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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacagtttttgatcctctctcttcctctgtatttttccttagccggatgtagatacagcacttcaattttcagtcaatccttctatagtttttcattttgcctctctcactcttattctccaattttactattttcttcaagttgattaccagtaggtactagcatgttaagctaacccagaagcttgtggtttgcagGAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGGTACTTCTTGAGGCAGATAGTGAACCGTGTGGTGGAAGTGACCGATAACA

Basic information

species Physcomitrella patens
transcript PP1S495_14V6.1
intron # 4
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|162194076|gb|FC370251.1|FC370251
EST:     GGACGAGCCCCACAAATCATCTGGATATTCCTTCAAAAGAAATGCTTGAG                         GAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGG
genomic: GGACGAG-CCCACAAATCATCTGGATATTCCTTCAAAGGAAATGCTTGAGgtaacagttt ... tggtttgcagGAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGG
EST: gi|162168211|gb|FC344941.1|FC344941
EST:     TGGACGAGCCCACAAATCATCTGGATATTCCTTCAAAGGAAATGCTTGAG                         GAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGG
genomic: TGGACGAGCCCACAAATCATCTGGATATTCCTTCAAAGGAAATGCTTGAGgtaacagttt ... tggtttgcagGAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGG
EST: gi|162269948|gb|FC445946.1|FC445946
EST:     TGGACGAGCCCACAAATCATCTGGATATTCCTTCAAAGGAAATGCTTGAG                         GAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGG
genomic: TGGACGAGCCCACAAATCATCTGGATATTCCTTCAAAGGAAATGCTTGAGgtaacagttt ... tggtttgcagGAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGG
EST: gi|162173200|gb|FC349254.1|FC349254
EST:     TGGACGAGCCCACAAATCATCTGGATATTCCTTCAAAGGAAATGCTTGAG                         GAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGG
genomic: TGGACGAGCCCACAAATCATCTGGATATTCCTTCAAAGGAAATGCTTGAGgtaacagttt ... tggtttgcagGAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGG
EST: gi|18368890|gb|BJ200975.1|BJ200975
EST:     TGGACGAGCCCACAAATCATCTGGATATTCCTTCAAAGGAAATGCTTGAG                         GAAGCATTGAGGGAGTATAAG
genomic: TGGACGAGCCCACAAATCATCTGGATATTCCTTCAAAGGAAATGCTTGAGgtaacagttt ... tggtttgcagGAAGCATTGAGGGAGTATAAG
EST: gi|162197640|gb|FC374474.1|FC374474
EST:     AGGAAATGCTTGAG                         GAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGG
genomic: AGGAAATGCTTGAGgtaacagttt ... tggtttgcagGAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGG
EST: gi|162194077|gb|FC370252.1|FC370252
EST:     TGGACGAGCCCACAAATCATCTGGATATTCCTTCAAAGGAAATGCTTGAG                         GAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGG
genomic: TGGACGAGCCCACAAATCATCTGGATATTCCTTCAAAGGAAATGCTTGAGgtaacagttt ... tggtttgcagGAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGG
EST: gi|162150677|gb|FC327573.1|FC327573
EST:     AGCCCACAAATCATCTGGATATTCCTTCAAAGGAAATGCTTGAG                         GAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGG
genomic: AGCCCACAAATCATCTGGATATTCCTTCAAAGGAAATGCTTGAGgtaacagttt ... tggtttgcagGAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGG
EST: gi|162246026|gb|FC421889.1|FC421889
EST:     AAATGCTTGAG                         GAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGG
genomic: AAATGCTTGAGgtaacagttt ... tggtttgcagGAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGG
EST: gi|162164376|gb|FC341021.1|FC341021
EST:     TGGACGAGCCCACAAATCATCTGGATATTCCTTCAAAGGAAATGCTTGAG                         GAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGG
genomic: TGGACGAGCCCACAAATCATCTGGATATTCCTTCAAAGGAAATGCTTGAGgtaacagttt ... tggtttgcagGAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGG
EST: gi|162192497|gb|FC369127.1|FC369127
EST:     TGGACGAGCCCACAAATCATCTGGATATTCCTTCAAAGGAAATGCTTGAG                         GAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGG
genomic: TGGACGAGCCCACAAATCATCTGGATATTCCTTCAAAGGAAATGCTTGAGgtaacagttt ... tggtttgcagGAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGG
EST: gi|162169804|gb|FC346160.1|FC346160
EST:     TGGACGAGCCCACAAATCATCTGGATATTCCTTCAAAGGAAATGCTTGAG                         GAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGG
genomic: TGGACGAGCCCACAAATCATCTGGATATTCCTTCAAAGGAAATGCTTGAGgtaacagttt ... tggtttgcagGAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGG
EST: gi|162174172|gb|FC350375.1|FC350375
EST:     TGGACGAGCCCACAAATCATCTGGATATTCCTTCAAAGGAAATGCTTGAG                         GAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGG
genomic: TGGACGAGCCCACAAATCATCTGGATATTCCTTCAAAGGAAATGCTTGAGgtaacagttt ... tggtttgcagGAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGG
EST: gi|162152733|gb|FC329739.1|FC329739
EST:     TGGACGAGCCCACAAATCATCTGGATATTCCTTCAAAGGAAATGCTTGAG                         GAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGG
genomic: TGGACGAGCCCACAAATCATCTGGATATTCCTTCAAAGGAAATGCTTGAGgtaacagttt ... tggtttgcagGAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGG
EST: gi|162194863|gb|FC370527.1|FC370527
EST:     TGGACGAGCCCACAAATCATCTGGATATTCCTTCAAAGGAAATGCTTGAG                         GAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGG
genomic: TGGACGAGCCCACAAATCATCTGGATATTCCTTCAAAGGAAATGCTTGAGgtaacagttt ... tggtttgcagGAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGG
EST: gi|162165977|gb|FC340976.1|FC340976
EST:     TGGACGAGCCCACAAATCATCTGGATATTCCTTCAAAGGAAATGCTTGAG                         GAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGG
genomic: TGGACGAGCCCACAAATCATCTGGATATTCCTTCAAAGGAAATGCTTGAGgtaacagttt ... tggtttgcagGAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGG
EST: gi|162150678|gb|FC327574.1|FC327574
EST:     TGGACGAGCCCACAAATCATCTGGATATTCCTTCAAAGGAAATGCTTGAG                         GAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGG
genomic: TGGACGAGCCCACAAATCATCTGGATATTCCTTCAAAGGAAATGCTTGAGgtaacagttt ... tggtttgcagGAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGG

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: 34 (upstream exon), 33 (downstream exon)
Score: 75

GCGGCTATCGTTGTGCAAGTTCATGGTCACACCTTCAACTGTCCTAGTACTGGACGAGCCCACAAATCATCTGGATATTCCTTCAAAGGAAATGCTTGAGgtaacagttt ... tggtttgcagGAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGGTACTTCTTGAGGCAGATAGTGAACCGTGTGGTGGAAGTGACCGATAACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattaccagtaggtactagcatgttaagctaacccagaagcttgtggtttgcagGAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGGTACTTCTTGAGGCAGATAGTGAACCGTGTGGTGGAAGTGACCGATAACA
                           agctaac  putative branch site (score: 75)
                     atgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacagtttttgatcctctctcttcctctgtatttttccttagccggatgtagatacagcacttcaattttcagtcaatccttctatagtttttcattttgcctctctcactcttattctccaattttactattttcttcaagttgattaccagtaggtactagcatgttaagctaacccagaagcttgtggtttgcagGAAGCATTGAGGGAGTATAAGGGTACAGTCATCGCAGTTTCTCACGACCGGTACTTCTTGAGGCAGATAGTGAACCGTGTGGTGGAAGTGACCGATAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG