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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatttcaggctgtgaagtttccagcgtcaagctttcttctgcagatagtatgtttctcacgtttacaaccatatttaagtacttgtatttgtgttgcagAACAAGGCACCATCAAAAGCATCTCTCATGTTTTCTGGAACTCAGGAGAAGTGCATTGCTTGCAGCAAAACTGTGTATCCCATTGAAAAG

Basic information

species Physcomitrella patens
transcript PP1S80_3V6.1
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|162264935|gb|FC441438.1|FC441438
EST:     GAAGGATTGAAAAAGGCTGAGAAAGGAGAG                         AACAAGGCACCATCAAAAGCATCTCTCATGTTTTCTGGAACTCAGGAGAAG
genomic: GAAGGATTGAAAAAGGCTGAGAAAGGAGAGgtacgtttga ... tgtgttgcagAACAAGGCACCATCAAAAGCATCTCTCATGTTTTCTGGAACTCAGGAGAAG
EST: gi|208387435|gb|DC949220.1|DC949220
EST:     GATTGAAAAAGGCTGAGAAAGGAGAG                         AACAAGGCACCATCAAAAGCATCTCTCATGTTTTCTGGAACTCAGGAGAAG
genomic: GATTGAAAAAGGCTGAGAAAGGAGAGgtacgtttga ... tgtgttgcagAACAAGGCACCATCAAAAGCATCTCTCATGTTTTCTGGAACTCAGGAGAAG
EST: gi|208365845|gb|DC955448.1|DC955448
EST:     AAAAGGCTGAGAAAGGAGAG                         ANCANGNC-CCATCAAAAGCATCTCTCATGTTTTCTGGAACTCAGGAGAAG
genomic: AAAAGGCTGAGAAAGGAGAGgtacgtttga ... tgtgttgcagAACAAGGCACCATCAAAAGCATCTCTCATGTTTTCTGGAACTCAGGAGAAG
EST: gi|67695765|gb|BJ955998.1|BJ955998
EST:     GATTGAAAAAGGCTGAGAAAGGAGAG                         AACAAGGCACCATCAAAAGCATCTCTCATGTTTTCTGGAACTCAGGAGAAG
genomic: GATTGAAAAAGGCTGAGAAAGGAGAGgtacgtttga ... tgtgttgcagAACAAGGCACCATCAAAAGCATCTCTCATGTTTTCTGGAACTCAGGAGAAG
EST: gi|162264936|gb|FC441439.1|FC441439
EST:     GATTGAAAAAGGCTGAGAAAGGAGAG                         AACAAGGCACCATCAAAAGCATCTCTCATGTTTTCTGGAACTCAGGAGAAG
genomic: GATTGAAAAAGGCTGAGAAAGGAGAGgtacgtttga ... tgtgttgcagAACAAGGCACCATCAAAAGCATCTCTCATGTTTTCTGGAACTCAGGAGAAG
EST: gi|162201813|gb|FC377747.1|FC377747
EST:     GATTGAAAAAGGCTGAGAAAGGAGAG                         AACAAGGCACCATCAAAAGCATCTCTCATGTTTTCTGGAACTCAGGAGAAG
genomic: GATTGAAAAAGGCTGAGAAAGGAGAGgtacgtttga ... tgtgttgcagAACAAGGCACCATCAAAAGCATCTCTCATGTTTTCTGGAACTCAGGAGAAG
EST: gi|162155897|gb|FC332446.1|FC332446
EST:     GATTGAAAAAGGCTGAGAAAGGAGAG                         AACAAGGCACCATCAAAAGCATCTCTCATGTTTTCTGGAACTCAGGAGAAG
genomic: GATTGAAAAAGGCTGAGAAAGGAGAGgtacgtttga ... tgtgttgcagAACAAGGCACCATCAAAAGCATCTCTCATGTTTTCTGGAACTCAGGAGAAG
EST: gi|208379342|gb|DC922928.1|DC922928
EST:     AAGGCTGAGAAAGGAGAG                         AACAAGGCACCATCAAAAGCATCTCTCATGTTTTCTGGAACTCAGGAGAAG
genomic: AAGGCTGAGAAAGGAGAGgtacgtttga ... tgtgttgcagAACAAGGCACCATCAAAAGCATCTCTCATGTTTTCTGGAACTCAGGAGAAG
EST: gi|162259609|gb|FC435536.1|FC435536
EST:     GATTGAAAAAGGCTGAGAAAGGAGAG                         ANCAAGGCACCATCAAAAGCATCTCTCATG-TTTCTGGAACTCAGGAGAAG
genomic: GATTGAAAAAGGCTGAGAAAGGAGAGgtacgtttga ... tgtgttgcagAACAAGGCACCATCAAAAGCATCTCTCATGTTTTCTGGAACTCAGGAGAAG
EST: gi|67697433|gb|BJ957666.1|BJ957666
EST:     TGAAGGATTGAAAAANGGCTGAGAAAGGAGAG                         AACAAGGCACCATCAAAAGCATCTCTCATGTTTTCTGGAACTCAGGAGAAG
genomic: TGAAGGATTGAAAAA-GGCTGAGAAAGGAGAGgtacgtttga ... tgtgttgcagAACAAGGCACCATCAAAAGCATCTCTCATGTTTTCTGGAACTCAGGAGAAG
EST: gi|162155898|gb|FC332447.1|FC332447
EST:     GATTGAAAAAGGCTGAGAAAGGAGAG                         AACAAGGCACCATCAAAAGCATCTCTCATGTTTTCTGGAACTCAGGAGAAG
genomic: GATTGAAAAAGGCTGAGAAAGGAGAGgtacgtttga ... tgtgttgcagAACAAGGCACCATCAAAAGCATCTCTCATGTTTTCTGGAACTCAGGAGAAG
EST: gi|67698662|gb|BJ958895.1|BJ958895
EST:     GATTGAAAAAGGCTGAGAAAGGAGAG                         AACAAGGCACCATCAAAAGCATCTCTCATGTTTTCTGGAACTCAGGAGAAG
genomic: GATTGAAAAAGGCTGAGAAAGGAGAGgtacgtttga ... tgtgttgcagAACAAGGCACCATCAAAAGCATCTCTCATGTTTTCTGGAACTCAGGAGAAG
EST: gi|162150285|gb|FC326370.1|FC326370
EST:     GATTGAAAAAGGCTGAGAAAGGAGAG                         AACAAGGCACCATCAAAAGCATCTCTCATGTTTTCTGGAACTCAGGAGAAG
genomic: GATTGAAAAAGGCTGAGAAAGGAGAGgtacgtttga ... tgtgttgcagAACAAGGCACCATCAAAAGCATCTCTCATGTTTTCTGGAACTCAGGAGAAG
EST: gi|162243581|gb|FC419518.1|FC419518
EST:     GATTGAAAAAGGCTGAGAAAGGAGAG                         AACAAGGCACCATCAAAAGCATCTCTCATGTTTTCTGGAACTCAGGAGAAG
genomic: GATTGAAAAAGGCTGAGAAAGGAGAGgtacgtttga ... tgtgttgcagAACAAGGCACCATCAAAAGCATCTCTCATGTTTTCTGGAACTCAGGAGAAG
EST: gi|162211924|gb|FC387796.1|FC387796
EST:     GATTGAAAAAGGCTGAGAAAGGAGAG                         AACAAGGCACCATCAAAAGCATCTCTCATGTTTTCTGGAACTCAGGAGAAG
genomic: GATTGAAAAAGGCTGAGAAAGGAGAGgtacgtttga ... tgtgttgcagAACAAGGCACCATCAAAAGCATCTCTCATGTTTTCTGGAACTCAGGAGAAG
EST: gi|162201814|gb|FC377748.1|FC377748
EST:     GATTGAAAAAGGCTGAGAAAGGAGAG                         AACAAGGCACCATCAAAAGCATCTCTCATGTTTTCTGGAACTCAGGAGAAG
genomic: GATTGAAAAAGGCTGAGAAAGGAGAGgtacgtttga ... tgtgttgcagAACAAGGCACCATCAAAAGCATCTCTCATGTTTTCTGGAACTCAGGAGAAG

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: 26 (upstream exon), 29 (downstream exon)
Score: 3

GATTGAAAAAGGCTGAGAAAGGAGAGgtacgtttga ... tgtgttgcagAACAAGGCACCATCAAAAGCATCTCTCATGTTTTCTGGAACTCAGGAGAAGTGCATTGCTTGCAGCAAAACTGTGTATCCCATTGAAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagtatgtttctcacgtttacaaccatatttaagtacttgtatttgtgttgcagAACAAGGCACCATCAAAAGCATCTCTCATGTTTTCTGGAACTCAGGAGAAGTGCATTGCTTGCAGCAAAACTGTGTATCCCATTGAAAAG
         ttctcac  putative branch site (score: 3)
                          atatttaagtactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caatttcaggctgtgaagtttccagcgtcaagctttcttctgcagatagtatgtttctcacgtttacaaccatatttaagtacttgtatttgtgttgcagAACAAGGCACCATCAAAAGCATCTCTCATGTTTTCTGGAACTCAGGAGAAGTGCATTGCTTGCAGCAAAACTGTGTATCCCATTGAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - -ttctgca