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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCAAGAACCTCGAGCTCTTGGTGACTGCTGGTGTGGGATCCGACCACATTGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAGgtatgtgcttggattcccataaaacctcaaggaatagcataaagcaaaaccaaaagattgcgtatcacggcgggactatttgtaatgcgattgggtccttgatatataaatttcag

Basic information

species Physcomitrella patens
transcript PP1S106_16V6.1
intron # 4
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|208384946|gb|DC903453.1|DC903453
EST:     TGACCTTCATGCTGCTGCTGAAANGG-CCNTACGGTGTCAGANGTCACAG                         GAAGCAACGTGACGTCAGTT
genomic: TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAGgtatgtgctt ... taaatttcagGAAGCAACGTGACGTCAGTT
EST: gi|162272414|gb|FC449053.1|FC449053
EST:     TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAG                         GAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGTTC
genomic: TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAGgtatgtgctt ... taaatttcagGAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGTTC
EST: gi|208385885|gb|DC956723.1|DC956723
EST:     TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAG                         GAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGTTC
genomic: TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAGgtatgtgctt ... taaatttcagGAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGTTC
EST: gi|100388263|gb|BY951865.1|BY951865
EST:     GACCTTCATGCTGCTGCTGAAAAGG-CCTTNACGGTGTCAGAGGTCACAG                         GGAGCAACGTGACGTCAGTTGC
genomic: GACCTTCATGCTGCTGCTGAAAAGGGCCTT-ACGGTGTCAGAGGTCACAGgtatgtgctt ... taaatttcagGAAGCAACGTGACGTCAGTTGC
EST: gi|100398640|gb|BY990442.1|BY990442
EST:     TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAG                         GAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGTTC
genomic: TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAGgtatgtgctt ... taaatttcagGAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGTTC
EST: gi|100385283|gb|BY950875.1|BY950875
EST:     TGACCTTCATGCTGCTGCTGAAAAGGGGCTTACGGTGTCAGAGGTCACAG                         GAAGCAACGTGACGTCAG
genomic: TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAGgtatgtgctt ... taaatttcagGAAGCAACGTGACGTCAG
EST: gi|162269932|gb|FC445423.1|FC445423
EST:     TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAG                         GAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGTTC
genomic: TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAGgtatgtgctt ... taaatttcagGAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGTTC
EST: gi|100358870|gb|BY946730.1|BY946730
EST:     TGACCTTCATGCTGCTGCTGNAAAGGGCCTTACGGTGTCAGAGGTCACAG                         GAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACT
genomic: TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAGgtatgtgctt ... taaatttcagGAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACT
EST: gi|208361729|gb|DC934969.1|DC934969
EST:     TGACCTTCATGCTGCTGCTGAAAAGG-CCTTACGGTGTCAGAGGTCACAG                         GAAGCANCGTGACGTCAGT
genomic: TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAGgtatgtgctt ... taaatttcagGAAGCAACGTGACGTCAGT
EST: gi|100402552|gb|BY954892.1|BY954892
EST:     TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAG                         GAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACGGGTTC
genomic: TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAGgtatgtgctt ... taaatttcagGAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGTTC
EST: gi|162264750|gb|FC440317.1|FC440317
EST:     TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAG                         GAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGTTC
genomic: TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAGgtatgtgctt ... taaatttcagGAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGTTC
EST: gi|208361815|gb|DC939037.1|DC939037
EST:     TGACCTTCATGCTGCTGCTGAAAAGGGCCTNACGGTGTCAGAAGTCACAG                         GAAGCAACGTGACGTCAGTT
genomic: TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAGgtatgtgctt ... taaatttcagGAAGCAACGTGACGTCAGTT
EST: gi|100398916|gb|BY990580.1|BY990580
EST:     TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAG                         GAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGTTC
genomic: TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAGgtatgtgctt ... taaatttcagGAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGTTC
EST: gi|208363654|gb|DC935349.1|DC935349
EST:     TGACCTTCATGCTGCTGCTGAAA-GGGCCTTACGGTGTCAGANGTCACAG                         GAAGCANCGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGTTC
genomic: TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAGgtatgtgctt ... taaatttcagGAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGTTC
EST: gi|67574343|gb|BJ947167.1|BJ947167
EST:     TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAG                         GAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGTT
genomic: TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAGgtatgtgctt ... taaatttcagGAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGTT
EST: gi|162266592|gb|FC441978.1|FC441978
EST:     TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAG                         GAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGTTC
genomic: TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAGgtatgtgctt ... taaatttcagGAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGTTC
EST: gi|208386186|gb|DC949097.1|DC949097
EST:     TCAGA-GTCACA-                         GAAGCAACGTGACNTCAGTTGCNGAGGATGAAGTGCTGCGTATANTGGTTT
genomic: TCAGAGGTCACAGgtatgtgctt ... taaatttcagGAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGTTC
EST: gi|162274536|gb|FC450979.1|FC450979
EST:     TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAG                         GAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGTTC
genomic: TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAGgtatgtgctt ... taaatttcagGAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGTTC
EST: gi|22491841|gb|BU051764.1|BU051764
EST:     TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAG                         GAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGTTC
genomic: TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAGgtatgtgctt ... taaatttcagGAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGTTC
EST: gi|162262253|gb|FC437164.1|FC437164
EST:     TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAG                         GAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGTTC
genomic: TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAGgtatgtgctt ... taaatttcagGAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGTTC
EST: gi|100388495|gb|BY952097.1|BY952097
EST:     TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGGGTCAGAAGTCACAG                         GAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCG
genomic: TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAGgtatgtgctt ... taaatttcagGAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCG
EST: gi|100446294|gb|CJ970593.1|CJ970593
EST:     TGACCTTCATGCTGCTGCTGAAA-GGGCCTTACGGTGTCAGANGTCACAG                         GAAGCANCGTGACGTCAGTTGCGGANGATGAAGTGCTGCGTATAC
genomic: TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAGgtatgtgctt ... taaatttcagGAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATAC
EST: gi|100445835|gb|CJ970134.1|CJ970134
EST:     TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGANGTCACAG                         GAAGCANCGTGACGTCAGTTGCGAAGGATGAAGTGCTGCGTA
genomic: TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAGgtatgtgctt ... taaatttcagGAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTA
EST: gi|100361912|gb|BY947689.1|BY947689
EST:     TGACCTTCATGCTGCTGCTGANNAGGGC-TTACGGTGTCAGAAGTCACAG                         GAAGCAACGTGACGTCAGTTGCGGAAGAATGA-GTGCTGCGTATACTGGTT
genomic: TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAGgtatgtgctt ... taaatttcagGAAGCAACGTGACGTCAGTTGCGGAGGA-TGAAGTGCTGCGTATACTGGTT
EST: gi|208384825|gb|DC907438.1|DC907438
EST:     TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGANGTCACAG                         GAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGT
genomic: TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAGgtatgtgctt ... taaatttcagGAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGT
EST: gi|100397747|gb|BY990380.1|BY990380
EST:     TGACCTTCATGCTGCTGCTGNAAAGGGCCTTACGGTGTCAGAGGTCACAG                         GAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGTTC
genomic: TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAGgtatgtgctt ... taaatttcagGAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGTTC
EST: gi|100364728|gb|BY947878.1|BY947878
EST:     TGAC-TTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAG                         GAAGCAACGTGACGTCAGTTTGCG-AGGATGAAGTGCTGCGTATACTGGTT
genomic: -GACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAGgtatgtgctt ... taaatttcagGAAGCAACGTGACGTCAGTT-GCGGAGGATGAAGTGCTGCGTATACTGGTT
EST: gi|100401401|gb|BY990984.1|BY990984
EST:     TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAG                         GAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGTTC
genomic: TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAGgtatgtgctt ... taaatttcagGAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGTTC
EST: gi|100362785|gb|BY947527.1|BY947527
EST:     GACCTTCATGCTGCTGCTGAAAAGGGCCCTTACG-TGTCAGAGGTCACAG                         GAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGTTC
genomic: GACCTTCATGCTGCTGCTGAAAAGGGCC-TTACGGTGTCAGAGGTCACAGgtatgtgctt ... taaatttcagGAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGTTC
EST: gi|162272578|gb|FC448542.1|FC448542
EST:     TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAG                         GAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGTTC
genomic: TGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAGgtatgtgctt ... taaatttcagGAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGTTC

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: 29 (upstream exon), 33 (downstream exon)
Score: 24

GCCAAGAACCTCGAGCTCTTGGTGACTGCTGGTGTGGGATCCGACCACATTGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAGgtatgtgctt ... taaatttcagGAAGCAACGTGACGTCAGTTGCGGAGGATGAAGTGCTGCGTATACTGGTTCTGGTCCGAAACTTTGCACCAGGATGGAAGCAGGTCTCCGAAGGTGGTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCAAGAACCTCGAGCTCTTGGTGACTGCTGGTGTGGGATCCGACCACATTGACCTTCATGCTGCTGCTGAAAAGGGCCTTACGGTGTCAGAGGTCACAGgtatgtgcttggattcccataaaacctcaaggaatagcataaagcaaaaccaaaagattgcgtatcacggcgggactatttgtaatgcgattgggtccttgatatataaatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT