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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttaccggtttggttgattacaatggaatgcaatcgtatgatgatcagattctatcggtgtcgaaagagccacacacacaagttgtttcgttggttccgtttcttgagcttatgtattgtatgcatcatccagcaagctctttacaagtcttggacttttctgttcgcagTTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAATGCTAAATGGTGGGGTTTCTGTATTGCGATTGGCTTCATAAG

Basic information

species Physcomitrella patens
transcript PP1S8_288V6.1
intron # 32
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|162181732|gb|FC358762.1|FC358762
EST:     ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAG                         TTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
genomic: ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAGgtgagtttac ... ctgttcgcagTTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
EST: gi|162175272|gb|FC351470.1|FC351470
EST:     ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAG                         TTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
genomic: ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAGgtgagtttac ... ctgttcgcagTTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
EST: gi|162189371|gb|FC366529.1|FC366529
EST:     ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAG                         TTTGTGATCCTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
genomic: ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAGgtgagtttac ... ctgttcgcagTTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
EST: gi|162186820|gb|FC363064.1|FC363064
EST:     ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAG                         TTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
genomic: ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAGgtgagtttac ... ctgttcgcagTTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
EST: gi|18336099|gb|BJ168121.1|BJ168121
EST:     ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAG                         TTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
genomic: ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAGgtgagtttac ... ctgttcgcagTTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
EST: gi|162189370|gb|FC366528.1|FC366528
EST:     ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAG                         TTTGTGATCCTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
genomic: ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAGgtgagtttac ... ctgttcgcagTTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
EST: gi|162191835|gb|FC367984.1|FC367984
EST:     ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAG                         TTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
genomic: ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAGgtgagtttac ... ctgttcgcagTTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
EST: gi|162208803|gb|FC384939.1|FC384939
EST:     ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAG                         TTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
genomic: ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAGgtgagtttac ... ctgttcgcagTTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
EST: gi|162181320|gb|FC358415.1|FC358415
EST:     ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAG                         TTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
genomic: ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAGgtgagtttac ... ctgttcgcagTTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
EST: gi|37849039|gb|BJ607047.1|BJ607047
EST:     ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAG                         TTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
genomic: ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAGgtgagtttac ... ctgttcgcagTTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
EST: gi|37849985|gb|BJ607993.1|BJ607993
EST:     ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAG                         TTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
genomic: ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAGgtgagtttac ... ctgttcgcagTTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
EST: gi|162197899|gb|FC373953.1|FC373953
EST:     ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAG                         TTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
genomic: ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAGgtgagtttac ... ctgttcgcagTTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
EST: gi|162259196|gb|FC435216.1|FC435216
EST:     ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAG                         TTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
genomic: ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAGgtgagtttac ... ctgttcgcagTTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
EST: gi|162153021|gb|FC330051.1|FC330051
EST:     ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAG                         TTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
genomic: ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAGgtgagtttac ... ctgttcgcagTTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
EST: gi|162256238|gb|FC432294.1|FC432294
EST:     ACAAGAATTATCTCTTCCTTGGCATTATTTTCATTGAAGAGATTCTCCAG                         TTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
genomic: ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAGgtgagtttac ... ctgttcgcagTTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
EST: gi|37853493|gb|BJ611501.1|BJ611501
EST:     ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAG                         TTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
genomic: ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAGgtgagtttac ... ctgttcgcagTTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
EST: gi|162245992|gb|FC421881.1|FC421881
EST:     ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAG                         TTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
genomic: ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAGgtgagtttac ... ctgttcgcagTTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
EST: gi|162186821|gb|FC363065.1|FC363065
EST:     ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAG                         TTTGTGATCGTGCAGTTTTTGAACAAATTTGCC
genomic: ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAGgtgagtttac ... ctgttcgcagTTTGTGATCGTGCAGTTTTTGAACAAATTTGCC
EST: gi|162272382|gb|FC449034.1|FC449034
EST:     ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAG                         TTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
genomic: ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAGgtgagtttac ... ctgttcgcagTTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
EST: gi|162162455|gb|FC338367.1|FC338367
EST:     ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAG                         TTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
genomic: ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAGgtgagtttac ... ctgttcgcagTTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
EST: gi|162272381|gb|FC449033.1|FC449033
EST:     ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAG                         TTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
genomic: ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAGgtgagtttac ... ctgttcgcagTTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
EST: gi|37850518|gb|BJ608526.1|BJ608526
EST:     ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAG                         TTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTTAA
genomic: ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAGgtgagtttac ... ctgttcgcagTTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGC-TTAA
EST: gi|162155066|gb|FC330860.1|FC330860
EST:     ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAG                         TTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
genomic: ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAGgtgagtttac ... ctgttcgcagTTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
EST: gi|162166639|gb|FC343531.1|FC343531
EST:     ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAG                         TTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
genomic: ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAGgtgagtttac ... ctgttcgcagTTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
EST: gi|162205304|gb|FC380986.1|FC380986
EST:     ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAG                         TTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
genomic: ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAGgtgagtttac ... ctgttcgcagTTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
EST: gi|162256676|gb|FC433194.1|FC433194
EST:     ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAG                         TTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT
genomic: ACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAGgtgagtttac ... ctgttcgcagTTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAAT

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), 35 (downstream exon)
Score: 48

CGAAATCAACGCAAGGAGACCTGACAAATTTAATATTTTCGAAGGCATTCACAAGAATTATCTCTTCCTTGGCATTATTCTCATTGAAGTGATTCTCCAGgtgagtttac ... ctgttcgcagTTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAATGCTAAATGGTGGGGTTTCTGTATTGCGATTGGCTTCATAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtatgcatcatccagcaagctctttacaagtcttggacttttctgttcgcagTTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAATGCTAAATGGTGGGGTTTCTGTATTGCGATTGGCTTCATAAG
                                        cttttctgttc  CT-rich tract
                         tttacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtttaccggtttggttgattacaatggaatgcaatcgtatgatgatcagattctatcggtgtcgaaagagccacacacacaagttgtttcgttggttccgtttcttgagcttatgtattgtatgcatcatccagcaagctctttacaagtcttggacttttctgttcgcagTTTGTGATCGTGCAGTTTTTGAACAAATTTGCCCAAACAACGAAGCTTAATGCTAAATGGTGGGGTTTCTGTATTGCGATTGGCTTCATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG