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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGACGGCAGTTTCATTGGAAGATAGTGTGAGACGCGTACAGTCAATCGCCGACGCAGCTTATGAAGTCAATCCAGAGATCATTGTACTCTGCCATGGTGgtgagtgttttctttcgcctacccatttattgggaactcatcccacaaatatttactgtgattttcaaaagcaagggcttgatattaatctacttcacgagaagaattctgacataattttttatcctgtatgagacccttatcactgcacaacaaaatgaccatgaataatgttgcag

Basic information

species Physcomitrella patens
transcript PP1S9_334V6.1
intron # 9
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|37844563|gb|BJ602571.1|BJ602571
EST:     CGACGCAGCTTATGAAGTCAATCCAGAGATCATTGTACTCTGCCATGGTG                         GGCCTATATCTGGACCAAAGGAAGCAGAGTATGTATTGCAAAGAACAAAGA
genomic: CGACGCAGCTTATGAAGTCAATCCAGAGATCATTGTACTCTGCCATGGTGgtgagtgttt ... aatgttgcagGGCCTATATCTGGACCAAAGGAAGCAGAGTATGTATTGCAAAGAACAAAGA
EST: gi|162238883|gb|FC415086.1|FC415086
EST:     CGACGCAGCTTATGAAGTCAATCCAGAGATCATTGTACTCTGCCATGGTG                         GGCCTATATCTGGACCAAAGGAAGCAGAGTATGTATTGCAAAGAACAAAGA
genomic: CGACGCAGCTTATGAAGTCAATCCAGAGATCATTGTACTCTGCCATGGTGgtgagtgttt ... aatgttgcagGGCCTATATCTGGACCAAAGGAAGCAGAGTATGTATTGCAAAGAACAAAGA
EST: gi|161979171|gb|EE296309.1|EE296309
EST:     ACTCTGCCATGGTG                         GGCCTATATCTGGACCAAAGGAAGCAGAGTATGTATTGCAAAGAACAAAGA
genomic: ACTCTGCCATGGTGgtgagtgttt ... aatgttgcagGGCCTATATCTGGACCAAAGGAAGCAGAGTATGTATTGCAAAGAACAAAGA
EST: gi|37844514|gb|BJ602522.1|BJ602522
EST:     CGACGCAGCTTATGAAGTCAATCCAGAGATCATTGTACTCTGCCATGGTG                         GGCCTATATCTGGACCAAAGGAAGCAGAGTATGTATTGCAAAGAACAAAGA
genomic: CGACGCAGCTTATGAAGTCAATCCAGAGATCATTGTACTCTGCCATGGTGgtgagtgttt ... aatgttgcagGGCCTATATCTGGACCAAAGGAAGCAGAGTATGTATTGCAAAGAACAAAGA
EST: gi|37842335|gb|BJ600343.1|BJ600343
EST:     CGACGCAGCTTATGAAGTCAATCCAGAGATCATTGTACTCTGCCATGGTG                         GGCCTATATCTGGACCAAAGGAAGCAGAGTATGTATTGCAAAGAACAAAGA
genomic: CGACGCAGCTTATGAAGTCAATCCAGAGATCATTGTACTCTGCCATGGTGgtgagtgttt ... aatgttgcagGGCCTATATCTGGACCAAAGGAAGCAGAGTATGTATTGCAAAGAACAAAGA
EST: gi|162246377|gb|FC421070.1|FC421070
EST:     CGACGCAGCTTATGAAGTCAATCCAGAGATCATTGTACTCTGCCATGGTG                         GGCCTATATCTGGACCAAAGGAAGCAGAGTATGTATTGCAAAGAACAAAGA
genomic: CGACGCAGCTTATGAAGTCAATCCAGAGATCATTGTACTCTGCCATGGTGgtgagtgttt ... aatgttgcagGGCCTATATCTGGACCAAAGGAAGCAGAGTATGTATTGCAAAGAACAAAGA
EST: gi|37838990|gb|BJ596998.1|BJ596998
EST:     CGACGCAGCTTATGAAGTCAATCCAGAGATCATTGTACTCTGCCATGGTG                         GGCCTATATCTGGACCAAAGGAAGCAGAGTATGTATTGCAAAGAACAAAGA
genomic: CGACGCAGCTTATGAAGTCAATCCAGAGATCATTGTACTCTGCCATGGTGgtgagtgttt ... aatgttgcagGGCCTATATCTGGACCAAAGGAAGCAGAGTATGTATTGCAAAGAACAAAGA
EST: gi|37845029|gb|BJ603037.1|BJ603037
EST:     CGACGCAGCTTATGAAGTCAATCCAGAGATCATTGTACTCTGCCATGGTG                         GGCCTATATCTGGACCAAAGGAAGCAGAGTATGTATTGCAAAGAACAAAGA
genomic: CGACGCAGCTTATGAAGTCAATCCAGAGATCATTGTACTCTGCCATGGTGgtgagtgttt ... aatgttgcagGGCCTATATCTGGACCAAAGGAAGCAGAGTATGTATTGCAAAGAACAAAGA
EST: gi|162175714|gb|FC351301.1|FC351301
EST:     CGACGCAGCTTATGAAGTCAATCCAGAGATCATTGTACTCTGCCATGGTG                         GGCCTATATCTGGACCAAAGGAAGCAGAGTATGTATTGCAAAGAACAAAGA
genomic: CGACGCAGCTTATGAAGTCAATCCAGAGATCATTGTACTCTGCCATGGTGgtgagtgttt ... aatgttgcagGGCCTATATCTGGACCAAAGGAAGCAGAGTATGTATTGCAAAGAACAAAGA
EST: gi|37834878|gb|BJ592890.1|BJ592890
EST:     CGACGCAGCTTATGAAGTCAATCCAGAGATCATTGTACTCTGCCATGGTG                         GGCCTATATCTGGACCAAAGGAAGCAGAGTATGTATTGCAAAGAACAAAGA
genomic: CGACGCAGCTTATGAAGTCAATCCAGAGATCATTGTACTCTGCCATGGTGgtgagtgttt ... aatgttgcagGGCCTATATCTGGACCAAAGGAAGCAGAGTATGTATTGCAAAGAACAAAGA
EST: gi|162226926|gb|FC403114.1|FC403114
EST:     CGACGCAGCTTATGAAGTCAATCCAGAGATCATTGTACTCTGCCATGGTG                         GGCCTATATCTGGACCAAAGGAAGCAGAGTATGTATTGCAAAGAACAAAGA
genomic: CGACGCAGCTTATGAAGTCAATCCAGAGATCATTGTACTCTGCCATGGTGgtgagtgttt ... aatgttgcagGGCCTATATCTGGACCAAAGGAAGCAGAGTATGTATTGCAAAGAACAAAGA
EST: gi|162246378|gb|FC421071.1|FC421071
EST:     CGACGCAGCTTATGAAGTCAATCCAGAGATCATTGTACTCTGCCATGGTG                         GGCCTATATCTGGACCAAAGGAAGCAGAGTATGTATTGCAAAGAACAAAGA
genomic: CGACGCAGCTTATGAAGTCAATCCAGAGATCATTGTACTCTGCCATGGTGgtgagtgttt ... aatgttgcagGGCCTATATCTGGACCAAAGGAAGCAGAGTATGTATTGCAAAGAACAAAGA
EST: gi|18334199|gb|BJ166215.1|BJ166215
EST:     CGACGCAGCTTATGAAGTCAATCCAGAGATCATTGTACTCTGCCATGGTG                         GGCCTATATCTGGACCAAAGGAAGCAGAGTATGTATTGCAAAGAACAAAGA
genomic: CGACGCAGCTTATGAAGTCAATCCAGAGATCATTGTACTCTGCCATGGTGgtgagtgttt ... aatgttgcagGGCCTATATCTGGACCAAAGGAAGCAGAGTATGTATTGCAAAGAACAAAGA
EST: gi|37839750|gb|BJ597758.1|BJ597758
EST:     CGACGCAGCTTATGAAGTCAATCCAGAGATCATTGTACTCTGCCATGGTG                         GGCCTATATCTGGACCAAAGGAAGCAGAGTATGTATTGCAAAGAACAAAGA
genomic: CGACGCAGCTTATGAAGTCAATCCAGAGATCATTGTACTCTGCCATGGTGgtgagtgttt ... aatgttgcagGGCCTATATCTGGACCAAAGGAAGCAGAGTATGTATTGCAAAGAACAAAGA
EST: gi|37850404|gb|BJ608412.1|BJ608412
EST:     CGACGCAGCTTATGAAGTCAATCCAGAGATCATTGTACTCTGCCATGGTG                         GGCCTATATCTGGACCAAAGGAAGCAGAGTATGTATTGCAAAGAACAAAGA
genomic: CGACGCAGCTTATGAAGTCAATCCAGAGATCATTGTACTCTGCCATGGTGgtgagtgttt ... aatgttgcagGGCCTATATCTGGACCAAAGGAAGCAGAGTATGTATTGCAAAGAACAAAGA
EST: gi|162184283|gb|FC360511.1|FC360511
EST:     CGACGCAGCTTATGAAGTCAATCCAGAGATCATTGTACTCTGCCATGGTG                         GGCCTATATCTGGACCAAAGGAAGCAGAGTATGTATTGCAAAGAACAAAGA
genomic: CGACGCAGCTTATGAAGTCAATCCAGAGATCATTGTACTCTGCCATGGTGgtgagtgttt ... aatgttgcagGGCCTATATCTGGACCAAAGGAAGCAGAGTATGTATTGCAAAGAACAAAGA

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), 34 (downstream exon)
Score: 13

AAGACGGCAGTTTCATTGGAAGATAGTGTGAGACGCGTACAGTCAATCGCCGACGCAGCTTATGAAGTCAATCCAGAGATCATTGTACTCTGCCATGGTGgtgagtgttt ... aatgttgcagGGCCTATATCTGGACCAAAGGAAGCAGAGTATGTATTGCAAAGAACAAAGAATGTTCATGGGTTTTATGGAGCATCAAGCATGGAGCGTTTGCCAGTTGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGACGGCAGTTTCATTGGAAGATAGTGTGAGACGCGTACAGTCAATCGCCGACGCAGCTTATGAAGTCAATCCAGAGATCATTGTACTCTGCCATGGTGgtgagtgttttctttcgcctacccatttattgggaactcatcccacaaatatttactgtgattttcaaaagcaagggcttgatattaatctacttcacgagaagaattctgacataattttttatcctgtatgagacccttatcactgcacaacaaaatgaccatgaataatgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA