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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCATGGAGATCACGCCTCGCATAAGGAGGTGATTGATCTTGTGCGAGAATTCAACAAAGAAGCGCACGCGAATGTCATTGCTCTCATGTTGGATACAAAGgtttgtgttgctctcgatggaacatcgtgttttgtttaagagtaatttatttatttgtttgtttgttggattttttggtgcatagcaattcctagcagaattaaatcgctttcatcagctgaaattcttttttctgaggctttcgtatgtaaatatatttaagaaagagtcttactacctcacag

Basic information

species Physcomitrella patens
transcript PP1S318_21V6.1
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|100412938|gb|BY992509.1|BY992509
EST:     TCAACAAAGAAGCGCACGCGAATGTCATTGCTCTCATGTTGGATACAAAG                         GGTCCAGAGGTTAGAAGTGGAGACCTGCCTCAGCCAATTATGCTGAAGAAG
genomic: TCAACAAAGAAGCGCACGCGAATGTCATTGCTCTCATGTTGGATACAAAGgtttgtgttg ... tacctcacagGGTCCAGAGGTTAGAAGTGGAGACCTGCCTCAGCCAATTATGCTGAAGAAG
EST: gi|208387754|gb|DC941323.1|DC941323
EST:     TCAACAAAGAAGCGCACGCGAATGTCATTGCTCTCATGTTGGATACAAAG                         GGTCCAGANGTTAAAAGTGGAGACCTGCCTCA-CCNATTATGCTGAAAAAG
genomic: TCAACAAAGAAGCGCACGCGAATGTCATTGCTCTCATGTTGGATACAAAGgtttgtgttg ... tacctcacagGGTCCAGAGGTTAGAAGTGGAGACCTGCCTCAGCCAATTATGCTGAAGAAG
EST: gi|162154587|gb|FC330797.1|FC330797
EST:     TCAACAAAGAAGCGCACGCGAATGTCATTGCTCTCATGTTGGATACAAAG                         GGTCCAGAGGTTAGAAGTGGAGA
genomic: TCAACAAAGAAGCGCACGCGAATGTCATTGCTCTCATGTTGGATACAAAGgtttgtgttg ... tacctcacagGGTCCAGAGGTTAGAAGTGGAGA
EST: gi|100359954|gb|BY947205.1|BY947205
EST:     CA-CAAAGAAGCGCACGCGAATGTCATTGCTCTCATNGT-GGATACAAAG                         GGTCCAGAAGGT-AGAAGTGGAGACCTGCCTCAGCCAATTATGCTNGA-GA
genomic: CAACAAAGAAGCGCACGCGAATGTCATTGCTCTCAT-GTTGGATACAAAGgtttgtgttg ... tacctcacagGGTCCAGA-GGTTAGAAGTGGAGACCTGCCTCAGCCAATTATGCT-GAAGA
EST: gi|100386829|gb|BY988098.1|BY988098
EST:     CAACAAAGAAGCGCACGCGAATGTCATTGCTCTCATGT-GGNATACAAAG                         GGTCCAGAGGTTAGAAG
genomic: CAACAAAGAAGCGCACGCGAATGTCATTGCTCTCATGTTGG-ATACAAAGgtttgtgttg ... tacctcacagGGTCCAGAGGTTAGAAG
EST: gi|162202022|gb|FC377228.1|FC377228
EST:     TCAACAAAGAAGCGCACGCGAATGTCATTGCTCTCATGTTGGATACAAAG                         GGTCCAGAGGTTAGAAGTGGAGACCTGCCTCAGCCAATTATGCTGAAGAAG
genomic: TCAACAAAGAAGCGCACGCGAATGTCATTGCTCTCATGTTGGATACAAAGgtttgtgttg ... tacctcacagGGTCCAGAGGTTAGAAGTGGAGACCTGCCTCAGCCAATTATGCTGAAGAAG
EST: gi|162155347|gb|FC331246.1|FC331246
EST:     TCAACAAAGAAGCGCACGCGAATGTCATTGCTCTCATGTTGGATACAAAG                         GGTCCAGAGGTTAGAAGTGGAGACCTGCCTCAGCCAATTATGCTGAAGAAG
genomic: TCAACAAAGAAGCGCACGCGAATGTCATTGCTCTCATGTTGGATACAAAGgtttgtgttg ... tacctcacagGGTCCAGAGGTTAGAAGTGGAGACCTGCCTCAGCCAATTATGCTGAAGAAG
EST: gi|208398035|gb|DC908207.1|DC908207
EST:     TCAACAAAGAAGCGCACGCGAATGTCATTGCTCTCATGTTGGATACAAAG                         GGTCCAGAGGTTANAAGTGGANACCTGCCTCANCCAATTATGCTGAAAAAN
genomic: TCAACAAAGAAGCGCACGCGAATGTCATTGCTCTCATGTTGGATACAAAGgtttgtgttg ... tacctcacagGGTCCAGAGGTTAGAAGTGGAGACCTGCCTCAGCCAATTATGCTGAAGAAG
EST: gi|162158981|gb|FC334828.1|FC334828
EST:     TCAACAAAGAAGCGCACGCGAATGTCATTGCTCTCATGTTGGATACAAAG                         GGTCCAGAGGTTAGAAGTGGAGACCTGCCTCAGCCAATTATGCTGAAGAAG
genomic: TCAACAAAGAAGCGCACGCGAATGTCATTGCTCTCATGTTGGATACAAAGgtttgtgttg ... tacctcacagGGTCCAGAGGTTAGAAGTGGAGACCTGCCTCAGCCAATTATGCTGAAGAAG
EST: gi|162256310|gb|FC432320.1|FC432320
EST:     TCAACAAAGAAGCGCACGCGAATGTCATTGCTCTCATGTTGGATACAAAG                         GGTCCAGAGGTTAGAAGTGGAGACCTGCCTCAGCCAATTATGCTGAAGAAG
genomic: TCAACAAAGAAGCGCACGCGAATGTCATTGCTCTCATGTTGGATACAAAGgtttgtgttg ... tacctcacagGGTCCAGAGGTTAGAAGTGGAGACCTGCCTCAGCCAATTATGCTGAAGAAG
EST: gi|162267890|gb|FC444491.1|FC444491
EST:     TCAACAAAGAAGCGCACGCGAATGTCATTGCTCTCATGTTGGATACAAAG                         GGTCCAGAGGTTAGAAGTGGAGACCTGCCTCAGCCAATTATGCTGAAGAAG
genomic: TCAACAAAGAAGCGCACGCGAATGTCATTGCTCTCATGTTGGATACAAAGgtttgtgttg ... tacctcacagGGTCCAGAGGTTAGAAGTGGAGACCTGCCTCAGCCAATTATGCTGAAGAAG
EST: gi|100388218|gb|BY951820.1|BY951820
EST:     TCA-CAAAGAAGCGCACGCGAATGTCATTGCTCTCATGTTGAATACAAAG                         GGTCCAGAGGTTAGAAGTGGAGACCTGCTTCAGCCAATTATGCTGAGGAAG
genomic: TCAACAAAGAAGCGCACGCGAATGTCATTGCTCTCATGTTGGATACAAAGgtttgtgttg ... tacctcacagGGTCCAGAGGTTAGAAGTGGAGACCTGCCTCAGCCAATTATGCTGAAGAAG
EST: gi|100390194|gb|BY952602.1|BY952602
EST:     TCAACAAAGAAGCGCACGCGAATGTCATTGCTCTCATGTTGGATACAAAG                         GGTCCCGAGGTTAGAAGTGG
genomic: TCAACAAAGAAGCGCACGCGAATGTCATTGCTCTCATGTTGGATACAAAGgtttgtgttg ... tacctcacagGGTCCAGAGGTTAGAAGTGG
EST: gi|100398109|gb|BY954092.1|BY954092
EST:     TCAACAAAGA-GCGCACGCGAATGTCATTGCTCTCATGTTGGATACAAAG                         GGTCCAGAGGTTAGAAGTGGAGACCTGCCTCAGCCAATTATGCTGAAGAAG
genomic: -CAACAAAGAAGCGCACGCGAATGTCATTGCTCTCATGTTGGATACAAAGgtttgtgttg ... tacctcacagGGTCCAGAGGTTAGAAGTGGAGACCTGCCTCAGCCAATTATGCTGAAGAAG
EST: gi|100369821|gb|BY967400.1|BY967400
EST:     TCAACAAAGAAGCGCACGCGAATGTCATTGCTCTCATGTTGGATACAAAG                         GGTCCAGAGGTTAGAAGTGGAGACCTGCCTCAGCCAATTATGCTGAAGAAG
genomic: TCAACAAAGAAGCGCACGCGAATGTCATTGCTCTCATGTTGGATACAAAGgtttgtgttg ... tacctcacagGGTCCAGAGGTTAGAAGTGGAGACCTGCCTCAGCCAATTATGCTGAAGAAG
EST: gi|100379690|gb|BY949895.1|BY949895
EST:     CNNACAA-GAAGCGCACGCGAATGTCATTGCTCTCATGTTGGATACAAAG                         GGTC-AGAAGGT-AGAAGTGGAGACCTGCCTCAGCCNAAT-ATGCTGAAGA
genomic: CA-ACAAAGAAGCGCACGCGAATGTCATTGCTCTCATGTTGGATACAAAGgtttgtgttg ... tacctcacagGGTCCAGA-GGTTAGAAGTGGAGACCTGCCTCAGCC-AATTATGCTGAAGA

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: 31 (upstream exon), 32 (downstream exon)
Score: 9

CCATGGAGATCACGCCTCGCATAAGGAGGTGATTGATCTTGTGCGAGAATTCAACAAAGAAGCGCACGCGAATGTCATTGCTCTCATGTTGGATACAAAGgtttgtgttg ... tacctcacagGGTCCAGAGGTTAGAAGTGGAGACCTGCCTCAGCCAATTATGCTGAAGAAGGGCGATCCATTCACCTTCACAATTAAGCGCGGCGTGGGAACCGATACCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCATGGAGATCACGCCTCGCATAAGGAGGTGATTGATCTTGTGCGAGAATTCAACAAAGAAGCGCACGCGAATGTCATTGCTCTCATGTTGGATACAAAGgtttgtgttgctctcgatggaacatcgtgttttgtttaagagtaatttatttatttgtttgtttgttggattttttggtgcatagcaattcctagcagaattaaatcgctttcatcagctgaaattcttttttctgaggctttcgtatgtaaatatatttaagaaagagtcttactacctcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC