATTTTGGTGgtatggatag ... tcgtttgcagCTTGTACAACAACATTTTGCAACCTAGCAAGCTGATTGCTGG
EST: gi|208397568|gb|DC912186.1|DC912186
EST:     AGCTCTCTGCGTTCCGTCTACACGTTTCACACTGTTGAGGAATTTTGGTG                         CTTGTACAACAACATTTTGCAACCTAGCAAGCTGATTGCTGGGGCAGATTT
genomic: AGCTCTCTGCGTTCCGTCTACACGTTTCACACTGTTGAGGAATTTTGGTGgtatggatag ... tcgtttgcagCTTGTACAACAACATTTTGCAACCTAGCAAGCTGATTGCTGGGGCAGATTT
EST: gi|67575463|gb|BJ948287.1|BJ948287
EST:     AGCTCTCTGCGTTCCGTCTACACGTTTCACACTGTTGAGGAATTTTGGTG                         CTTGTACAACAACATTT
genomic: AGCTCTCTGCGTTCCGTCTACACGTTTCACACTGTTGAGGAATTTTGGTGgtatggatag ... tcgtttgcagCTTGTACAACAACATTT
EST: gi|18354376|gb|BJ186432.1|BJ186432
EST:     AGCTCTCTGCGTTCCGTCTACACGTTTCACACTGTTGAGGAATTTTGGTG                         CTTGTACAACAACATTTTGCAACCTAGCAAGCTGATTGCTGGGGCAGATTT
genomic: AGCTCTCTGCGTTCCGTCTACACGTTTCACACTGTTGAGGAATTTTGGTGgtatggatag ... tcgtttgcagCTTGTACAACAACATTTTGCAACCTAGCAAGCTGATTGCTGGGGCAGATTT

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: 31 (upstream exon), 33 (downstream exon)
Score: 16

CGTTTTGGTTTGACAATCCGAACGGGAAACAGAAGCAGGCCACATGGGGGAGCTCTCTGCGTTCCGTCTACACGTTTCACACTGTTGAGGAATTTTGGTGgtatggatag ... tcgtttgcagCTTGTACAACAACATTTTGCAACCTAGCAAGCTGATTGCTGGGGCAGATTTTCACTGCTTCAAGAGCGGAATTGAGCCTAAATGGGAGGACCCTAAGTGT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagttgatttgttccggaagtactgacattgtactgcttgtcattcgtttgcagCTTGTACAACAACATTTTGCAACCTAGCAAGCTGATTGCTGGGGCAGATTTTCACTGCTTCAAGAGCGGAATTGAGCCTAAATGGGAGGACCCTAAGTGT
                     tactgac  putative branch site (score: 16)
                                            ttcgttt  putative PPT
       atttgtt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcgtgttttaggatggtattgattctacaaacttttgatgtaggttagttgatttgttccggaagtactgacattgtactgcttgtcattcgtttgcagCTTGTACAACAACATTTTGCAACCTAGCAAGCTGATTGCTGGGGCAGATTTTCACTGCTTCAAGAGCGGAATTGAGCCTAAATGGGAGGACCCTAAGTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA