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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagacccgacctcaaatttgcaacctttgcacacggatttctcatggtttagagctacaatcggtgttgaatgctgaatggaaatttggtgcatgatgccacttcatgaaatgagagggttaatgggattctgtccctgaatcagAACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCCAAGAGATATCTTGAGGACGTGTGCGCTCACAAGCAAGCTGTTCCTTTCC

Basic information

species Physcomitrella patens
transcript PP1S97_78V6.2
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|67696433|gb|BJ956666.1|BJ956666
EST:     CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG                         AACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
genomic: CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAGgtgagacccg ... cctgaatcagAACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
EST: gi|67571063|gb|BJ943887.1|BJ943887
EST:     CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG                         AACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
genomic: CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAGgtgagacccg ... cctgaatcagAACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
EST: gi|67571535|gb|BJ944359.1|BJ944359
EST:     CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG                         AACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
genomic: CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAGgtgagacccg ... cctgaatcagAACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
EST: gi|162260531|gb|FC435105.1|FC435105
EST:     CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG                         AACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
genomic: CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAGgtgagacccg ... cctgaatcagAACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
EST: gi|67572512|gb|BJ945336.1|BJ945336
EST:     CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG                         AACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
genomic: CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAGgtgagacccg ... cctgaatcagAACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
EST: gi|67696650|gb|BJ956883.1|BJ956883
EST:     CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG                         AACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
genomic: CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAGgtgagacccg ... cctgaatcagAACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
EST: gi|162279259|gb|FC455806.1|FC455806
EST:     CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG                         AACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
genomic: CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAGgtgagacccg ... cctgaatcagAACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
EST: gi|162278150|gb|FC454385.1|FC454385
EST:     CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG                         AACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
genomic: CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAGgtgagacccg ... cctgaatcagAACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
EST: gi|18332577|gb|BJ164590.1|BJ164590
EST:     CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG                         AACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
genomic: CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAGgtgagacccg ... cctgaatcagAACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
EST: gi|67569399|gb|BJ942223.1|BJ942223
EST:     CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG                         AACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
genomic: CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAGgtgagacccg ... cctgaatcagAACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
EST: gi|162279258|gb|FC455805.1|FC455805
EST:     CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG                         AACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
genomic: CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAGgtgagacccg ... cctgaatcagAACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
EST: gi|162260530|gb|FC435104.1|FC435104
EST:     CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG                         AACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
genomic: CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAGgtgagacccg ... cctgaatcagAACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
EST: gi|67578333|gb|BJ950500.1|BJ950500
EST:     CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG                         AACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
genomic: CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAGgtgagacccg ... cctgaatcagAACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
EST: gi|67699663|gb|BJ959896.1|BJ959896
EST:     CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG                         AACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
genomic: CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAGgtgagacccg ... cctgaatcagAACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
EST: gi|67573050|gb|BJ945874.1|BJ945874
EST:     CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG                         AACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
genomic: CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAGgtgagacccg ... cctgaatcagAACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
EST: gi|162246687|gb|FC425280.1|FC425280
EST:     CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG                         AACACTAGAGAGGCAGCGCAAGCCTTCAAGCATATGGAGTTGGCTAAGGCC
genomic: CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAGgtgagacccg ... cctgaatcagAACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
EST: gi|67571332|gb|BJ944156.1|BJ944156
EST:     CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG                         AACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
genomic: CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAGgtgagacccg ... cctgaatcagAACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
EST: gi|162246688|gb|FC425281.1|FC425281
EST:     CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG                         AACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
genomic: CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAGgtgagacccg ... cctgaatcagAACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
EST: gi|67694652|gb|BJ954885.1|BJ954885
EST:     CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG                         AACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
genomic: CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAGgtgagacccg ... cctgaatcagAACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
EST: gi|67573265|gb|BJ946089.1|BJ946089
EST:     CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG                         AACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
genomic: CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAGgtgagacccg ... cctgaatcagAACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
EST: gi|67576166|gb|BJ948990.1|BJ948990
EST:     CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG                         AACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
genomic: CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAGgtgagacccg ... cctgaatcagAACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
EST: gi|67692660|gb|BJ952893.1|BJ952893
EST:     CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG                         AACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
genomic: CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAGgtgagacccg ... cctgaatcagAACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
EST: gi|67695885|gb|BJ956118.1|BJ956118
EST:     CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG                         AACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
genomic: CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAGgtgagacccg ... cctgaatcagAACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
EST: gi|67572806|gb|BJ945630.1|BJ945630
EST:     CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG                         AACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
genomic: CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAGgtgagacccg ... cctgaatcagAACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
EST: gi|67694374|gb|BJ954607.1|BJ954607
EST:     CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG                         AACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
genomic: CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAGgtgagacccg ... cctgaatcagAACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
EST: gi|67572841|gb|BJ945665.1|BJ945665
EST:     CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG                         AACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
genomic: CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAGgtgagacccg ... cctgaatcagAACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
EST: gi|67695151|gb|BJ955384.1|BJ955384
EST:     ATCGGATTTGCGTGTGCATTTTAAG                         AACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
genomic: ATCGGATTTGCGTGTGCATTTTAAGgtgagacccg ... cctgaatcagAACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
EST: gi|67571783|gb|BJ944607.1|BJ944607
EST:     CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG                         AACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
genomic: CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAGgtgagacccg ... cctgaatcagAACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
EST: gi|18329135|gb|BJ161141.1|BJ161141
EST:     CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG                         AACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
genomic: CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAGgtgagacccg ... cctgaatcagAACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
EST: gi|67694876|gb|BJ955109.1|BJ955109
EST:     CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAG                         AACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC
genomic: CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAGgtgagacccg ... cctgaatcagAACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCC

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: 98

CCTGTAAGGCCAGGGGATCGGATTTGCGTGTGCATTTTAAGgtgagacccg ... cctgaatcagAACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCCAAGAGATATCTTGAGGACGTGTGCGCTCACAAGCAAGCTGTTCCTTTCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatgatgccacttcatgaaatgagagggttaatgggattctgtccctgaatcagAACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCCAAGAGATATCTTGAGGACGTGTGCGCTCACAAGCAAGCTGTTCCTTTCC
                           ggttaat  putative branch site (score: 98)
                                      ttctgtccct  putative PPT
               atgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagacccgacctcaaatttgcaacctttgcacacggatttctcatggtttagagctacaatcggtgttgaatgctgaatggaaatttggtgcatgatgccacttcatgaaatgagagggttaatgggattctgtccctgaatcagAACACTAGAGAGGCAGCGCAAGCCATCAAGCATATGGAGTTGGCTAAGGCCAAGAGATATCTTGAGGACGTGTGCGCTCACAAGCAAGCTGTTCCTTTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT