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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGACGAACGAGCCAATAGAAATGTGGATATCCTACGTGACTTTGCTCGTGAGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctgtttctgcagttgtacgtctcgtgtctttttgcaaaaaacgccagaagagcgttatatgtgcatattacgagtagacaacgtcttacttag...

Basic information

species Physcomitrella patens
transcript PP1S227_66V6.1
intron # 4
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|162278618|gb|FC455016.1|FC455016
EST:     AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGG                         GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
genomic: AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctg ... acttgcgcagGCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
EST: gi|19790555|gb|BQ041934.1|BQ041934
EST:     AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGG                         GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
genomic: AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctg ... acttgcgcagGCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
EST: gi|100388195|gb|BY951797.1|BY951797
EST:     AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGG                         GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
genomic: AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctg ... acttgcgcagGCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
EST: gi|100440503|gb|BY962232.1|BY962232
EST:     AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGG                         GCCAATCCAGATTTACA-GGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGG
genomic: AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctg ... acttgcgcagGCCAATCCAGATT-ACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGG
EST: gi|208389895|gb|DC937726.1|DC937726
EST:     AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGG                         GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGANGGC
genomic: AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctg ... acttgcgcagGCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
EST: gi|100413212|gb|BY956563.1|BY956563
EST:     AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGG                         GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
genomic: AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctg ... acttgcgcagGCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
EST: gi|67717186|gb|BJ967445.1|BJ967445
EST:     AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGG                         GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTC
genomic: AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctg ... acttgcgcagGCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTC
EST: gi|100388007|gb|BY988480.1|BY988480
EST:     AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGG                         GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
genomic: AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctg ... acttgcgcagGCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
EST: gi|100444345|gb|BY982374.1|BY982374
EST:     AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGG                         GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGC
genomic: AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctg ... acttgcgcagGCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGC
EST: gi|100361431|gb|BY965837.1|BY965837
EST:     AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGG                         GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
genomic: AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctg ... acttgcgcagGCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
EST: gi|100364743|gb|BY947886.1|BY947886
EST:     AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGG                         GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
genomic: AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctg ... acttgcgcagGCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
EST: gi|100362006|gb|BY947736.1|BY947736
EST:     GCAAGACATNCA-GTATTTCTACGACATTACTGATAGGAGCAACTTTCGG                         GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCNAGGAGG-
genomic: GCAAGACAT-CAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctg ... acttgcgcagGCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGC-AGGAGGG
EST: gi|100428300|gb|BY977734.1|BY977734
EST:     AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGG                         GCCAATCCAGATTACAAGGGA
genomic: AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctg ... acttgcgcagGCCAATCCAGATTACAAGGGA
EST: gi|100438751|gb|BY961784.1|BY961784
EST:     AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGG                         GCCAATCCAGA
genomic: AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctg ... acttgcgcagGCCAATCCAGA
EST: gi|67718911|gb|BJ969170.1|BJ969170
EST:     AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGG                         GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
genomic: AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctg ... acttgcgcagGCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
EST: gi|100384785|gb|BY950775.1|BY950775
EST:     GCAAGACATNCA-GTATTTCTACGACATTACTGATAGGAGCAACTTTCGG                         GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
genomic: GCAAGACAT-CAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctg ... acttgcgcagGCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
EST: gi|162172982|gb|FC347892.1|FC347892
EST:     AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGG                         GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
genomic: AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctg ... acttgcgcagGCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
EST: gi|100442174|gb|BY963067.1|BY963067
EST:     AGCAAGACATCAAGTACTTCTACGACATTACTGATAGGAGCAACTTTCGG                         GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
genomic: AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctg ... acttgcgcagGCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
EST: gi|162158369|gb|FC334164.1|FC334164
EST:     AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGG                         GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
genomic: AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctg ... acttgcgcagGCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
EST: gi|162199219|gb|FC375055.1|FC375055
EST:     AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGG                         GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
genomic: AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctg ... acttgcgcagGCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
EST: gi|162258438|gb|FC434445.1|FC434445
EST:     AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGG                         GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
genomic: AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctg ... acttgcgcagGCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
EST: gi|208344467|gb|DC905028.1|DC905028
EST:     AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGG                         GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCANGAGGGC
genomic: AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctg ... acttgcgcagGCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
EST: gi|100410814|gb|BY956200.1|BY956200
EST:     AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGG                         GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
genomic: AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctg ... acttgcgcagGCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
EST: gi|100353093|gb|BY945602.1|BY945602
EST:     AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGG                         GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
genomic: AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctg ... acttgcgcagGCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
EST: gi|208361763|gb|DC935003.1|DC935003
EST:     AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGG                         GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGANGGC
genomic: AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctg ... acttgcgcagGCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
EST: gi|162198077|gb|FC372104.1|FC372104
EST:     AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGG                         GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
genomic: AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctg ... acttgcgcagGCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
EST: gi|100390972|gb|BY952982.1|BY952982
EST:     AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGG                         GCCAATCCAGATTNACA-GGGAGTTTGCCATGTGGCTCTGGCGCAGGAGGG
genomic: AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctg ... acttgcgcagGCCAATCCAGATT-ACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGG
EST: gi|100406831|gb|BY955742.1|BY955742
EST:     CAAGACATCAAGTATTTCTACGACATTACTGGAT-GGAGCAACTTTTCGG                         GC-AATCCAGA
genomic: CAAGACATCAAGTATTTCTACGACATTACTG-ATAGGAGCAACTTT-CGGgtacgtcctg ... acttgcgcagGCCAATCCAGA
EST: gi|100362852|gb|BY947561.1|BY947561
EST:     AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGG                         GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTGGCGCAGGAGGGC
genomic: AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctg ... acttgcgcagGCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
EST: gi|162222838|gb|FC399300.1|FC399300
EST:     AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGG                         GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
genomic: AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctg ... acttgcgcagGCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
EST: gi|19780614|gb|BQ039583.1|BQ039583
EST:     AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGG                         GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
genomic: AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctg ... acttgcgcagGCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
EST: gi|162163969|gb|FC339879.1|FC339879
EST:     AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGG                         GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
genomic: AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctg ... acttgcgcagGCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
EST: gi|100385562|gb|BY969899.1|BY969899
EST:     AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGG                         GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGG
genomic: AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctg ... acttgcgcagGCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGG
EST: gi|162216862|gb|FC392212.1|FC392212
EST:     AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGG                         GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
genomic: AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctg ... acttgcgcagGCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
EST: gi|22492336|gb|BU052259.1|BU052259
EST:     AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGG                         GCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC
genomic: AGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctg ... acttgcgcagGCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGC

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: 33 (upstream exon), 34 (downstream exon)
Score: 20

AGACGAACGAGCCAATAGAAATGTGGATATCCTACGTGACTTTGCTCGTGAGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctg ... acttgcgcagGCCAATCCAGATTACAAGGGAGTTTGCCATGTGGCTCTTGCGCAGGAGGGCCATTGTCGCCCTGGAGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGACGAACGAGCCAATAGAAATGTGGATATCCTACGTGACTTTGCTCGTGAGCAAGACATCAAGTATTTCTACGACATTACTGATAGGAGCAACTTTCGGgtacgtcctgtttctgcagttgtacgtctcgtgtctttttgcaaaaaacgccagaagagcgttatatgtgcatattacgagtagacaacgtcttacttag

- - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaaaaac