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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTCGTCGCCCCAGCTCTTCTGTAGCCTCGAATTTTTGCAGTTTAGGCGGTGCGAACCTCTCTTTCAACATGGCAACTCAGATGAGCAAGAAGCGGAAGgtggaattcttcgcttgtgaacaagtttttgagactttggctgtttttttttttaaatgatttttaattgttttttttgctgaaaactcactagggcacatttcgagtagatcacagcactcatgtttgttttatctcttttctcacag

Basic information

species Physcomitrella patens
transcript PP1S31_178V6.1
intron # 1
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|162232978|gb|FC407566.1|FC407566
EST:     GTGCGAACCTCTCTTTC-ACATGGCAACTCAGATGAGCAAGAAGCGGAAG                         TTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
genomic: GTGCGAACCTCTCTTTCAACATGGCAACTCAGATGAGCAAGAAGCGGAAGgtggaattct ... tttctcacagTTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
EST: gi|162278299|gb|FC454177.1|FC454177
EST:     GTGCGAACCTCTCTTTCAACATGGCAACTCAGATGAGCAAGAAGCGGAAG                         TTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
genomic: GTGCGAACCTCTCTTTCAACATGGCAACTCAGATGAGCAAGAAGCGGAAGgtggaattct ... tttctcacagTTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
EST: gi|18328342|gb|BJ160346.1|BJ160346
EST:     GTGCGAACCTCTCTTTCAACATGGCAACTCAGATGAGCAAGAAGCGGAAG                         TTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
genomic: GTGCGAACCTCTCTTTCAACATGGCAACTCAGATGAGCAAGAAGCGGAAGgtggaattct ... tttctcacagTTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
EST: gi|18372625|gb|BJ204227.1|BJ204227
EST:     GTGCGAACCTCTCTTTCAACATGGCAACTCAGATGAGCAAGAAGCGGAAG                         TTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
genomic: GTGCGAACCTCTCTTTCAACATGGCAACTCAGATGAGCAAGAAGCGGAAGgtggaattct ... tttctcacagTTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
EST: gi|162208528|gb|FC384491.1|FC384491
EST:     GTGCGAACCTCTCTTTC-ACATGGCAACTCAGATGAGCAAGAAGCGGAAG                         TTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
genomic: GTGCGAACCTCTCTTTCAACATGGCAACTCAGATGAGCAAGAAGCGGAAGgtggaattct ... tttctcacagTTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
EST: gi|162265194|gb|FC441281.1|FC441281
EST:     GTGCGAACCTCTCTTTC-ACATGGCAACTCAGATGAGCAAGAAGCGGAAG                         TTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
genomic: GTGCGAACCTCTCTTTCAACATGGCAACTCAGATGAGCAAGAAGCGGAAGgtggaattct ... tttctcacagTTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
EST: gi|67727225|gb|BJ977484.1|BJ977484
EST:     GTGCGAACCTCTCTTTCAACATGGCAACTCAGATGAGCAAGAAGCGGAAG                         TTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
genomic: GTGCGAACCTCTCTTTCAACATGGCAACTCAGATGAGCAAGAAGCGGAAGgtggaattct ... tttctcacagTTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
EST: gi|162232977|gb|FC407565.1|FC407565
EST:     ACATGGCAACTCAGATGAGCAAGAAGCGGAAG                         TTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
genomic: ACATGGCAACTCAGATGAGCAAGAAGCGGAAGgtggaattct ... tttctcacagTTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
EST: gi|18359275|gb|BJ191335.1|BJ191335
EST:     GTGCGAACCTCTCTTTCAACATGGCAACTCAGATGAGCAAGAAGCGGAAG                         TTTGTAGCAGACGGTGTTTTCTTCGCAGAGCTCAATGAGCTTCTCACCCGC
genomic: GTGCGAACCTCTCTTTCAACATGGCAACTCAGATGAGCAAGAAGCGGAAGgtggaattct ... tttctcacagTTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
EST: gi|67718871|gb|BJ969130.1|BJ969130
EST:     GTGCGAACCTCTCTTTCAACATGGCAACTCAGATGAGCAAGAAGCGGAAG                         TTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
genomic: GTGCGAACCTCTCTTTCAACATGGCAACTCAGATGAGCAAGAAGCGGAAGgtggaattct ... tttctcacagTTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
EST: gi|18349896|gb|BJ181947.1|BJ181947
EST:     GTGCGAACCTCTCTTTCAACATGGCAACTCAGATGAGCAAGAAGCGGAAG                         TTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
genomic: GTGCGAACCTCTCTTTCAACATGGCAACTCAGATGAGCAAGAAGCGGAAGgtggaattct ... tttctcacagTTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
EST: gi|162259149|gb|FC435195.1|FC435195
EST:     GTGCGAACCTCTCTTTC-ACATGGCAACTCAGATGAGCAAGAAGCGGAAG                         TTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
genomic: GTGCGAACCTCTCTTTCAACATGGCAACTCAGATGAGCAAGAAGCGGAAGgtggaattct ... tttctcacagTTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
EST: gi|162208527|gb|FC384490.1|FC384490
EST:     TTCAACATGGCAACTCAGATGAGCAAGAAGCGGAAG                         TTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
genomic: TTCAACATGGCAACTCAGATGAGCAAGAAGCGGAAGgtggaattct ... tttctcacagTTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
EST: gi|18372947|gb|BJ204549.1|BJ204549
EST:     GTGCGAACCTCTCTTTCAACATGGCAACTCAGATGAGCAAGAAGCGGAAG                         TTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
genomic: GTGCGAACCTCTCTTTCAACATGGCAACTCAGATGAGCAAGAAGCGGAAGgtggaattct ... tttctcacagTTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
EST: gi|162277243|gb|FC453673.1|FC453673
EST:     GTGCGAACCTCTCTTTC-ACATGGCAACTCAGATGAGCAAGAAGCGGAAG                         TTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
genomic: GTGCGAACCTCTCTTTCAACATGGCAACTCAGATGAGCAAGAAGCGGAAGgtggaattct ... tttctcacagTTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
EST: gi|37828865|gb|BJ586877.1|BJ586877
EST:     CAACATGGCAACTCAGATGAGCAAGAAGCGGAAG                         TTTGTAGCAGACGGTGTTTTNTTCGCCGAGCTCAATGAGCTTCTCACCCGC
genomic: CAACATGGCAACTCAGATGAGCAAGAAGCGGAAGgtggaattct ... tttctcacagTTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
EST: gi|37852687|gb|BJ610695.1|BJ610695
EST:     AACTCAGATGAGCAAGAAGCGGAAG                         TTTGTAGCAGACGGTGTTTTCTTCGCAGAGCTCAATGAGCTTCTCACCCGC
genomic: AACTCAGATGAGCAAGAAGCGGAAGgtggaattct ... tttctcacagTTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
EST: gi|162271941|gb|FC448151.1|FC448151
EST:     GTGCGAACCTCTCTTTC-ACATGGCAACTCAGATGAGCAAGAAGCGGAAG                         TTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
genomic: GTGCGAACCTCTCTTTCAACATGGCAACTCAGATGAGCAAGAAGCGGAAGgtggaattct ... tttctcacagTTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
EST: gi|67702967|gb|BJ963200.1|BJ963200
EST:     GTGCGAACCTCTCTTTCAACATGGCAACTCAGATGAGCAAGAAGCGGAAG                         TTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
genomic: GTGCGAACCTCTCTTTCAACATGGCAACTCAGATGAGCAAGAAGCGGAAGgtggaattct ... tttctcacagTTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
EST: gi|162206672|gb|FC382430.1|FC382430
EST:     GTGCGAACCTCTCTTT-TACATGGCAACTCAGATGAGCAAGAAGCGGAAG                         TTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
genomic: GTGCGAACCTCTCTTTCAACATGGCAACTCAGATGAGCAAGAAGCGGAAGgtggaattct ... tttctcacagTTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
EST: gi|37852142|gb|BJ610150.1|BJ610150
EST:     ATGGCAACTCAGATGAGCAAGAAGCGGAAG                         TTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC
genomic: ATGGCAACTCAGATGAGCAAGAAGCGGAAGgtggaattct ... tttctcacagTTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGC

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), 35 (downstream exon)
Score: 30

GCTTCGTCGCCCCAGCTCTTCTGTAGCCTCGAATTTTTGCAGTTTAGGCGGTGCGAACCTCTCTTTCAACATGGCAACTCAGATGAGCAAGAAGCGGAAGgtggaattct ... tttctcacagTTTGTAGCAGACGGTGTTTTCTTCGCCGAGCTCAATGAGCTTCTCACCCGCGAGCTCGCCGAAGATGGCTATTCTGGAGTGGAAGTGCGCGTCACTCCCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTCGTCGCCCCAGCTCTTCTGTAGCCTCGAATTTTTGCAGTTTAGGCGGTGCGAACCTCTCTTTCAACATGGCAACTCAGATGAGCAAGAAGCGGAAGgtggaattcttcgcttgtgaacaagtttttgagactttggctgtttttttttttaaatgatttttaattgttttttttgctgaaaactcactagggcacatttcgagtagatcacagcactcatgtttgttttatctcttttctcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC