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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGTGACTGACATACTTCTGGCCGCTGGAGTAGCGAAGGAAAAAATTCTTCTAAATTTTTGAGGAGATTTTCGTTCAGTGgtaaggcaatcacaaacaaaaaaacatatcacttttttaaagagaagaagttgtctatttcaatttatgcgctcatgatttaagccccaagtttttagtt...

Basic information

species Physcomitrella patens
transcript PP1S4_215V6.1
intron # 6
splice site 5'
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|22491814|gb|BU051737.1|BU051737
EST:     TAGCGAAGGAAAAAATTCTTCTAAATTTTTGAGGAGATTTTCGTTCAGTG                         CAGATTTGAAGATGAAAACACGAAGCTCTCCAGGATGTCTTCGAAATATTG
genomic: TAGCGAAGGAAAAAATTCTTCTAAATTTTTGAGGAGATTTTCGTTCAGTGgtaaggcaat ... aaaatgttagCAGATTTGAAGATGAAAACACGAAGCTCTCCAGGATGTCTTCGAAATATTG
EST: gi|162264332|gb|FC440498.1|FC440498
EST:     TAGCGAAGGAAAAAATTCTTCTAAATTTTTGAGGAGATTTTCGTTCAGTG                         -A--TTTGAAGATGAAAACACGAAGCTCTCCAGGATGTCTTCGAAATATTG
genomic: TAGCGAAGGAAAAAATTCTTCTAAATTTTTGAGGAGATTTTCGTTCAGTGgtaaggcaat ... aaaatgttagCAGATTTGAAGATGAAAACACGAAGCTCTCCAGGATGTCTTCGAAATATTG
EST: gi|18333863|gb|BJ165879.1|BJ165879
EST:     TAGCGAAGGAAAAAATTCTTCTAAATTTTTGAGGAGATTTTCGTTCAGTG                         -A--TTTGAAGATGAAAACACGAAGCTCTCCAGGATGTCTTCGAAATATTG
genomic: TAGCGAAGGAAAAAATTCTTCTAAATTTTTGAGGAGATTTTCGTTCAGTGgtaaggcaat ... aaaatgttagCAGATTTGAAGATGAAAACACGAAGCTCTCCAGGATGTCTTCGAAATATTG
EST: gi|18332708|gb|BJ164721.1|BJ164721
EST:     TAGCGAAGGAAAAAATTCTTCTAAATTTTTGAGGAGATTTTCGTTCAGTG                         -A--TTTGAAGATGAAAACACGAAGCTCTCCAGGATGTCTTCGAAATATTG
genomic: TAGCGAAGGAAAAAATTCTTCTAAATTTTTGAGGAGATTTTCGTTCAGTGgtaaggcaat ... aaaatgttagCAGATTTGAAGATGAAAACACGAAGCTCTCCAGGATGTCTTCGAAATATTG
EST: gi|19789046|gb|BQ041060.1|BQ041060
EST:     TAGCGAAGGAAAAAATTCTTCTAAATTTTTGAGGAGATTTTCGTTCAGT-                         --GATTTGAAGATGAAAACACGAAGCTCTCCAGGATGTCTTCGAAATATTG
genomic: TAGCGAAGGAAAAAATTCTTCTAAATTTTTGAGGAGATTTTCGTTCAGTGgtaaggcaat ... aaaatgttagCAGATTTGAAGATGAAAACACGAAGCTCTCCAGGATGTCTTCGAAATATTG
EST: gi|162245009|gb|FC424967.1|FC424967
EST:     TAGCGAAGGAAAAAATTCTTCTAAATTTTTGAGGAGATTTTCGTTCAGT-                         --GATTTGAAGATGAAAACACGAAGCTCTCCAGGATGTCTTCGAAATATTG
genomic: TAGCGAAGGAAAAAATTCTTCTAAATTTTTGAGGAGATTTTCGTTCAGTGgtaaggcaat ... aaaatgttagCAGATTTGAAGATGAAAACACGAAGCTCTCCAGGATGTCTTCGAAATATTG
EST: gi|208371352|gb|DC944516.1|DC944516
EST:     TAGCGAAGGAAAAAATTCTTCTAAATTTTTGAGGAGATTTTCGTTCAGTG                         -A--TTTGAAGATGAAAACACGAAGCTCTCCAGGATGTCTTCGAAATATTG
genomic: TAGCGAAGGAAAAAATTCTTCTAAATTTTTGAGGAGATTTTCGTTCAGTGgtaaggcaat ... aaaatgttagCAGATTTGAAGATGAAAACACGAAGCTCTCCAGGATGTCTTCGAAATATTG
EST: gi|6102388|gb|AW126858.1|AW126858
EST:     TAGCGAAGGAAAAAATTCTTCTAAATTTTTGAGGAGATTTTCGTTCAGT-                         --GATTTGAAGATGAAAACACGAAGCTCTCCAGGATGTCTTCGAAATATTG
genomic: TAGCGAAGGAAAAAATTCTTCTAAATTTTTGAGGAGATTTTCGTTCAGTGgtaaggcaat ... aaaatgttagCAGATTTGAAGATGAAAACACGAAGCTCTCCAGGATGTCTTCGAAATATTG
EST: gi|162245008|gb|FC424966.1|FC424966
EST:     TAGCGAAGGAAAAAATTCTTCTAAATTTTTGAGGAGATTTTCGTTCAGT-                         --GATTTGAAGATGAAAACACGAAGCTCTCCAGGATGTCTTCGAAATATTG
genomic: TAGCGAAGGAAAAAATTCTTCTAAATTTTTGAGGAGATTTTCGTTCAGTGgtaaggcaat ... aaaatgttagCAGATTTGAAGATGAAAACACGAAGCTCTCCAGGATGTCTTCGAAATATTG
EST: gi|67696462|gb|BJ956695.1|BJ956695
EST:     TAGCGAAGGAAAAAATTCTTCTAAATTTTTGAGGAGATTTTCGTTCAGTG                         -A--TTTGAAGATGAAAACACGAAGCTCTCCAGGATGTCTTCGAAATATTG
genomic: TAGCGAAGGAAAAAATTCTTCTAAATTTTTGAGGAGATTTTCGTTCAGTGgtaaggcaat ... aaaatgttagCAGATTTGAAGATGAAAACACGAAGCTCTCCAGGATGTCTTCGAAATATTG
EST: gi|162238938|gb|FC417702.1|FC417702
EST:     TAGCGAAGGAAAAAATTCTTCTAAATTTTTGAGGAGATTTTCGTTCAGTG                         -A--TTTGAAGATGAAAACACGAAGCTCTCCAGGATGTCTTCGAAATATTG
genomic: TAGCGAAGGAAAAAATTCTTCTAAATTTTTGAGGAGATTTTCGTTCAGTGgtaaggcaat ... aaaatgttagCAGATTTGAAGATGAAAACACGAAGCTCTCCAGGATGTCTTCGAAATATTG
EST: gi|162179827|gb|FC356418.1|FC356418
EST:     TAGCGAAGGAAAAAATTCTTCTAAATTTTTGAGGAGATTTTCGTTCAGTG                         -A--TTTGAAGATGAAAACACGAAGCTCTCCAGGATGTCTTCGAAATATTG
genomic: TAGCGAAGGAAAAAATTCTTCTAAATTTTTGAGGAGATTTTCGTTCAGTGgtaaggcaat ... aaaatgttagCAGATTTGAAGATGAAAACACGAAGCTCTCCAGGATGTCTTCGAAATATTG
EST: gi|162264333|gb|FC440499.1|FC440499
EST:     TAGCGAAGGAAAAAATTCTTCTAAATTTTTGAGGAGATTTTCGTTCAGTG                         -A--TTTGAAGATGAAAACACGAAGCTCTCCAGGATGTCTTCGAAATATTG
genomic: TAGCGAAGGAAAAAATTCTTCTAAATTTTTGAGGAGATTTTCGTTCAGTGgtaaggcaat ... aaaatgttagCAGATTTGAAGATGAAAACACGAAGCTCTCCAGGATGTCTTCGAAATATTG
EST: gi|7584099|gb|AW699997.1|AW699997
EST:     AAATTCTTCTAAATTTTTGAGGAGATTTTCGTTCAGT-                         --GATTTGAAGATGAAAACACGAAGCTCTCCAGGATGTCTTCGAAATATTG
genomic: AAATTCTTCTAAATTTTTGAGGAGATTTTCGTTCAGTGgtaaggcaat ... aaaatgttagCAGATTTGAAGATGAAAACACGAAGCTCTCCAGGATGTCTTCGAAATATTG
EST: gi|162235909|gb|FC411652.1|FC411652
EST:     TAGCGAAGGAAAAAATTCTTCTAAATTTTTGAGGAGATTTTCGTTCAGTG                         -A--TTTGAAGATGAAAACACGAAGCTCTCCAGGATGTCTTCGAAATATTG
genomic: TAGCGAAGGAAAAAATTCTTCTAAATTTTTGAGGAGATTTTCGTTCAGTGgtaaggcaat ... aaaatgttagCAGATTTGAAGATGAAAACACGAAGCTCTCCAGGATGTCTTCGAAATATTG
EST: gi|162199674|gb|FC375913.1|FC375913
EST:     TAGCGAAGGAAAAAATTCTTCTAAATTTTTGAGGAGATTTTCGTTCAGTG                         CAGATTTGAAGATGAAAACACGAAGCTCTCCAGGATGTCTTCGAAATATTG
genomic: TAGCGAAGGAAAAAATTCTTCTAAATTTTTGAGGAGATTTTCGTTCAGTGgtaaggcaat ... aaaatgttagCAGATTTGAAGATGAAAACACGAAGCTCTCCAGGATGTCTTCGAAATATTG

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), 29 (downstream exon)
Score: 19

GATGTGACTGACATACTTCTGGCCGCTGGAGTAGCGAAGGAAAAAATTCTTCTAAATTTTTGAGGAGATTTTCGTTCAGTGgtaaggcaat ... aaaatgttagCAGATTTGAAGATGAAAACACGAAGCTCTCCAGGATGTCTTCGAAATATTGCCTTCCGCTAGTAACCTTGGAGAAATATTCTTGTACTTTTTGCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGTGACTGACATACTTCTGGCCGCTGGAGTAGCGAAGGAAAAAATTCTTCTAAATTTTTGAGGAGATTTTCGTTCAGTGgtaaggcaatcacaaacaaaaaaacatatcacttttttaaagagaagaagttgtctatttcaatttatgcgctcatgatttaagccccaagtttttagtt

- - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaagagaa