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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggttcacttttctcatcatcaaattctctatatttcattcaggagactgtgattcactatggctctctcgtgcctgtgaagctactaaggtttttgcataattctgtagGTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAA

Basic information

species Physcomitrella patens
transcript PP1S14_298V6.1
intron # 3
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|162171350|gb|FC346443.1|FC346443
EST:     CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAG                         GTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
genomic: CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAGgtaggttcac ... aattctgtagGTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
EST: gi|162203804|gb|FC379901.1|FC379901
EST:     CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAG                         GTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
genomic: CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAGgtaggttcac ... aattctgtagGTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
EST: gi|67717000|gb|BJ967259.1|BJ967259
EST:     CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAG                         GTTGTTGCAGCGGGAGCCAATCCAGTACAGATCA
genomic: CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAGgtaggttcac ... aattctgtagGTTGTTGCAGCGGGAGCCAATCCAGTACAGATCA
EST: gi|208371103|gb|DC931563.1|DC931563
EST:     CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGANGGCGTCAAG                         GTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
genomic: CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAGgtaggttcac ... aattctgtagGTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
EST: gi|208353715|gb|DC929716.1|DC929716
EST:     CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGANGGCGTCAAG                         GTTGTTGCANCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
genomic: CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAGgtaggttcac ... aattctgtagGTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
EST: gi|67709685|gb|BJ965501.1|BJ965501
EST:     CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGANGGCGTCAAG                         GTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
genomic: CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAGgtaggttcac ... aattctgtagGTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
EST: gi|100399573|gb|BY972786.1|BY972786
EST:     CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAG                         GTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
genomic: CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAGgtaggttcac ... aattctgtagGTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
EST: gi|162195954|gb|FC372151.1|FC372151
EST:     CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAG                         GTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
genomic: CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAGgtaggttcac ... aattctgtagGTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
EST: gi|208351065|gb|DC913501.1|DC913501
EST:     CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAG                         GTTGTTGCAGCGGGAGCCAATCCGGTACAGATCACAAGAGGCATTGAAAAA
genomic: CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAGgtaggttcac ... aattctgtagGTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
EST: gi|162170824|gb|FC347438.1|FC347438
EST:     CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAG                         GTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
genomic: CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAGgtaggttcac ... aattctgtagGTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
EST: gi|162157418|gb|FC333195.1|FC333195
EST:     CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAG                         GTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
genomic: CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAGgtaggttcac ... aattctgtagGTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
EST: gi|100446886|gb|CJ971185.1|CJ971185
EST:     CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAG                         GTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
genomic: CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAGgtaggttcac ... aattctgtagGTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
EST: gi|162187436|gb|FC362658.1|FC362658
EST:     CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAG                         GTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
genomic: CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAGgtaggttcac ... aattctgtagGTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
EST: gi|162193667|gb|FC371246.1|FC371246
EST:     CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAG                         GTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
genomic: CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAGgtaggttcac ... aattctgtagGTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
EST: gi|162173847|gb|FC349439.1|FC349439
EST:     CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAG                         GTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
genomic: CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAGgtaggttcac ... aattctgtagGTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
EST: gi|162158432|gb|FC334227.1|FC334227
EST:     CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAG                         GTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
genomic: CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAGgtaggttcac ... aattctgtagGTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
EST: gi|100371786|gb|BY967552.1|BY967552
EST:     CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAG                         GTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
genomic: CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAGgtaggttcac ... aattctgtagGTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
EST: gi|100436275|gb|BY961135.1|BY961135
EST:     CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAG                         GTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
genomic: CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAGgtaggttcac ... aattctgtagGTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
EST: gi|162195933|gb|FC372143.1|FC372143
EST:     CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAG                         GTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
genomic: CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAGgtaggttcac ... aattctgtagGTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
EST: gi|208359427|gb|DC939152.1|DC939152
EST:     CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAG                         GTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
genomic: CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAGgtaggttcac ... aattctgtagGTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
EST: gi|208399108|gb|DC904517.1|DC904517
EST:     CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAG                         GTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
genomic: CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAGgtaggttcac ... aattctgtagGTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
EST: gi|162167160|gb|FC343636.1|FC343636
EST:     CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAG                         GTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
genomic: CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAGgtaggttcac ... aattctgtagGTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
EST: gi|162255992|gb|FC431756.1|FC431756
EST:     CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAG                         GTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
genomic: CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAGgtaggttcac ... aattctgtagGTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
EST: gi|162227587|gb|FC403529.1|FC403529
EST:     CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAG                         GTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
genomic: CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAGgtaggttcac ... aattctgtagGTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
EST: gi|208362500|gb|DC939480.1|DC939480
EST:     CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAG                         GTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
genomic: CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAGgtaggttcac ... aattctgtagGTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
EST: gi|162158158|gb|FC333953.1|FC333953
EST:     CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAG                         GTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
genomic: CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAGgtaggttcac ... aattctgtagGTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
EST: gi|162149659|gb|FC326710.1|FC326710
EST:     CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAG                         GTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
genomic: CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAGgtaggttcac ... aattctgtagGTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
EST: gi|100440490|gb|BY962227.1|BY962227
EST:     CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAG                         GTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA
genomic: CCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAGgtaggttcac ... aattctgtagGTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAA

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: 11

GTTGGTGAGGCAAGCGGCAGCCAAGACGAATGACTTGGCTGGTGACGGTACCACCACCTCTGTCGTTCTCGCACAAGGGCTCATTGCTGAGGGCGTCAAGgtaggttcac ... aattctgtagGTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactatggctctctcgtgcctgtgaagctactaaggtttttgcataattctgtagGTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAA
                                           ataattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggttcacttttctcatcatcaaattctctatatttcattcaggagactgtgattcactatggctctctcgtgcctgtgaagctactaaggtttttgcataattctgtagGTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA