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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGAACAACCAGGCCGTCGAAAGCCCCAGTGTACATTGCAAGGTTTCATTCGCAAGATTGAAGACATTAAGCTGAAAGAGgtaagttggcttatattgtatgcatacattgacatgttcgggaatcgaattcaagtctacttttatagtcatagtttgagttattgcatgtattggattt...

Basic information

species Physcomitrella patens
transcript PP1S207_101V6.1
intron # 2
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|162164254|gb|FC342069.1|FC342069
EST:     GTACATTGCAAGGTTTCATTCGCAAGATTGAAGACATTAAGCTGAAAGAG                         AGGCTTGAAATTGCTTGGGAGAGACGGTTTGCCTCAGAACAACATACCGCG
genomic: GTACATTGCAAGGTTTCATTCGCAAGATTGAAGACATTAAGCTGAAAGAGgtaagttggc ... tgtactgtagAGGCTTGAAATTGCTTGGGAGAGACGGTTTGCCTCAGAACAACATACCGCG
EST: gi|162164253|gb|FC342068.1|FC342068
EST:     GTACATTGCAAGGTTTCATTCGCAAGATTGAAGACATTAAGCTGAAAGAG                         AGGCTTGAAATTGCTTGGGAGAGACGGTTTGCCTCAGAACAACATACCGCG
genomic: GTACATTGCAAGGTTTCATTCGCAAGATTGAAGACATTAAGCTGAAAGAGgtaagttggc ... tgtactgtagAGGCTTGAAATTGCTTGGGAGAGACGGTTTGCCTCAGAACAACATACCGCG
EST: gi|37827260|gb|BJ585272.1|BJ585272
EST:     GTACATTGCAAGGTTTCATTCGCAAGATTGAAGACATTAAGCTGAAAGAG                         AGGCTTGAAATTGCTTGGGAGAGACGGTTTGCCTCAGAACAACATACCGCG
genomic: GTACATTGCAAGGTTTCATTCGCAAGATTGAAGACATTAAGCTGAAAGAGgtaagttggc ... tgtactgtagAGGCTTGAAATTGCTTGGGAGAGACGGTTTGCCTCAGAACAACATACCGCG
EST: gi|162157800|gb|FC334071.1|FC334071
EST:     GTACATTGCAAGGTTTCATTCGCAAGATTGAAGACATTAAGCTGAAAGAG                         AGGCTTGAAATTGCTTGGGAGAGACGGTTTGCCTCAGAACAACATACCGCG
genomic: GTACATTGCAAGGTTTCATTCGCAAGATTGAAGACATTAAGCTGAAAGAGgtaagttggc ... tgtactgtagAGGCTTGAAATTGCTTGGGAGAGACGGTTTGCCTCAGAACAACATACCGCG
EST: gi|162167944|gb|FC344882.1|FC344882
EST:     GTACATTGCAAGGTTTCATTCGCAAGATTGAAGACATTAAGCTGAAAGAG                         AGGCTTGAAATTGCTTGGGAGAGACGGTTTGCCTCAGAACAACATACCGCG
genomic: GTACATTGCAAGGTTTCATTCGCAAGATTGAAGACATTAAGCTGAAAGAGgtaagttggc ... tgtactgtagAGGCTTGAAATTGCTTGGGAGAGACGGTTTGCCTCAGAACAACATACCGCG
EST: gi|37835677|gb|BJ593689.1|BJ593689
EST:     GTACATTGCAAGGTTTCATTCGCAAGATTGAAGACATTAAGCTGAAAGAG                         AGGCTTGAAATTGCTTGGGAGAGACGGTTTGCCTCAGAACAACATACCGCG
genomic: GTACATTGCAAGGTTTCATTCGCAAGATTGAAGACATTAAGCTGAAAGAGgtaagttggc ... tgtactgtagAGGCTTGAAATTGCTTGGGAGAGACGGTTTGCCTCAGAACAACATACCGCG
EST: gi|67695975|gb|BJ956208.1|BJ956208
EST:     GTACATTGCAAGGTTTCATTCGCAAGATTGAAGACATTAAGCTGAAAGAG                         AGGCTTGAAATTGCTTGGGAGAGACGGTTTGCCTCAGAACAACATACCGCG
genomic: GTACATTGCAAGGTTTCATTCGCAAGATTGAAGACATTAAGCTGAAAGAGgtaagttggc ... tgtactgtagAGGCTTGAAATTGCTTGGGAGAGACGGTTTGCCTCAGAACAACATACCGCG
EST: gi|162226413|gb|FC402406.1|FC402406
EST:     GTACATTGCAAGGTTTCATTCGCAAGATTGAAGACATTAAGCTGAAAGAG                         AGGCTTGAAATTGCTTGGGAGAGACGGTTTGCCTCAGAACAACATACCGCG
genomic: GTACATTGCAAGGTTTCATTCGCAAGATTGAAGACATTAAGCTGAAAGAGgtaagttggc ... tgtactgtagAGGCTTGAAATTGCTTGGGAGAGACGGTTTGCCTCAGAACAACATACCGCG
EST: gi|208396881|gb|DC924381.1|DC924381
EST:     GTACATTGCAAGGTTTCATTCGCAAGATTGAAGACATTAAGCTGAAAGAG                         AGGCTTGAAATTGCTTGGGAGAGACGGTTTGCCTCAGAACAACATACCGCG
genomic: GTACATTGCAAGGTTTCATTCGCAAGATTGAAGACATTAAGCTGAAAGAGgtaagttggc ... tgtactgtagAGGCTTGAAATTGCTTGGGAGAGACGGTTTGCCTCAGAACAACATACCGCG
EST: gi|18335447|gb|BJ167467.1|BJ167467
EST:     GTACATTGCAAGGTTTCATTCGCAAGATTGAAGACATTAAGCTGAAAGAG                         AGGCTTGAAATTGCTTGGGAGAGACGGTTTGCCTCAGAACAACATACCGCG
genomic: GTACATTGCAAGGTTTCATTCGCAAGATTGAAGACATTAAGCTGAAAGAGgtaagttggc ... tgtactgtagAGGCTTGAAATTGCTTGGGAGAGACGGTTTGCCTCAGAACAACATACCGCG
EST: gi|162201291|gb|FC376810.1|FC376810
EST:     GTACATTGCAAGGTTTCATTCGCAAGATTGAAGACATTAAGCTGAAAGAG                         AGGCTTGAAATTGCTTGGGAGAGACGGTTTGCCTCAGAACAACATACCGCG
genomic: GTACATTGCAAGGTTTCATTCGCAAGATTGAAGACATTAAGCTGAAAGAGgtaagttggc ... tgtactgtagAGGCTTGAAATTGCTTGGGAGAGACGGTTTGCCTCAGAACAACATACCGCG
EST: gi|162157801|gb|FC334072.1|FC334072
EST:     GTACATTGCAAGGTTTCATTCGCAAGATTGAAGACATTAAGCTGAAAGAG                         AGGCTTGAAATTGCTTGGGAGAGACGGTTTGCCTCAGAACAACATACCGCG
genomic: GTACATTGCAAGGTTTCATTCGCAAGATTGAAGACATTAAGCTGAAAGAGgtaagttggc ... tgtactgtagAGGCTTGAAATTGCTTGGGAGAGACGGTTTGCCTCAGAACAACATACCGCG
EST: gi|162273484|gb|FC449629.1|FC449629
EST:     GTACATTGCAAGGTTTCATTCGCAAGATTGAAGACATTAAGCTGAAAGAG                         AGGCTTGAAATTGCTTGGGAGAGACGGTTTGCCTCAGAACAACATACCGCG
genomic: GTACATTGCAAGGTTTCATTCGCAAGATTGAAGACATTAAGCTGAAAGAGgtaagttggc ... tgtactgtagAGGCTTGAAATTGCTTGGGAGAGACGGTTTGCCTCAGAACAACATACCGCG
EST: gi|67700953|gb|BJ961186.1|BJ961186
EST:     GTACATTGCAAGGTTTCATTCGCAAGATTGAAGACATTAAGCTGAAAGAG                         AGGCTTGAAATTGCTTGGGAGAGACGGTTTGCCTCAGAACAACATACCGCG
genomic: GTACATTGCAAGGTTTCATTCGCAAGATTGAAGACATTAAGCTGAAAGAGgtaagttggc ... tgtactgtagAGGCTTGAAATTGCTTGGGAGAGACGGTTTGCCTCAGAACAACATACCGCG
EST: gi|100386436|gb|BY951232.1|BY951232
EST:     GTACATTGCAAGGTTTCATTCGCAAGATTGAAGACATTAAGCTGAAAGAG                         AGGCTTGAA-TTGCTTGGGAGAGACGGTTTGCCTCAGAANCA-CATACCGC
genomic: GTACATTGCAAGGTTTCATTCGCAAGATTGAAGACATTAAGCTGAAAGAGgtaagttggc ... tgtactgtagAGGCTTGAAATTGCTTGGGAGAGACGGTTTGCCTCAGAA-CAACATACCGC
EST: gi|208386501|gb|DC956849.1|DC956849
EST:     GTACATTGCAAGGTTTCATTCGCAAGATTGAAGACATTAAGCTGAAAGAG                         AGGCTTGTAATTGCTTGGGAGAGACGGTTTGCCTCAGAACAACATACCGCG
genomic: GTACATTGCAAGGTTTCATTCGCAAGATTGAAGACATTAAGCTGAAAGAGgtaagttggc ... tgtactgtagAGGCTTGAAATTGCTTGGGAGAGACGGTTTGCCTCAGAACAACATACCGCG

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), 27 (downstream exon)
Score: 4

TTGGAACAACCAGGCCGTCGAAAGCCCCAGTGTACATTGCAAGGTTTCATTCGCAAGATTGAAGACATTAAGCTGAAAGAGgtaagttggc ... tgtactgtagAGGCTTGAAATTGCTTGGGAGAGACGGTTTGCCTCAGAACAACATACCGCGGGTGACGACTTATATGTTATGAATGTTGAGCAAGTACTACAATCTCCGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGGAACAACCAGGCCGTCGAAAGCCCCAGTGTACATTGCAAGGTTTCATTCGCAAGATTGAAGACATTAAGCTGAAAGAGgtaagttggcttatattgtatgcatacattgacatgttcgggaatcgaattcaagtctacttttatagtcatagtttgagttattgcatgtattggattt

- - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA