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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaaggttttctattgctttcccagtttattactagtgactctcgtactagaaacagctattgaggataagaactgaacttttacaatcttgctttgcagTATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGAGATGAAGACATAATGATGCTCAACAATGGTTGCATGTGTTGCACTGTTC

Basic information

species Physcomitrella patens
transcript PP1S31_130V6.1
intron # 2
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|100390810|gb|BY989293.1|BY989293
EST:     ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAG                         TATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
genomic: ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAGgtacgaaatt ... tgctttgcagTATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
EST: gi|67716934|gb|BJ967193.1|BJ967193
EST:     ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAG                         TATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
genomic: ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAGgtacgaaatt ... tgctttgcagTATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
EST: gi|162184555|gb|FC360029.1|FC360029
EST:     ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAG                         TATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
genomic: ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAGgtacgaaatt ... tgctttgcagTATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
EST: gi|162176071|gb|FC351865.1|FC351865
EST:     ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAG                         TATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
genomic: ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAGgtacgaaatt ... tgctttgcagTATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
EST: gi|162156787|gb|FC333599.1|FC333599
EST:     ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAG                         TATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
genomic: ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAGgtacgaaatt ... tgctttgcagTATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
EST: gi|208358154|gb|DC934487.1|DC934487
EST:     ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAG                         TATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
genomic: ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAGgtacgaaatt ... tgctttgcagTATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
EST: gi|162253297|gb|FC428891.1|FC428891
EST:     ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAG                         TATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
genomic: ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAGgtacgaaatt ... tgctttgcagTATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
EST: gi|162152362|gb|FC328549.1|FC328549
EST:     ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAG                         TATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
genomic: ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAGgtacgaaatt ... tgctttgcagTATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
EST: gi|162195573|gb|FC371874.1|FC371874
EST:     ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAG                         TATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
genomic: ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAGgtacgaaatt ... tgctttgcagTATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
EST: gi|100354739|gb|BY983541.1|BY983541
EST:     ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAG                         TATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
genomic: ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAGgtacgaaatt ... tgctttgcagTATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
EST: gi|208359157|gb|DC934660.1|DC934660
EST:     ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAG                         TATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
genomic: ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAGgtacgaaatt ... tgctttgcagTATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
EST: gi|100382598|gb|BY986875.1|BY986875
EST:     ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAG                         TATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
genomic: ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAGgtacgaaatt ... tgctttgcagTATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
EST: gi|18352228|gb|BJ184282.1|BJ184282
EST:     ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAG                         TATGGGGAGGNGGGATATTGATGGTTCCCTAGTAGCTTC
genomic: ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAGgtacgaaatt ... tgctttgcagTATGGGGAGGTGG-ATATTGATGGTTCCCTAGTAGCTTC
EST: gi|162159887|gb|FC336140.1|FC336140
EST:     ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAG                         TATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
genomic: ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAGgtacgaaatt ... tgctttgcagTATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
EST: gi|208397777|gb|DC912000.1|DC912000
EST:     ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAG                         TATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
genomic: ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAGgtacgaaatt ... tgctttgcagTATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
EST: gi|100394903|gb|BY989983.1|BY989983
EST:     ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAG                         TATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
genomic: ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAGgtacgaaatt ... tgctttgcagTATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
EST: gi|100406754|gb|BY955718.1|BY955718
EST:     ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAG                         TATGGGGAGGTGGATATTGATGGNTTCC-TAGTAGCTTTCAAAGCAACA-G
genomic: ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAGgtacgaaatt ... tgctttgcagTATGGGGAGGTGGATATTGATGG-TTCCCTAGTAGCTT-CAAAGCAACAAG
EST: gi|162242562|gb|FC419217.1|FC419217
EST:     ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAG                         TATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
genomic: ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAGgtacgaaatt ... tgctttgcagTATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
EST: gi|100353131|gb|BY945621.1|BY945621
EST:     ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAG                         TATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
genomic: ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAGgtacgaaatt ... tgctttgcagTATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
EST: gi|208370345|gb|DC931757.1|DC931757
EST:     ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGANAACGAG                         TATGGGGAGGTGGATATTGATGGTTCCCTAGTANCTTCAAAGCAACNAGGA
genomic: ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAGgtacgaaatt ... tgctttgcagTATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
EST: gi|162187277|gb|FC363227.1|FC363227
EST:     ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAG                         TATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
genomic: ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAGgtacgaaatt ... tgctttgcagTATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
EST: gi|18330321|gb|BJ162327.1|BJ162327
EST:     ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAG                         TATGGGGAGGTGGATATTGATGGT
genomic: ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAGgtacgaaatt ... tgctttgcagTATGGGGAGGTGGATATTGATGGT
EST: gi|162162412|gb|FC339169.1|FC339169
EST:     ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAG                         TATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
genomic: ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAGgtacgaaatt ... tgctttgcagTATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
EST: gi|162151814|gb|FC328060.1|FC328060
EST:     ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAG                         TATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
genomic: ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAGgtacgaaatt ... tgctttgcagTATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
EST: gi|100392220|gb|BY953254.1|BY953254
EST:     ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAG                         TATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
genomic: ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAGgtacgaaatt ... tgctttgcagTATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
EST: gi|100386028|gb|BY969967.1|BY969967
EST:     ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAG                         TATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
genomic: ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAGgtacgaaatt ... tgctttgcagTATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
EST: gi|100446745|gb|CJ971044.1|CJ971044
EST:     ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAG                         TATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA
genomic: ACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAGgtacgaaatt ... tgctttgcagTATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGA

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: 18

ACTACGCTGTTGAATCACATTCTCACCATGCAGCACGGAAAACGGATTGCCGTCATTGAGAACGAGgtacgaaatt ... tgctttgcagTATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGAGATGAAGACATAATGATGCTCAACAATGGTTGCATGTGTTGCACTGTTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactagaaacagctattgaggataagaactgaacttttacaatcttgctttgcagTATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGAGATGAAGACATAATGATGCTCAACAATGGTTGCATGTGTTGCACTGTTC
                                          tcttgcttt  CT-rich tract
                                  ttttacaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaaggttttctattgctttcccagtttattactagtgactctcgtactagaaacagctattgaggataagaactgaacttttacaatcttgctttgcagTATGGGGAGGTGGATATTGATGGTTCCCTAGTAGCTTCAAAGCAACAAGGAGATGAAGACATAATGATGCTCAACAATGGTTGCATGTGTTGCACTGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA